Research

colonic-mucosa


Publications

All FacultyMyles Brown, M.D.Shirley LiuRamesh Shivdasani, M.D., Ph.D.Kornelia Polyak, M.D., Ph.D.Matthew Freedman

Zhang X; Eliassen AH; Tamimi RM; Hazra A; Beck AH; Brown M; Collins LC; Rosner B; Hankinson SE, 2015. Adult body size and physical activity in relation to risk of breast cancer according to tumor androgen receptor status.  Cancer Epidemiol Biomarkers Prev.

Janiszewska M; Polyak K, 2015. Clonal evolution in cancer: a tale of twisted twines.  Cell Stem Cell 16(1):11-2

Fan D; Liu SY; van Hasselt CA; Vlantis AC; Ng EK; Zhang H; Dong Y; Ng SK; Chu R; Chan AB; Du J; Wei W; Liu X; Liu Z; Xing M; Chen GG, 2015. Estrogen Receptor α Induces Prosurvival Autophagy in Papillary Thyroid Cancer via Stimulating Reactive Oxygen Species and Extracellular Signal Regulated Kinases.  J Clin Endocrinol Metab 100(4):E561-71

Wang H; Zang C; Liu XS; Aster JC, 2015. The role of Notch receptors in transcriptional regulation.  J Cell Physiol 230(5):982-8

Bailey ST; Westerling T; Brown M, 2015. Loss of estrogen-regulated microRNA expression increases HER2 signaling and is prognostic of poor outcome in luminal breast cancer.  Cancer Res 75(2):436-45

Chu R; Liu SY; Vlantis AC; van Hasselt CA; Ng EK; Fan MD; Ng SK; Chan AB; Du J; Wei W; Liu X; Liu Z; Chen GG, 2015. Inhibition of Foxp3 in cancer cells induces apoptosis of thyroid cancer cells.  Mol Cell Endocrinol 399:228-34

Penney KL; Sinnott JA; Tyekucheva S; Gerke T; Shui IM; Kraft P; Sesso HD; Freedman ML; Loda M; Mucci LA; Stampfer MJ, 2015. Association of prostate cancer risk variants with gene expression in normal and tumor tissue.  Cancer Epidemiol Biomarkers Prev 24(1):255-60

van Kruchten M; de Vries EG; Glaudemans AW; van Lanschot MC; van Faassen M; Kema IP; Brown M; Schröder CP; de Vries EF; Hospers GA, 2015. Measuring residual estrogen receptor availability during fulvestrant therapy in patients with metastatic breast cancer.  Cancer Discov 5(1):72-81

Schumacher MA; Aihara E; Feng R; Engevik A; Shroyer NF; Ottemann KM; Worrell RT; Montrose MH; Shivdasani RA; Zavros Y, 2015. The use of murine-derived fundic organoids in studies of gastric physiology.  J Physiol.

San Roman AK; Aronson BE; Krasinski SD; Shivdasani RA; Verzi MP, 2015. Transcription factors GATA4 and HNF4A control distinct aspects of intestinal homeostasis in conjunction with transcription factor CDX2.  J Biol Chem 290(3):1850-60

Wang X; Bu HF; Liu SX; De Plaen IG; Tan XD, 2015. Molecular mechanisms underlying the regulation of the MFG-E8 gene promoter activity in physiological and inflammatory conditions.  J Cell Biochem.

Liu SY; Wong SK; Lam CC; Yung MY; Kong AP; Ng EK, 2015. Long-term Results on Weight Loss and Diabetes Remission after Laparoscopic Sleeve Gastrectomy for A Morbidly Obese Chinese Population.  Obes Surg.

Brown M; Chinnaiyan A; Farsetti A; Livingston DM; Loda M; Schuele R; Mihich E, 2015. 26th pezcoller symposium: cancers driven by hormones.  Cancer Res 75(7):1177-80

Hsieh CL; Botta G; Gao S; Li T; Van Allen EM; Treacy DJ; Cai C; He HH; Sweeney CJ; Brown M; Balk SP; Nelson PS; Garraway LA; Kantoff PW, 2015. PLZF, a Tumor Suppressor Genetically Lost in Metastatic Castration Resistant Prostate Cancer, is a Mediator of Resistance to Androgen Deprivation Therapy.  Cancer Res.

Huh SJ; Clement K; Jee D; Merlini A; Choudhury S; Maruyama R; Yoo R; Chytil A; Boyle P; Ran FA; Moses HL; Barcellos-Hoff MH; Jackson-Grusby L; Meissner A; Polyak K, 2015. Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells.  Stem Cell Reports 4(2):297-311

Yoshida T; Kim JH; Carver K; Su Y; Weremowicz S; Mulvey L; Yamamoto S; Brennan C; Mei S; Long H; Yao J; Polyak K, 2015. CLK2 Is an Oncogenic Kinase and Splicing Regulator in Breast Cancer.  Cancer Res 75(7):1516-26

Sabnis A; Carrasco R; Liu SX; Yan X; Managlia E; Chou PM; Tan XD; De Plaen IG, 2015. Intestinal vascular endothelial growth factor is decreased in necrotizing enterocolitis.  Neonatology 107(3):191-8

Jiang P; Liu XS, 2015. Big data mining yields novel insights on cancer.  Nat Genet 47(2):103-4

Watanabe H; Ma Q; Peng S; Adelmant G; Swain D; Song W; Fox C; Francis JM; Pedamallu CS; DeLuca DS; Brooks AN; Wang S; Que J; Rustgi AK; Wong KK; Ligon KL; Liu XS; Marto JA; Meyerson M; Bass AJ, 2014. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.  J Clin Invest 124(4):1636-45

Shivdasani RA, 2014. Radiation redux: reserve intestinal stem cells miss the call to duty.  Cell Stem Cell 14(2):135-6

Almendro V; Cheng YK; Randles A; Itzkovitz S; Marusyk A; Ametller E; Gonzalez-Farre X; Muñoz M; Russnes HG; Helland A; Rye IH; Borresen-Dale AL; Maruyama R; van Oudenaarden A; Dowsett M; Jones RL; Reis-Filho J; Gascon P; Gönen M; Michor F; Polyak K, 2014. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.  Cell Rep 6(3):514-27

San Roman AK; Jayewickreme CD; Murtaugh LC; Shivdasani RA, 2014. Wnt secretion from epithelial cells and subepithelial myofibroblasts is not required in the mouse intestinal stem cell niche in vivo.  Stem Cell Reports 2(2):127-34

Godinho SA; Picone R; Burute M; Dagher R; Su Y; Leung CT; Polyak K; Brugge JS; Théry M; Pellman D, 2014. Oncogene-like induction of cellular invasion from centrosome amplification.  Nature 510(7503):167-71

Chen X; Iliopoulos D; Zhang Q; Tang Q; Greenblatt MB; Hatziapostolou M; Lim E; Tam WL; Ni M; Chen Y; Mai J; Shen H; Hu DZ; Adoro S; Hu B; Song M; Tan C; Landis MD; Ferrari M; Shin SJ; Brown M; Chang JC; Liu XS; Glimcher LH, 2014. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway.  Nature 508(7494):103-7

Lu T; Aron L; Zullo J; Pan Y; Kim H; Chen Y; Yang TH; Kim HM; Drake D; Liu XS; Bennett DA; Colaiácovo MP; Yankner BA, 2014. REST and stress resistance in ageing and Alzheimer's disease.  Nature 507(7493):448-54

Polyak K, 2014. Tumor heterogeneity confounds and illuminates: a case for Darwinian tumor evolution.  Nat Med 20(4):344-6

Hines WC; Su Y; Kuhn I; Polyak K; Bissell MJ, 2014. Sorting out the FACS: a devil in the details.  Cell Rep 6(5):779-81

Almendro V; Kim HJ; Cheng YK; Gönen M; Itzkovitz S; Argani P; van Oudenaarden A; Sukumar S; Michor F; Polyak K, 2014. Genetic and phenotypic diversity in breast tumor metastases.  Cancer Res 74(5):1338-48

Polyak K; Marusyk A, 2014. Cancer: Clonal cooperation.  Nature 508(7494):52-3

Sulahian R; Casey F; Shen J; Qian ZR; Shin H; Ogino S; Weir BA; Vazquez F; Liu XS; Hahn WC; Bass AJ; Chan V; Shivdasani RA, 2014. An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer.  Oncogene 33(49):5637-48

Wang Q; Huang J; Sun H; Liu J; Wang J; Wang Q; Qin Q; Mei S; Zhao C; Yang X; Liu XS; Zhang Y, 2014. CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse.  Nucleic Acids Res 42(Database issue):D450-8

Chu R; van Hasselt A; Vlantis AC; Ng EK; Liu SY; Fan MD; Ng SK; Chan AB; Liu Z; Li XY; Chen GG, 2014. The cross-talk between estrogen receptor and peroxisome proliferator-activated receptor gamma in thyroid cancer.  Cancer 120(1):142-53

Marrus N; Veenstra-Vanderweele J; Hellings JA; Stigler KA; Szymanski L; King BH; Carlisle LL; Cook EH Jr; Pruett JR Jr, 2014. Training of child and adolescent psychiatry fellows in autism and intellectual disability.  Autism 18(4):471-5

Lee RK; Liu SY; Tong CS; Lee PS; Ng EK; Ahuja AT, 2014. Morphologic change in computed tomography of aldosterone-producing adenoma after radiofrequency ablation.  Can Assoc Radiol J 65(1):86-90

Zhang Y; Vastenhouw NL; Feng J; Fu K; Wang C; Ge Y; Pauli A; van Hummelen P; Schier AF; Liu XS, 2014. Canonical nucleosome organization at promoters forms during genome activation.  Genome Res 24(2):260-6

Hsieh CL; Fei T; Chen Y; Li T; Gao Y; Wang X; Sun T; Sweeney CJ; Lee GS; Chen S; Balk SP; Liu XS; Brown M; Kantoff PW, 2014. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation.  Proc Natl Acad Sci U S A 111(20):7319-24

Jeselsohn R; Yelensky R; Buchwalter G; Frampton G; Meric-Bernstam F; Gonzalez-Angulo AM; Ferrer-Lozano J; Perez-Fidalgo JA; Cristofanilli M; Gómez H; Arteaga CL; Giltnane J; Balko JM; Cronin MT; Jarosz M; Sun J; Hawryluk M; Lipson D; Otto G; Ross JS; Dvir A; Soussan-Gutman L; Wolf I; Rubinek T; Gilmore L; Schnitt S; Come SE; Pusztai L; Stephens P; Brown M; Miller VA, 2014. Emergence of constitutively active estrogen receptor-α mutations in pretreated advanced estrogen receptor-positive breast cancer.  Clin Cancer Res 20(7):1757-67

Wang H; Zang C; Taing L; Arnett KL; Wong YJ; Pear WS; Blacklow SC; Liu XS; Aster JC, 2014. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers.  Proc Natl Acad Sci U S A 111(2):705-10

Chin YR; Yoshida T; Marusyk A; Beck AH; Polyak K; Toker A, 2014. Targeting Akt3 signaling in triple-negative breast cancer.  Cancer Res 74(3):964-73

Bailey ST; Miron PL; Choi YJ; Kochupurakkal B; Maulik G; Rodig SJ; Tian R; Foley KM; Bowman T; Miron A; Brown M; Iglehart JD; Biswas DK, 2014. NF-κB activation-induced anti-apoptosis renders HER2-positive cells drug resistant and accelerates tumor growth.  Mol Cancer Res 12(3):408-20

Kim TH; Li F; Ferreiro-Neira I; Ho LL; Luyten A; Nalapareddy K; Long H; Verzi M; Shivdasani RA, 2014. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity.  Nature 506(7489):511-5

He HH; Meyer CA; Hu SS; Chen MW; Zang C; Liu Y; Rao PK; Fei T; Xu H; Long H; Liu XS; Brown M, 2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.  Nat Methods 11(1):73-8

Pathania S; Bade S; Le Guillou M; Burke K; Reed R; Bowman-Colin C; Su Y; Ting DT; Polyak K; Richardson AL; Feunteun J; Garber JE; Livingston DM, 2014. BRCA1 haploinsufficiency for replication stress suppression in primary cells.  Nat Commun 5:5496

Zou MR; Cao J; Liu Z; Huh SJ; Polyak K; Yan Q, 2014. Histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) controls mammary gland development by regulating key developmental and lineage specification genes.  J Biol Chem 289(25):17620-33

Hu Y; Petit SA; Ficarro SB; Toomire KJ; Xie A; Lim E; Cao SA; Park E; Eck MJ; Scully R; Brown M; Marto JA; Livingston DM, 2014. PARP1-driven poly-ADP-ribosylation regulates BRCA1 function in homologous recombination-mediated DNA repair.  Cancer Discov 4(12):1430-47

Meyer CA; Liu XS, 2014. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.  Nat Rev Genet 15(11):709-21

Al Olama AA; Kote-Jarai Z; Berndt SI; Conti DV; Schumacher F; Han Y; Benlloch S; Hazelett DJ; Wang Z; Saunders E; Leongamornlert D; Lindstrom S; Jugurnauth-Little S; Dadaev T; Tymrakiewicz M; Stram DO; Rand K; Wan P; Stram A; Sheng X; Pooler LC; Park K; Xia L; Tyrer J; Kolonel LN; Le Marchand L; Hoover RN; Machiela MJ; Yeager M; Burdette L; Chung CC; Hutchinson A; Yu K; Goh C; Ahmed M; Govindasami K; Guy M; Tammela TL; Auvinen A; Wahlfors T; Schleutker J; Visakorpi T; Leinonen KA; Xu J; Aly M; Donovan J; Travis RC; Key TJ; Siddiq A; Canzian F; Khaw KT; Takahashi A; Kubo M; Pharoah P; Pashayan N; Weischer M; Nordestgaard BG; Nielsen SF; Klarskov P; Røder MA; Iversen P; Thibodeau SN; McDonnell SK; Schaid DJ; Stanford JL; Kolb S; Holt S; Knudsen B; Coll AH; Gapstur SM; Diver WR; Stevens VL; Maier C; Luedeke M; Herkommer K; Rinckleb AE; Strom SS; Pettaway C; Yeboah ED; Tettey Y; Biritwum RB; Adjei AA; Tay E; Truelove A; Niwa S; Chokkalingam AP; Cannon-Albright L; Cybulski C; Wokołorczyk D; Kluźniak W; Park J; Sellers T; Lin HY; Isaacs WB; Partin AW; Brenner H; Dieffenbach AK; Stegmaier C; Chen C; Giovannucci EL; Ma J; Stampfer M; Penney KL; Mucci L; John EM; Ingles SA; Kittles RA; Murphy AB; Pandha H; Michael A; Kierzek AM; Blot W; Signorello LB; Zheng W; Albanes D; Virtamo J; Weinstein S; Nemesure B; Carpten J; Leske C; Wu SY; Hennis A; Kibel AS; Rybicki BA; Neslund-Dudas C; Hsing AW; Chu L; Goodman PJ; Klein EA; Zheng SL; Batra J; Clements J; Spurdle A; Teixeira MR; Paulo P; Maia S; Slavov C; Kaneva R; Mitev V; Witte JS; Casey G; Gillanders EM; Seminara D; Riboli E; Hamdy FC; Coetzee GA; Li Q; Freedman ML; Hunter DJ; Muir K; Gronberg H; Neal DE; Southey M; Giles GG; Severi G; Cook MB; Nakagawa H; Wiklund F; Kraft P; Chanock SJ; Henderson BE; Easton DF; Eeles RA; Haiman CA, 2014. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.  Nat Genet 46(10):1103-9

Cato L; Neeb A; Brown M; Cato AC, 2014. Control of steroid receptor dynamics and function by genomic actions of the cochaperones p23 and Bag-1L.  Nucl Recept Signal 12:e005

Cuiffo BG; Campagne A; Bell GW; Lembo A; Orso F; Lien EC; Bhasin MK; Raimo M; Hanson SE; Marusyk A; El-Ashry D; Hematti P; Polyak K; Mechta-Grigoriou F; Mariani O; Volinia S; Vincent-Salomon A; Taverna D; Karnoub AE, 2014. MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis.  Cell Stem Cell 15(6):762-74

Meng FL; Du Z; Federation A; Hu J; Wang Q; Kieffer-Kwon KR; Meyers RM; Amor C; Wasserman CR; Neuberg D; Casellas R; Nussenzweig MC; Bradner JE; Liu XS; Alt FW, 2014. Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability.  Cell 159(7):1538-48

Cai C; He HH; Gao S; Chen S; Yu Z; Gao Y; Chen S; Chen MW; Zhang J; Ahmed M; Wang Y; Metzger E; Schüle R; Liu XS; Brown M; Balk SP, 2014. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity.  Cell Rep 9(5):1618-27

Liu SY; Wong SK; Ng EK, 2014. Novel oesophago-gastro-duodenal stenting for gastric leaks after laparoscopic sleeve gastrectomy.  Obes Res Clin Pract.

Li W; Xu H; Xiao T; Cong L; Love MI; Zhang F; Irizarry RA; Liu JS; Brown M; Liu XS, 2014. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.  Genome Biol 15(12):554

Luyten A; Zang C; Liu XS; Shivdasani RA, 2014. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells.  Genes Dev 28(16):1827-39

Janiszewska M; Beca F; Polyak K, 2014. Tumor heterogeneity: the Lernaean hydra of oncology?  Oncology (Williston Park) 28(9):781-2, 784

Hu CY; Mohtat D; Yu Y; Ko YA; Shenoy N; Bhattacharya S; Izquierdo MC; Park AS; Giricz O; Vallumsetla N; Gundabolu K; Ware K; Bhagat TD; Suzuki M; Pullman J; Liu XS; Greally JM; Susztak K; Verma A, 2014. Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival.  Clin Cancer Res 20(16):4349-60

Yoo S; Pettersson A; Jordahl KM; Lis RT; Lindstrom S; Meisner A; Nuttall EJ; Stack EC; Stampfer MJ; Kraft P; Brown M; Loda M; Giovannucci EL; Kantoff PW; Mucci LA, 2014. Androgen receptor CAG repeat polymorphism and risk of TMPRSS2:ERG-positive prostate cancer.  Cancer Epidemiol Biomarkers Prev 23(10):2027-31

Li Q; Stram A; Chen C; Kar S; Gayther S; Pharoah P; Haiman C; Stranger B; Kraft P; Freedman ML, 2014. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.  Hum Mol Genet 23(19):5294-302

Feng R; Aihara E; Kenny S; Yang L; Li J; Varro A; Montrose MH; Shroyer NF; Wang TC; Shivdasani RA; Zavros Y, 2014. Indian Hedgehog mediates gastrin-induced proliferation in stomach of adult mice.  Gastroenterology 147(3):655-666.e9

Wang J; Lin X; Wang S; Wang C; Wang Q; Duan X; Lu P; Wang Q; Wang C; Liu XS; Huang J, 2014. PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression.  Sci Rep 4:5008

Morris SA; Cahan P; Li H; Zhao AM; San Roman AK; Shivdasani RA; Collins JJ; Daley GQ, 2014. Dissecting engineered cell types and enhancing cell fate conversion via CellNet.  Cell 158(4):889-902

Yamamoto S; Wu Z; Russnes HG; Takagi S; Peluffo G; Vaske C; Zhao X; Moen Vollan HK; Maruyama R; Ekram MB; Sun H; Kim JH; Carver K; Zucca M; Feng J; Almendro V; Bessarabova M; Rueda OM; Nikolsky Y; Caldas C; Liu XS; Polyak K, 2014. JARID1B is a luminal lineage-driving oncogene in breast cancer.  Cancer Cell 25(6):762-77

Stoeck A; Lejnine S; Truong A; Pan L; Wang H; Zang C; Yuan J; Ware C; MacLean J; Garrett-Engele PW; Kluk M; Laskey J; Haines BB; Moskaluk C; Zawel L; Fawell S; Gilliland G; Zhang T; Kremer BE; Knoechel B; Bernstein BE; Pear WS; Liu XS; Aster JC; Sathyanarayanan S, 2014. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma.  Cancer Discov 4(10):1154-67

Marusyk A; Tabassum DP; Altrock PM; Almendro V; Michor F; Polyak K, 2014. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity.  Nature 514(7520):54-8

Dreijerink KM; Goudet P; Burgess JR; Valk GD, 2014. Breast-cancer predisposition in multiple endocrine neoplasia type 1.  N Engl J Med 371(6):583-4

Gordon FK; Vallaster CS; Westerling T; Iyer LK; Brown M; Schnitzler GR, 2014. Research resource: Aorta- and liver-specific ERα-binding patterns and gene regulation by estrogen.  Mol Endocrinol 28(8):1337-51

Shin H; Liu T; Duan X; Zhang Y; Liu XS, 2013. Computational methodology for ChIP-seq analysis.  Quant Biol 1(1):54-70

Cai C; Wang H; He HH; Chen S; He L; Ma F; Mucci L; Wang Q; Fiore C; Sowalsky AG; Loda M; Liu XS; Brown M; Balk SP; Yuan X, 2013. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.  J Clin Invest 123(3):1109-22

Ho LL; Sinha A; Verzi M; Bernt KM; Armstrong SA; Shivdasani RA, 2013. DOT1L-mediated H3K79 methylation in chromatin is dispensable for Wnt pathway-specific and other intestinal epithelial functions.  Mol Cell Biol 33(9):1735-45

Mahdavi A; Segall-Shapiro TH; Kou S; Jindal GA; Hoff KG; Liu S; Chitsaz M; Ismagilov RF; Silberg JJ; Tirrell DA, 2013. A genetically encoded and gate for cell-targeted metabolic labeling of proteins.  J Am Chem Soc 135(8):2979-82

Bergmann KR; Liu SX; Tian R; Kushnir A; Turner JR; Li HL; Chou PM; Weber CR; De Plaen IG, 2013. Bifidobacteria stabilize claudins at tight junctions and prevent intestinal barrier dysfunction in mouse necrotizing enterocolitis.  Am J Pathol 182(5):1595-606

Zhang X; Peterson KA; Liu XS; McMahon AP; Ohba S, 2013. Gene regulatory networks mediating canonical Wnt signal-directed control of pluripotency and differentiation in embryo stem cells.  Stem Cells 31(12):2667-79

Sun H; Qin B; Liu T; Wang Q; Liu J; Wang J; Lin X; Yang Y; Taing L; Rao PK; Brown M; Zhang Y; Long HW; Liu XS, 2013. CistromeFinder for ChIP-seq and DNase-seq data reuse.  Bioinformatics 29(10):1352-4

Verzi MP; Shin H; San Roman AK; Liu XS; Shivdasani RA, 2013. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.  Mol Cell Biol 33(2):281-92

Ni M; Chen Y; Fei T; Li D; Lim E; Liu XS; Brown M, 2013. Amplitude modulation of androgen signaling by c-MYC.  Genes Dev 27(7):734-48

Almendro V; Marusyk A; Polyak K, 2013. Cellular heterogeneity and molecular evolution in cancer.  Annu Rev Pathol 8:277-302

Chiu PW; Wu JC; Teoh AY; Chan Y; Wong SK; Liu SY; Yung MY; Lam CC; Sung JJ; Chan FK; Lau JY; Ng EK, 2013. Peroral endoscopic myotomy for treatment of achalasia: from bench to bedside (with video).  Gastrointest Endosc 77(1):29-38

Schutz FA; Pomerantz MM; Gray KP; Atkins MB; Rosenberg JE; Hirsch MS; McDermott DF; Lampron ME; Lee GS; Signoretti S; Kantoff PW; Freedman ML; Choueiri TK, 2013. Single nucleotide polymorphisms and risk of recurrence of renal-cell carcinoma: a cohort study.  Lancet Oncol 14(1):81-7

Trynka G; Sandor C; Han B; Xu H; Stranger BE; Liu XS; Raychaudhuri S, 2013. Chromatin marks identify critical cell types for fine mapping complex trait variants.  Nat Genet 45(2):124-30

Li Q; Seo JH; Stranger B; McKenna A; Pe'er I; Laframboise T; Brown M; Tyekucheva S; Freedman ML, 2013. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.  Cell 152(3):633-41

Marusyk A; Polyak K, 2013. Cancer. Cancer cell phenotypes, in fifty shades of grey.  Science 339(6119):528-9

Du Z; Li H; Wei Q; Zhao X; Wang C; Zhu Q; Yi X; Xu W; Liu XS; Jin W; Su Z, 2013. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.  Mol Plant 6(5):1463-72

Lobo GP; Amengual J; Baus D; Shivdasani RA; Taylor D; von Lintig J, 2013. Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX.  J Biol Chem 288(13):9017-27

Seo JH; Li Q; Fatima A; Eklund A; Szallasi Z; Polyak K; Richardson AL; Freedman ML, 2013. Deconvoluting complex tissues for expression quantitative trait locus-based analyses.  Philos Trans R Soc Lond B Biol Sci 368(1620):20120363

Francis JM; Kiezun A; Ramos AH; Serra S; Pedamallu CS; Qian ZR; Banck MS; Kanwar R; Kulkarni AA; Karpathakis A; Manzo V; Contractor T; Philips J; Nickerson E; Pho N; Hooshmand SM; Brais LK; Lawrence MS; Pugh T; McKenna A; Sivachenko A; Cibulskis K; Carter SL; Ojesina AI; Freeman S; Jones RT; Voet D; Saksena G; Auclair D; Onofrio R; Shefler E; Sougnez C; Grimsby J; Green L; Lennon N; Meyer T; Caplin M; Chung DC; Beutler AS; Ogino S; Thirlwell C; Shivdasani R; Asa SL; Harris CR; Getz G; Kulke M; Meyerson M, 2013. Somatic mutation of CDKN1B in small intestine neuroendocrine tumors.  Nat Genet 45(12):1483-6

Timmerman LA; Holton T; Yuneva M; Louie RJ; Padró M; Daemen A; Hu M; Chan DA; Ethier SP; van 't Veer LJ; Polyak K; McCormick F; Gray JW, 2013. Glutamine sensitivity analysis identifies the xCT antiporter as a common triple-negative breast tumor therapeutic target.  Cancer Cell 24(4):450-65

Wang H; Meyer CA; Fei T; Wang G; Zhang F; Liu XS, 2013. A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer.  BMC Genomics 14:680

Merenbakh-Lamin K; Ben-Baruch N; Yeheskel A; Dvir A; Soussan-Gutman L; Jeselsohn R; Yelensky R; Brown M; Miller VA; Sarid D; Rizel S; Klein B; Rubinek T; Wolf I, 2013. D538G mutation in estrogen receptor-α: A novel mechanism for acquired endocrine resistance in breast cancer.  Cancer Res 73(23):6856-64

Wang S; Sun H; Ma J; Zang C; Wang C; Wang J; Tang Q; Meyer CA; Zhang Y; Liu XS, 2013. Target analysis by integration of transcriptome and ChIP-seq data with BETA.  Nat Protoc 8(12):2502-15

Nan H; Morikawa T; Suuriniemi M; Imamura Y; Werner L; Kuchiba A; Yamauchi M; Hunter DJ; Kraft P; Giovannucci EL; Fuchs CS; Ogino S; Freedman ML; Chan AT, 2013. Aspirin use, 8q24 single nucleotide polymorphism rs6983267, and colorectal cancer according to CTNNB1 alterations.  J Natl Cancer Inst 105(24):1852-61

Eswaran J; Horvath A; Godbole S; Reddy SD; Mudvari P; Ohshiro K; Cyanam D; Nair S; Fuqua SA; Polyak K; Florea LD; Kumar R, 2013. RNA sequencing of cancer reveals novel splicing alterations.  Sci Rep 3:1689

Masiello CA; Chen Y; Gao X; Liu S; Cheng HY; Bennett MR; Rudgers JA; Wagner DS; Zygourakis K; Silberg JJ, 2013. Biochar and microbial signaling: production conditions determine effects on microbial communication.  Environ Sci Technol 47(20):11496-503

Catic A; Suh CY; Hill CT; Daheron L; Henkel T; Orford KW; Dombkowski DM; Liu T; Liu XS; Scadden DT, 2013. Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation.  Cell 155(6):1380-95

McLaughlin SK; Olsen SN; Dake B; De Raedt T; Lim E; Bronson RT; Beroukhim R; Polyak K; Brown M; Kuperwasser C; Cichowski K, 2013. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor.  Cancer Cell 24(3):365-78

Du Z; Fei T; Verhaak RG; Su Z; Zhang Y; Brown M; Chen Y; Liu XS, 2013. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.  Nat Struct Mol Biol 20(7):908-13

Pignon JC; Grisanzio C; Geng Y; Song J; Shivdasani RA; Signoretti S, 2013. p63-expressing cells are the stem cells of developing prostate, bladder, and colorectal epithelia.  Proc Natl Acad Sci U S A 110(20):8105-10

Jeselsohn RM; Werner L; Regan MM; Fatima A; Gilmore L; Collins LC; Beck AH; Bailey ST; He HH; Buchwalter G; Brown M; Iglehart JD; Richardson A; Come SE, 2013. Digital quantification of gene expression in sequential breast cancer biopsies reveals activation of an immune response.  PLoS One 8(5):e64225

Pantel K; Diaz LA Jr; Polyak K, 2013. Tracking tumor resistance using 'liquid biopsies'.  Nat Med 19(6):676-7

Choudhury S; Almendro V; Merino VF; Wu Z; Maruyama R; Su Y; Martins FC; Fackler MJ; Bessarabova M; Kowalczyk A; Conway T; Beresford-Smith B; Macintyre G; Cheng YK; Lopez-Bujanda Z; Kaspi A; Hu R; Robens J; Nikolskaya T; Haakensen VD; Schnitt SJ; Argani P; Ethington G; Panos L; Grant M; Clark J; Herlihy W; Lin SJ; Chew G; Thompson EW; Greene-Colozzi A; Richardson AL; Rosson GD; Pike M; Garber JE; Nikolsky Y; Blum JL; Au A; Hwang ES; Tamimi RM; Michor F; Haviv I; Liu XS; Sukumar S; Polyak K, 2013. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics.  Cell Stem Cell 13(1):117-30

Buchwalter G; Hickey MM; Cromer A; Selfors LM; Gunawardane RN; Frishman J; Jeselsohn R; Lim E; Chi D; Fu X; Schiff R; Brown M; Brugge JS, 2013. PDEF promotes luminal differentiation and acts as a survival factor for ER-positive breast cancer cells.  Cancer Cell 23(6):753-67

Steenbergen RD; Ongenaert M; Snellenberg S; Trooskens G; van der Meide WF; Pandey D; Bloushtain-Qimron N; Polyak K; Meijer CJ; Snijders PJ; Van Criekinge W, 2013. Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis.  J Pathol 231(1):53-62

Liu SH; Heiland F, 2012. Should we get married? The effect of parents' marriage on out-of-wedlock children.  Econ Inq 50(1):17-38

Polyak K, 2012. On chromatin remodeling in mammary gland differentiation and breast tumorigenesis.  Cold Spring Harb Perspect Biol 4.

Polyak K; Vogt PK, 2012. Progress in breast cancer research.  Proc Natl Acad Sci U S A 109(8):2715-7

Kim TH; Escudero S; Shivdasani RA, 2012. Intact function of Lgr5 receptor-expressing intestinal stem cells in the absence of Paneth cells.  Proc Natl Acad Sci U S A 109(10):3932-7

Qin B; Zhou M; Ge Y; Taing L; Liu T; Wang Q; Wang S; Chen J; Shen L; Duan X; Hu S; Li W; Long H; Zhang Y; Liu XS, 2012. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.  Bioinformatics 28(10):1411-2

Marusyk A; Almendro V; Polyak K, 2012. Intra-tumour heterogeneity: a looking glass for cancer?  Nat Rev Cancer 12(5):323-34

He HH; Meyer CA; Chen MW; Jordan VC; Brown M; Liu XS, 2012. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.  Genome Res 22(6):1015-25

Mehta MM; Liu S; Silberg JJ, 2012. A transposase strategy for creating libraries of circularly permuted proteins.  Nucleic Acids Res 40(9):e71

Wang C; Tian R; Zhao Q; Xu H; Meyer CA; Li C; Zhang Y; Liu XS, 2012. Computational inference of mRNA stability from histone modification and transcriptome profiles.  Nucleic Acids Res 40(14):6414-23

Shivdasani RA, 2012. GEFs on the RhoAd to a colossal nucleus.  Dev Cell 22(3):471-2

Sun T; Yang M; Chen S; Balk S; Pomerantz M; Hsieh CL; Brown M; Lee GS; Kantoff PW, 2012. The altered expression of MiR-221/-222 and MiR-23b/-27b is associated with the development of human castration resistant prostate cancer.  Prostate 72(10):1093-103

Shrestha Y; Schafer EJ; Boehm JS; Thomas SR; He F; Du J; Wang S; Barretina J; Weir BA; Zhao JJ; Polyak K; Golub TR; Beroukhim R; Hahn WC, 2012. PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling.  Oncogene 31(29):3397-408

Kostic AD; Gevers D; Pedamallu CS; Michaud M; Duke F; Earl AM; Ojesina AI; Jung J; Bass AJ; Tabernero J; Baselga J; Liu C; Shivdasani RA; Ogino S; Birren BW; Huttenhower C; Garrett WS; Meyerson M, 2012. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.  Genome Res 22(2):292-8

Li JC; Leung KL; Ng SS; Liu SY; Lee JF; Hon SS, 2012. Laparoscopic-assisted versus open resection of right-sided colonic cancer--a prospective randomized controlled trial.  Int J Colorectal Dis 27(1):95-102

Maruyama R; Shipitsin M; Choudhury S; Wu Z; Protopopov A; Yao J; Lo PK; Bessarabova M; Ishkin A; Nikolsky Y; Liu XS; Sukumar S; Polyak K, 2012. Altered antisense-to-sense transcript ratios in breast cancer.  Proc Natl Acad Sci U S A 109(8):2820-4

Ho Sui SJ; Begley K; Reilly D; Chapman B; McGovern R; Rocca-Sera P; Maguire E; Altschuler GM; Hansen TA; Sompallae R; Krivtsov A; Shivdasani RA; Armstrong SA; Culhane AC; Correll M; Sansone SA; Hofmann O; Hide W, 2012. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.  Nucleic Acids Res 40(Database issue):D984-91

Chen Y; Negre N; Li Q; Mieczkowska JO; Slattery M; Liu T; Zhang Y; Kim TK; He HH; Zieba J; Ruan Y; Bickel PJ; Myers RM; Wold BJ; White KP; Lieb JD; Liu XS, 2012. Systematic evaluation of factors influencing ChIP-seq fidelity.  Nat Methods 9(6):609-14

Jiao X; Wood LD; Lindman M; Jones S; Buckhaults P; Polyak K; Sukumar S; Carter H; Kim D; Karchin R; Sjöblom T, 2012. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers.  Genes Chromosomes Cancer 51(5):480-9

Balko JM; Miller TW; Morrison MM; Hutchinson K; Young C; Rinehart C; Sánchez V; Jee D; Polyak K; Prat A; Perou CM; Arteaga CL; Cook RS, 2012. The receptor tyrosine kinase ErbB3 maintains the balance between luminal and basal breast epithelium.  Proc Natl Acad Sci U S A 109(1):221-6

Vu MT; Zhai P; Lee J; Guerra C; Liu S; Gustin MC; Silberg JJ, 2012. The DNLZ/HEP zinc-binding subdomain is critical for regulation of the mitochondrial chaperone HSPA9.  Protein Sci 21(2):258-67

Horst D; Chen J; Morikawa T; Ogino S; Kirchner T; Shivdasani RA, 2012. Differential WNT activity in colorectal cancer confers limited tumorigenic potential and is regulated by MAPK signaling.  Cancer Res 72(6):1547-56

Martins FC; De S; Almendro V; Gönen M; Park SY; Blum JL; Herlihy W; Ethington G; Schnitt SJ; Tung N; Garber JE; Fetten K; Michor F; Polyak K, 2012. Evolutionary pathways in BRCA1-associated breast tumors.  Cancer Discov 2(6):503-11

Landt SG; Marinov GK; Kundaje A; Kheradpour P; Pauli F; Batzoglou S; Bernstein BE; Bickel P; Brown JB; Cayting P; Chen Y; DeSalvo G; Epstein C; Fisher-Aylor KI; Euskirchen G; Gerstein M; Gertz J; Hartemink AJ; Hoffman MM; Iyer VR; Jung YL; Karmakar S; Kellis M; Kharchenko PV; Li Q; Liu T; Liu XS; Ma L; Milosavljevic A; Myers RM; Park PJ; Pazin MJ; Perry MD; Raha D; Reddy TE; Rozowsky J; Shoresh N; Sidow A; Slattery M; Stamatoyannopoulos JA; Tolstorukov MY; White KP; Xi S; Farnham PJ; Lieb JD; Wold BJ; Snyder M, 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.  Genome Res 22(9):1813-31

Meyer CA; Tang Q; Liu XS, 2012. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.  Mol Endocrinol 26(10):1651-9

Xu K; Wu ZJ; Groner AC; He HH; Cai C; Lis RT; Wu X; Stack EC; Loda M; Liu T; Xu H; Cato L; Thornton JE; Gregory RI; Morrissey C; Vessella RL; Montironi R; Magi-Galluzzi C; Kantoff PW; Balk SP; Liu XS; Brown M, 2012. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.  Science 338(6113):1465-9

Feng J; Meyer CA; Wang Q; Liu JS; Shirley Liu X; Zhang Y, 2012. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.  Bioinformatics 28(21):2782-8

Chiu PW; Wong TC; Teoh AY; To KF; Liu SY; Wong SK; Chan FK; Ng EK, 2012. Recognition of changes in microvascular and microstructural patterns upon magnifying endoscopy predicted the presence of extranodal gastric MALToma.  J Interv Gastroenterol 2(1):3-7

Benson MJ; Aijö T; Chang X; Gagnon J; Pape UJ; Anantharaman V; Aravind L; Pursiheimo JP; Oberdoerffer S; Liu XS; Lahesmaa R; Lähdesmäki H; Rao A, 2012. Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells.  Proc Natl Acad Sci U S A 109(40):16252-7

Xu Y; Xu C; Kato A; Tempel W; Abreu JG; Bian C; Hu Y; Hu D; Zhao B; Cerovina T; Diao J; Wu F; He HH; Cui Q; Clark E; Ma C; Barbara A; Veenstra GJ; Xu G; Kaiser UB; Liu XS; Sugrue SP; He X; Min J; Kato Y; Shi YG, 2012. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.  Cell 151(6):1200-13

Beck S; Bernstein BE; Campbell RM; Costello JF; Dhanak D; Ecker JR; Greally JM; Issa JP; Laird PW; Polyak K; Tycko B; Jones PA, 2012. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.  Cancer Res 72(24):6319-24

Bailey ST; Shin H; Westerling T; Liu XS; Brown M, 2012. Estrogen receptor prevents p53-dependent apoptosis in breast cancer.  Proc Natl Acad Sci U S A 109(44):18060-5

Takada K; Zhu D; Bird GH; Sukhdeo K; Zhao JJ; Mani M; Lemieux M; Carrasco DE; Ryan J; Horst D; Fulciniti M; Munshi NC; Xu W; Kung AL; Shivdasani RA; Walensky LD; Carrasco DR, 2012. Targeted disruption of the BCL9/β-catenin complex inhibits oncogenic Wnt signaling.  Sci Transl Med 4(148):148ra117

Polyak K; Metzger Filho O, 2012. SnapShot: breast cancer.  Cancer Cell 22(4):562-562.e1

Chiu PW; Teoh AY; To KF; Wong SK; Liu SY; Lam CC; Yung MY; Chan FK; Lau JY; Ng EK, 2012. Endoscopic submucosal dissection (ESD) compared with gastrectomy for treatment of early gastric neoplasia: a retrospective cohort study.  Surg Endosc 26(12):3584-91

Vegfors J; Petersson S; Kovács A; Polyak K; Enerbäck C, 2012. The expression of Psoriasin (S100A7) and CD24 is linked and related to the differentiation of mammary epithelial cells.  PLoS One 7(12):e53119

Fu K; Tang Q; Feng J; Liu XS; Zhang Y, 2012. DiNuP: a systematic approach to identify regions of differential nucleosome positioning.  Bioinformatics 28(15):1965-71

Grisanzio C; Werner L; Takeda D; Awoyemi BC; Pomerantz MM; Yamada H; Sooriakumaran P; Robinson BD; Leung R; Schinzel AC; Mills I; Ross-Adams H; Neal DE; Kido M; Yamamoto T; Petrozziello G; Stack EC; Lis R; Kantoff PW; Loda M; Sartor O; Egawa S; Tewari AK; Hahn WC; Freedman ML, 2012. Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis.  Proc Natl Acad Sci U S A 109(28):11252-7

Banerji S; Cibulskis K; Rangel-Escareno C; Brown KK; Carter SL; Frederick AM; Lawrence MS; Sivachenko AY; Sougnez C; Zou L; Cortes ML; Fernandez-Lopez JC; Peng S; Ardlie KG; Auclair D; Bautista-Piña V; Duke F; Francis J; Jung J; Maffuz-Aziz A; Onofrio RC; Parkin M; Pho NH; Quintanar-Jurado V; Ramos AH; Rebollar-Vega R; Rodriguez-Cuevas S; Romero-Cordoba SL; Schumacher SE; Stransky N; Thompson KM; Uribe-Figueroa L; Baselga J; Beroukhim R; Polyak K; Sgroi DC; Richardson AL; Jimenez-Sanchez G; Lander ES; Gabriel SB; Garraway LA; Golub TR; Melendez-Zajgla J; Toker A; Getz G; Hidalgo-Miranda A; Meyerson M, 2012. Sequence analysis of mutations and translocations across breast cancer subtypes.  Nature 486(7403):405-9

Kim TH; Shivdasani RA, 2012. Stem cell niches: famished Paneth cells, gluttonous stem cells.  Curr Biol 22(14):R579-80

Polyak K, 2012. On using functional genetics to understand breast cancer biology.  Cold Spring Harb Perspect Biol 4(7):a013516

Bhatia S; Frangioni JV; Hoffman RM; Iafrate AJ; Polyak K, 2012. The challenges posed by cancer heterogeneity.  Nat Biotechnol 30(7):604-10

Dulak AM; Schumacher SE; van Lieshout J; Imamura Y; Fox C; Shim B; Ramos AH; Saksena G; Baca SC; Baselga J; Tabernero J; Barretina J; Enzinger PC; Corso G; Roviello F; Lin L; Bandla S; Luketich JD; Pennathur A; Meyerson M; Ogino S; Shivdasani RA; Beer DG; Godfrey TE; Beroukhim R; Bass AJ, 2012. Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis.  Cancer Res 72(17):4383-93

Kim TH; Shivdasani RA, 2011. Notch signaling in stomach epithelial stem cell homeostasis.  J Exp Med 208(4):677-88

Verzi MP; Shin H; Ho LL; Liu XS; Shivdasani RA, 2011. Essential and redundant functions of caudal family proteins in activating adult intestinal genes.  Mol Cell Biol 31(10):2026-39

Bessarabova M; Pustovalova O; Shi W; Serebriyskaya T; Ishkin A; Polyak K; Velculescu VE; Nikolskaya T; Nikolsky Y, 2011. Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.  Cancer Res 71(10):3471-81

Feng D; Liu T; Sun Z; Bugge A; Mullican SE; Alenghat T; Liu XS; Lazar MA, 2011. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism.  Science 331(6022):1315-9

Meyer CA; He HH; Brown M; Liu XS, 2011. BINOCh: binding inference from nucleosome occupancy changes.  Bioinformatics 27(13):1867-8

Polyak K; Garber J, 2011. Targeting the missing links for cancer therapy.  Nat Med 17(3):283-4

Maruyama R; Choudhury S; Kowalczyk A; Bessarabova M; Beresford-Smith B; Conway T; Kaspi A; Wu Z; Nikolskaya T; Merino VF; Lo PK; Liu XS; Nikolsky Y; Sukumar S; Haviv I; Polyak K, 2011. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.  PLoS Genet 7(4):e1001369

Flavin RJ; Cook J; Fiorentino M; Bailey D; Brown M; Loda MF, 2011. β-Catenin is a useful adjunct immunohistochemical marker for the diagnosis of pulmonary lymphangioleiomyomatosis.  Am J Clin Pathol 135(5):776-82

Chaffer CL; Brueckmann I; Scheel C; Kaestli AJ; Wiggins PA; Rodrigues LO; Brooks M; Reinhardt F; Su Y; Polyak K; Arendt LM; Kuperwasser C; Bierie B; Weinberg RA, 2011. Normal and neoplastic nonstem cells can spontaneously convert to a stem-like state.  Proc Natl Acad Sci U S A 108(19):7950-5

Teoh AY; Yan Chiu PW; Wong TC; Liu SY; Hung Wong SK; Ng EK, 2011. Functional performance and quality of life in patients with squamous esophageal carcinoma receiving surgery or chemoradiation: results from a randomized trial.  Ann Surg 253(1):1-5

Mills JC; Shivdasani RA, 2011. Gastric epithelial stem cells.  Gastroenterology 140(2):412-24

Sun T; Mary LG; Oh WK; Freedman ML; Pomerantz M; Pienta KJ; Kantoff PW, 2011. Inherited variants in the chemokine CCL2 gene and prostate cancer aggressiveness in a Caucasian cohort.  Clin Cancer Res 17(6):1546-52

Pastor WA; Pape UJ; Huang Y; Henderson HR; Lister R; Ko M; McLoughlin EM; Brudno Y; Mahapatra S; Kapranov P; Tahiliani M; Daley GQ; Liu XS; Ecker JR; Milos PM; Agarwal S; Rao A, 2011. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.  Nature 473(7347):394-7

Liu T; Rechtsteiner A; Egelhofer TA; Vielle A; Latorre I; Cheung MS; Ercan S; Ikegami K; Jensen M; Kolasinska-Zwierz P; Rosenbaum H; Shin H; Taing S; Takasaki T; Iniguez AL; Desai A; Dernburg AF; Kimura H; Lieb JD; Ahringer J; Strome S; Liu XS, 2011. Broad chromosomal domains of histone modification patterns in C. elegans.  Genome Res 21(2):227-36

Cao Q; Zhou M; Wang X; Meyer CA; Zhang Y; Chen Z; Li C; Liu XS, 2011. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.  Nucleic Acids Res 39(Database issue):D968-74

Kim BM; Woo J; Kanellopoulou C; Shivdasani RA, 2011. Regulation of mouse stomach development and Barx1 expression by specific microRNAs.  Development 138(6):1081-6

Wang X; Laurie JD; Liu T; Wentz J; Liu XS, 2011. Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites.  Genomics 97(4):235-43

Kim TH; Shivdasani RA, 2011. Genetic evidence that intestinal Notch functions vary regionally and operate through a common mechanism of Math1 repression.  J Biol Chem 286(13):11427-33

Pomerantz MM; Werner L; Xie W; Regan MM; Lee GS; Sun T; Evan C; Petrozziello G; Nakabayashi M; Oh WK; Kantoff PW; Freedman ML, 2011. Association of prostate cancer risk Loci with disease aggressiveness and prostate cancer-specific mortality.  Cancer Prev Res (Phila) 4(5):719-28

Yang M; Xie W; Mostaghel E; Nakabayashi M; Werner L; Sun T; Pomerantz M; Freedman M; Ross R; Regan M; Sharifi N; Figg WD; Balk S; Brown M; Taplin ME; Oh WK; Lee GS; Kantoff PW, 2011. SLCO2B1 and SLCO1B3 may determine time to progression for patients receiving androgen deprivation therapy for prostate cancer.  J Clin Oncol 29(18):2565-73

Xu J; Liu S; Chen M; Ma J; Matthews KS, 2011. Altering residues N125 and D149 impacts sugar effector binding and allosteric parameters in Escherichia coli lactose repressor.  Biochemistry 50(42):9002-13

Sun T; Oh WK; Jacobus S; Regan M; Pomerantz M; Freedman ML; Lee GS; Kantoff PW, 2011. The impact of common genetic variations in genes of the sex hormone metabolic pathways on steroid hormone levels and prostate cancer aggressiveness.  Cancer Prev Res (Phila) 4(12):2044-50

Yonesaka K; Zejnullahu K; Okamoto I; Satoh T; Cappuzzo F; Souglakos J; Ercan D; Rogers A; Roncalli M; Takeda M; Fujisaka Y; Philips J; Shimizu T; Maenishi O; Cho Y; Sun J; Destro A; Taira K; Takeda K; Okabe T; Swanson J; Itoh H; Takada M; Lifshits E; Okuno K; Engelman JA; Shivdasani RA; Nishio K; Fukuoka M; Varella-Garcia M; Nakagawa K; Jänne PA, 2011. Activation of ERBB2 signaling causes resistance to the EGFR-directed therapeutic antibody cetuximab.  Sci Transl Med 3(99):99ra86

Marotta LL; Polyak K, 2011. Unraveling the complexity of basal-like breast cancer.  Oncotarget 2(8):588-9

Polyak K, 2011. Heterogeneity in breast cancer.  J Clin Invest 121(10):3786-8

Cai C; He HH; Chen S; Coleman I; Wang H; Fang Z; Chen S; Nelson PS; Liu XS; Brown M; Balk SP, 2011. Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1.  Cancer Cell 20(4):457-71

Wang X; Liu XS, 2011. Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.  Front Genet 2:25

Adams DJ; Berger B; Harismendy O; Huttenhower C; Liu XS; Myers CL; Oshlack A; Rinn JL; Walhout AJ, 2011. Genomics in 2011: challenges and opportunities.  Genome Biol 12(12):137

Place AE; Jin Huh S; Polyak K, 2011. The microenvironment in breast cancer progression: biology and implications for treatment.  Breast Cancer Res 13(6):227

Liu T; Ortiz JA; Taing L; Meyer CA; Lee B; Zhang Y; Shin H; Wong SS; Ma J; Lei Y; Pape UJ; Poidinger M; Chen Y; Yeung K; Brown M; Turpaz Y; Liu XS, 2011. Cistrome: an integrative platform for transcriptional regulation studies.  Genome Biol 12(8):R83

Pomerantz MM; Freedman ML, 2011. The genetics of cancer risk.  Cancer J 17(6):416-22

Scott SM; Brown M; Come SE, 2011. Emerging data on the efficacy and safety of fulvestrant, a unique antiestrogen therapy for advanced breast cancer.  Expert Opin Drug Saf 10(5):819-26

San Roman AK; Shivdasani RA, 2011. Boundaries, junctions and transitions in the gastrointestinal tract.  Exp Cell Res 317(19):2711-8

Marotta LL; Almendro V; Marusyk A; Shipitsin M; Schemme J; Walker SR; Bloushtain-Qimron N; Kim JJ; Choudhury SA; Maruyama R; Wu Z; Gönen M; Mulvey LA; Bessarabova MO; Huh SJ; Silver SJ; Kim SY; Park SY; Lee HE; Anderson KS; Richardson AL; Nikolskaya T; Nikolsky Y; Liu XS; Root DE; Hahn WC; Frank DA; Polyak K, 2011. The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors.  J Clin Invest 121(7):2723-35

Zhang J; Roberts TM; Shivdasani RA, 2011. Targeting PI3K signaling as a therapeutic approach for colorectal cancer.  Gastroenterology 141(1):50-61

Ni M; Chen Y; Lim E; Wimberly H; Bailey ST; Imai Y; Rimm DL; Liu XS; Brown M, 2011. Targeting androgen receptor in estrogen receptor-negative breast cancer.  Cancer Cell 20(1):119-31

Kim TH; Kim BM; Mao J; Rowan S; Shivdasani RA, 2011. Endodermal Hedgehog signals modulate Notch pathway activity in the developing digestive tract mesenchyme.  Development 138(15):3225-33

Freedman ML; Monteiro AN; Gayther SA; Coetzee GA; Risch A; Plass C; Casey G; De Biasi M; Carlson C; Duggan D; James M; Liu P; Tichelaar JW; Vikis HG; You M; Mills IG, 2011. Principles for the post-GWAS functional characterization of cancer risk loci.  Nat Genet 43(6):513-8

Woo J; Miletich I; Kim BM; Sharpe PT; Shivdasani RA, 2011. Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation.  PLoS One 6(7):e22493

Torres-Arzayus MI; Zhao J; Bronson R; Brown M, 2010. Estrogen-dependent and estrogen-independent mechanisms contribute to AIB1-mediated tumor formation.  Cancer Res 70(10):4102-11

Mao J; Kim BM; Rajurkar M; Shivdasani RA; McMahon AP, 2010. Hedgehog signaling controls mesenchymal growth in the developing mammalian digestive tract.  Development 137(10):1721-9

Wong YS; Liu SY; Ng SS; Wong VW; Mak OS; Li JC; Lee JF, 2010. Giant Meckel's diverticulitis: a rare condition complicating pregnancy.  Am J Surg 200(1):184-5

Petersen OW; Polyak K, 2010. Stem cells in the human breast.  Cold Spring Harb Perspect Biol 2(5):a003160

Kamata M; Liu S; Liang M; Nagaoka Y; Chen IS, 2010. Generation of human induced pluripotent stem cells bearing an anti-HIV transgene by a lentiviral vector carrying an internal murine leukemia virus promoter.  Hum Gene Ther 21(11):1555-67

Polyak K; Kalluri R, 2010. The role of the microenvironment in mammary gland development and cancer.  Cold Spring Harb Perspect Biol 2(11):a003244

Miron A; Varadi M; Carrasco D; Li H; Luongo L; Kim HJ; Park SY; Cho EY; Lewis G; Kehoe S; Iglehart JD; Dillon D; Allred DC; Macconaill L; Gelman R; Polyak K, 2010. PIK3CA mutations in in situ and invasive breast carcinomas.  Cancer Res 70(14):5674-8

Hirsch HA; Iliopoulos D; Joshi A; Zhang Y; Jaeger SA; Bulyk M; Tsichlis PN; Shirley Liu X; Struhl K, 2010. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.  Cancer Cell 17(4):348-61

Li JC; Liu SY; Lo AW; Hon SS; Ng SS; Lee JF; Leung KL, 2010. The learning curve for endorectal ultrasonography in rectal cancer staging.  Surg Endosc 24(12):3054-9

Ahmadiyeh N; Pomerantz MM; Grisanzio C; Herman P; Jia L; Almendro V; He HH; Brown M; Liu XS; Davis M; Caswell JL; Beckwith CA; Hills A; Macconaill L; Coetzee GA; Regan MM; Freedman ML, 2010. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC.  Proc Natl Acad Sci U S A 107(21):9742-6

Wolfer A; Wittner BS; Irimia D; Flavin RJ; Lupien M; Gunawardane RN; Meyer CA; Lightcap ES; Tamayo P; Mesirov JP; Liu XS; Shioda T; Toner M; Loda M; Brown M; Brugge JS; Ramaswamy S, 2010. MYC regulation of a "poor-prognosis" metastatic cancer cell state.  Proc Natl Acad Sci U S A 107(8):3698-703

Bienvenu F; Jirawatnotai S; Elias JE; Meyer CA; Mizeracka K; Marson A; Frampton GM; Cole MF; Odom DT; Odajima J; Geng Y; Zagozdzon A; Jecrois M; Young RA; Liu XS; Cepko CL; Gygi SP; Sicinski P, 2010. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.  Nature 463(7279):374-8

Sun T; Lee GS; Werner L; Pomerantz M; Oh WK; Kantoff PW; Freedman ML, 2010. Inherited variations in AR, ESR1, and ESR2 genes are not associated with prostate cancer aggressiveness or with efficacy of androgen deprivation therapy.  Cancer Epidemiol Biomarkers Prev 19(7):1871-8

Echtler K; Stark K; Lorenz M; Kerstan S; Walch A; Jennen L; Rudelius M; Seidl S; Kremmer E; Emambokus NR; von Bruehl ML; Frampton J; Isermann B; Genzel-Boroviczény O; Schreiber C; Mehilli J; Kastrati A; Schwaiger M; Shivdasani RA; Massberg S, 2010. Platelets contribute to postnatal occlusion of the ductus arteriosus.  Nat Med 16(1):75-82

Marusyk A; Polyak K, 2010. Tumor heterogeneity: causes and consequences.  Biochim Biophys Acta 1805(1):105-17

Park SY; Gönen M; Kim HJ; Michor F; Polyak K, 2010. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype.  J Clin Invest 120(2):636-44

Lauring J; Cosgrove DP; Fontana S; Gustin JP; Konishi H; Abukhdeir AM; Garay JP; Mohseni M; Wang GM; Higgins MJ; Gorkin D; Reis M; Vogelstein B; Polyak K; Cowherd M; Buckhaults PJ; Park BH, 2010. Knock in of the AKT1 E17K mutation in human breast epithelial cells does not recapitulate oncogenic PIK3CA mutations.  Oncogene 29(16):2337-45

Vastenhouw NL; Zhang Y; Woods IG; Imam F; Regev A; Liu XS; Rinn J; Schier AF, 2010. Chromatin signature of embryonic pluripotency is established during genome activation.  Nature 464(7290):922-6

He HH; Meyer CA; Shin H; Bailey ST; Wei G; Wang Q; Zhang Y; Xu K; Ni M; Lupien M; Mieczkowski P; Lieb JD; Zhao K; Brown M; Liu XS, 2010. Nucleosome dynamics define transcriptional enhancers.  Nat Genet 42(4):343-7

Park SY; Lee HE; Li H; Shipitsin M; Gelman R; Polyak K, 2010. Heterogeneity for stem cell-related markers according to tumor subtype and histologic stage in breast cancer.  Clin Cancer Res 16(3):876-87

Ji H; Liu XS, 2010. Analyzing 'omics data using hierarchical models.  Nat Biotechnol 28(4):337-40

Liu SY; Ng EK; Lee PS; Wong SK; Chiu PW; Mui WL; So WY; Chow FC, 2010. Radiofrequency ablation for benign aldosterone-producing adenoma: a scarless technique to an old disease.  Ann Surg 252(6):1058-64

Tian R; Liu SX; Williams C; Soltau TD; Dimmitt R; Zheng X; De Plaen IG, 2010. Characterization of a necrotizing enterocolitis model in newborn mice.  Int J Clin Exp Med 3(4):293-302

Ko M; Huang Y; Jankowska AM; Pape UJ; Tahiliani M; Bandukwala HS; An J; Lamperti ED; Koh KP; Ganetzky R; Liu XS; Aravind L; Agarwal S; Maciejewski JP; Rao A, 2010. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2.  Nature 468(7325):839-43

Wu ZJ; Meyer CA; Choudhury S; Shipitsin M; Maruyama R; Bessarabova M; Nikolskaya T; Sukumar S; Schwartzman A; Liu JS; Polyak K; Liu XS, 2010. Gene expression profiling of human breast tissue samples using SAGE-Seq.  Genome Res 20(12):1730-9

Verzi MP; Shivdasani RA, 2010. Stem cells: The intestinal-crypt casino.  Nature 467(7319):1055-6

Verzi MP; Shin H; He HH; Sulahian R; Meyer CA; Montgomery RK; Fleet JC; Brown M; Liu XS; Shivdasani RA, 2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26

Pomerantz MM; Shrestha Y; Flavin RJ; Regan MM; Penney KL; Mucci LA; Stampfer MJ; Hunter DJ; Chanock SJ; Schafer EJ; Chan JA; Tabernero J; Baselga J; Richardson AL; Loda M; Oh WK; Kantoff PW; Hahn WC; Freedman ML, 2010. Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis.  PLoS Genet 6(11):e1001204

Grisanzio C; Freedman ML, 2010. Chromosome 8q24-Associated Cancers and MYC.  Genes Cancer 1(6):555-9

Irie HY; Shrestha Y; Selfors LM; Frye F; Iida N; Wang Z; Zou L; Yao J; Lu Y; Epstein CB; Natesan S; Richardson AL; Polyak K; Mills GB; Hahn WC; Brugge JS, 2010. PTK6 regulates IGF-1-induced anchorage-independent survival.  PLoS One 5(7):e11729

Pomerantz MM; Freedman ML, 2010. Genetics of prostate cancer risk.  Mt Sinai J Med 77(6):643-54

Michor F; Polyak K, 2010. The origins and implications of intratumor heterogeneity.  Cancer Prev Res (Phila) 3(11):1361-4

Gerstein MB; Lu ZJ; Van Nostrand EL; Cheng C; Arshinoff BI; Liu T; Yip KY; Robilotto R; Rechtsteiner A; Ikegami K; Alves P; Chateigner A; Perry M; Morris M; Auerbach RK; Feng X; Leng J; Vielle A; Niu W; Rhrissorrakrai K; Agarwal A; Alexander RP; Barber G; Brdlik CM; Brennan J; Brouillet JJ; Carr A; Cheung MS; Clawson H; Contrino S; Dannenberg LO; Dernburg AF; Desai A; Dick L; Dosé AC; Du J; Egelhofer T; Ercan S; Euskirchen G; Ewing B; Feingold EA; Gassmann R; Good PJ; Green P; Gullier F; Gutwein M; Guyer MS; Habegger L; Han T; Henikoff JG; Henz SR; Hinrichs A; Holster H; Hyman T; Iniguez AL; Janette J; Jensen M; Kato M; Kent WJ; Kephart E; Khivansara V; Khurana E; Kim JK; Kolasinska-Zwierz P; Lai EC; Latorre I; Leahey A; Lewis S; Lloyd P; Lochovsky L; Lowdon RF; Lubling Y; Lyne R; MacCoss M; Mackowiak SD; Mangone M; McKay S; Mecenas D; Merrihew G; Miller DM 3rd; Muroyama A; Murray JI; Ooi SL; Pham H; Phippen T; Preston EA; Rajewsky N; Rätsch G; Rosenbaum H; Rozowsky J; Rutherford K; Ruzanov P; Sarov M; Sasidharan R; Sboner A; Scheid P; Segal E; Shin H; Shou C; Slack FJ; Slightam C; Smith R; Spencer WC; Stinson EO; Taing S; Takasaki T; Vafeados D; Voronina K; Wang G; Washington NL; Whittle CM; Wu B; Yan KK; Zeller G; Zha Z; Zhong M; Zhou X; Ahringer J; Strome S; Gunsalus KC; Micklem G; Liu XS; Reinke V; Kim SK; Hillier LW; Henikoff S; Piano F; Snyder M; Stein L; Lieb JD; Waterston RH, 2010. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.  Science 330(6012):1775-87

Nguyen PL; Ma J; Chavarro JE; Freedman ML; Lis R; Fedele G; Fiore C; Qiu W; Fiorentino M; Finn S; Penney KL; Eisenstein A; Schumacher FR; Mucci LA; Stampfer MJ; Giovannucci E; Loda M, 2010. Fatty acid synthase polymorphisms, tumor expression, body mass index, prostate cancer risk, and survival.  J Clin Oncol 28(25):3958-64

Kamata M; Liang M; Liu S; Nagaoka Y; Chen IS, 2010. Live cell monitoring of hiPSC generation and differentiation using differential expression of endogenous microRNAs.  PLoS One 5(7):e11834

Polyak K, 2010. Molecular markers for the diagnosis and management of ductal carcinoma in situ.  J Natl Cancer Inst Monogr 2010(41):210-3

Verzi MP; Hatzis P; Sulahian R; Philips J; Schuijers J; Shin H; Freed E; Lynch JP; Dang DT; Brown M; Clevers H; Liu XS; Shivdasani RA, 2010. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions.  Proc Natl Acad Sci U S A 107(34):15157-62

Polyak K, 2010. Going small is the new big.  Nat Methods 7(8):597, 599-600

Fan X; Moqtaderi Z; Jin Y; Zhang Y; Liu XS; Struhl K, 2010. Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.  Proc Natl Acad Sci U S A 107(42):17945-50

Horst D; Gu X; Bhasin M; Yang Q; Verzi M; Lin D; Joseph M; Zhang X; Chen W; Li YP; Shivdasani RA; Libermann TA, 2010. Requirement of the epithelium-specific Ets transcription factor Spdef for mucous gland cell function in the gastric antrum.  J Biol Chem 285(45):35047-55

Lupien M; Meyer CA; Bailey ST; Eeckhoute J; Cook J; Westerling T; Zhang X; Carroll JS; Rhodes DR; Liu XS; Brown M, 2010. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.  Genes Dev 24(19):2219-27

Sun T; Lee GS; Oh WK; Pomerantz M; Yang M; Xie W; Freedman ML; Kantoff PW, 2010. Single-nucleotide polymorphisms in p53 pathway and aggressiveness of prostate cancer in a Caucasian population.  Clin Cancer Res 16(21):5244-51

Lupien M; Eeckhoute J; Meyer CA; Krum SA; Rhodes DR; Liu XS; Brown M, 2009. Coactivator function defines the active estrogen receptor alpha cistrome.  Mol Cell Biol 29(12):3413-23

Polyak K; Weinberg RA, 2009. Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits.  Nat Rev Cancer 9(4):265-73

Liu SY; Lee KF; Lai PB, 2009. Needle track seeding: a real hazard after percutaneous radiofrequency ablation for colorectal liver metastasis.  World J Gastroenterol 15(13):1653-5

Sun T; Wang Q; Balk S; Brown M; Lee GS; Kantoff P, 2009. The role of microRNA-221 and microRNA-222 in androgen-independent prostate cancer cell lines.  Cancer Res 69(8):3356-63

Wuelling M; Kaiser FJ; Buelens LA; Braunholz D; Shivdasani RA; Depping R; Vortkamp A, 2009. Trps1, a regulator of chondrocyte proliferation and differentiation, interacts with the activator form of Gli3.  Dev Biol 328(1):40-53

Xia X; Lemieux ME; Li W; Carroll JS; Brown M; Liu XS; Kung AL, 2009. Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis.  Proc Natl Acad Sci U S A 106(11):4260-5

Liu SX; Tian R; Baskind H; Hsueh W; De Plaen IG, 2009. Platelet-activating factor induces the processing of nuclear factor-kappaB p105 into p50, which mediates acute bowel injury in mice.  Am J Physiol Gastrointest Liver Physiol 297(1):G76-81

Montgomery RK; Shivdasani RA, 2009. Prominin1 (CD133) as an intestinal stem cell marker: promise and nuance.  Gastroenterology 136(7):2051-4

Wang X; Elling AA; Li X; Li N; Peng Z; He G; Sun H; Qi Y; Liu XS; Deng XW, 2009. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize.  Plant Cell 21(4):1053-69

Nucera C; Eeckhoute J; Finn S; Carroll JS; Ligon AH; Priolo C; Fadda G; Toner M; Sheils O; Attard M; Pontecorvi A; Nose V; Loda M; Brown M, 2009. FOXA1 is a potential oncogene in anaplastic thyroid carcinoma.  Clin Cancer Res 15(11):3680-9

Eeckhoute J; Lupien M; Meyer CA; Verzi MP; Shivdasani RA; Liu XS; Brown M, 2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.  Genome Res 19(3):372-80

Polyak K; Haviv I; Campbell IG, 2009. Co-evolution of tumor cells and their microenvironment.  Trends Genet 25(1):30-8

Anderson KS; Wong J; Polyak K; Aronzon D; Enerbäck C, 2009. Detection of psoriasin/S100A7 in the sera of patients with psoriasis.  Br J Dermatol 160(2):325-32

Marotta LL; Polyak K, 2009. Cancer stem cells: a model in the making.  Curr Opin Genet Dev 19(1):44-50

Kolasinska-Zwierz P; Down T; Latorre I; Liu T; Liu XS; Ahringer J, 2009. Differential chromatin marking of introns and expressed exons by H3K36me3.  Nat Genet 41(3):376-81

Hu M; Peluffo G; Chen H; Gelman R; Schnitt S; Polyak K, 2009. Role of COX-2 in epithelial-stromal cell interactions and progression of ductal carcinoma in situ of the breast.  Proc Natl Acad Sci U S A 106(9):3372-7

Verzi MP; Stanfel MN; Moses KA; Kim BM; Zhang Y; Schwartz RJ; Shivdasani RA; Zimmer WE, 2009. Role of the homeodomain transcription factor Bapx1 in mouse distal stomach development.  Gastroenterology 136(5):1701-10

Bloushtain-Qimron N; Yao J; Shipitsin M; Maruyama R; Polyak K, 2009. Epigenetic patterns of embryonic and adult stem cells.  Cell Cycle 8(6):809-17

Haviv I; Polyak K; Qiu W; Hu M; Campbell I, 2009. Origin of carcinoma associated fibroblasts.  Cell Cycle 8(4):589-95

Campbell I; Polyak K; Haviv I, 2009. Clonal mutations in the cancer-associated fibroblasts: the case against genetic coevolution.  Cancer Res 69(17):6765-8; discussion 6769

Shin H; Liu T; Manrai AK; Liu XS, 2009. CEAS: cis-regulatory element annotation system.  Bioinformatics 25(19):2605-6

Boros J; Donaldson IJ; O'Donnell A; Odrowaz ZA; Zeef L; Lupien M; Meyer CA; Liu XS; Brown M; Sharrocks AD, 2009. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery.  Genome Res 19(11):1963-73

Huang J; Chen T; Liu X; Jiang J; Li J; Li D; Liu XS; Li W; Kang J; Pei G, 2009. More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells.  Cell Res 19(10):1127-38

Kunert S; Meyer I; Fleischhauer S; Wannack M; Fiedler J; Shivdasani RA; Schulze H, 2009. The microtubule modulator RanBP10 plays a critical role in regulation of platelet discoid shape and degranulation.  Blood 114(27):5532-40

MacConaill LE; Campbell CD; Kehoe SM; Bass AJ; Hatton C; Niu L; Davis M; Yao K; Hanna M; Mondal C; Luongo L; Emery CM; Baker AC; Philips J; Goff DJ; Fiorentino M; Rubin MA; Polyak K; Chan J; Wang Y; Fletcher JA; Santagata S; Corso G; Roviello F; Shivdasani R; Kieran MW; Ligon KL; Stiles CD; Hahn WC; Meyerson ML; Garraway LA, 2009. Profiling critical cancer gene mutations in clinical tumor samples.  PLoS One 4(11):e7887

Zhang Q; Gu J; Li L; Liu J; Luo B; Cheung HW; Boehm JS; Ni M; Geisen C; Root DE; Polyak K; Brown M; Richardson AL; Hahn WC; Kaelin WG Jr; Bommi-Reddy A, 2009. Control of cyclin D1 and breast tumorigenesis by the EglN2 prolyl hydroxylase.  Cancer Cell 16(5):413-24

Bass AJ; Watanabe H; Mermel CH; Yu S; Perner S; Verhaak RG; Kim SY; Wardwell L; Tamayo P; Gat-Viks I; Ramos AH; Woo MS; Weir BA; Getz G; Beroukhim R; O'Kelly M; Dutt A; Rozenblatt-Rosen O; Dziunycz P; Komisarof J; Chirieac LR; Lafargue CJ; Scheble V; Wilbertz T; Ma C; Rao S; Nakagawa H; Stairs DB; Lin L; Giordano TJ; Wagner P; Minna JD; Gazdar AF; Zhu CQ; Brose MS; Cecconello I; Jr UR; Marie SK; Dahl O; Shivdasani RA; Tsao MS; Rubin MA; Wong KK; Regev A; Hahn WC; Beer DG; Rustgi AK; Meyerson M, 2009. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.  Nat Genet 41(11):1238-42

Wang Q; Li W; Zhang Y; Yuan X; Xu K; Yu J; Chen Z; Beroukhim R; Wang H; Lupien M; Wu T; Regan MM; Meyer CA; Carroll JS; Manrai AK; Jänne OA; Balk SP; Mehra R; Han B; Chinnaiyan AM; Rubin MA; True L; Fiorentino M; Fiore C; Loda M; Kantoff PW; Liu XS; Brown M, 2009. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer.  Cell 138(2):245-56

Behbod F; Kittrell FS; LaMarca H; Edwards D; Kerbawy S; Heestand JC; Young E; Mukhopadhyay P; Yeh HW; Allred DC; Hu M; Polyak K; Rosen JM; Medina D, 2009. An intraductal human-in-mouse transplantation model mimics the subtypes of ductal carcinoma in situ.  Breast Cancer Res 11(5):R66

Pomerantz MM; Ahmadiyeh N; Jia L; Herman P; Verzi MP; Doddapaneni H; Beckwith CA; Chan JA; Hills A; Davis M; Yao K; Kehoe SM; Lenz HJ; Haiman CA; Yan C; Henderson BE; Frenkel B; Barretina J; Bass A; Tabernero J; Baselga J; Regan MM; Manak JR; Shivdasani R; Coetzee GA; Freedman ML, 2009. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer.  Nat Genet 41(8):882-4

Pomerantz MM; Beckwith CA; Regan MM; Wyman SK; Petrovics G; Chen Y; Hawksworth DJ; Schumacher FR; Mucci L; Penney KL; Stampfer MJ; Chan JA; Ardlie KG; Fritz BR; Parkin RK; Lin DW; Dyke M; Herman P; Lee S; Oh WK; Kantoff PW; Tewari M; McLeod DG; Srivastava S; Freedman ML, 2009. Evaluation of the 8q24 prostate cancer risk locus and MYC expression.  Cancer Res 69(13):5568-74

Chen Z; Shivdasani RA, 2009. Regulation of platelet biogenesis: insights from the May-Hegglin anomaly and other MYH9-related disorders.  J Thromb Haemost 7 Suppl 1:272-6

Eeckhoute J; Lupien M; Brown M, 2009. Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies.  Methods Mol Biol 556:155-64

Baba Y; Nosho K; Shima K; Freed E; Irahara N; Philips J; Meyerhardt JA; Hornick JL; Shivdasani RA; Fuchs CS; Ogino S, 2009. Relationship of CDX2 loss with molecular features and prognosis in colorectal cancer.  Clin Cancer Res 15(14):4665-73

Liu XS; Meyer CA, 2009. ChIP-Chip: algorithms for calling binding sites.  Methods Mol Biol 556:165-75

Snyder EL; Bailey D; Shipitsin M; Polyak K; Loda M, 2009. Identification of CD44v6(+)/CD24- breast carcinoma cells in primary human tumors by quantum dot-conjugated antibodies.  Lab Invest 89(8):857-66

Zhang Y; Moqtaderi Z; Rattner BP; Euskirchen G; Snyder M; Kadonaga JT; Liu XS; Struhl K, 2009. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.  Nat Struct Mol Biol 16(8):847-52

Souglakos J; Philips J; Wang R; Marwah S; Silver M; Tzardi M; Silver J; Ogino S; Hooshmand S; Kwak E; Freed E; Meyerhardt JA; Saridaki Z; Georgoulias V; Finkelstein D; Fuchs CS; Kulke MH; Shivdasani RA, 2009. Prognostic and predictive value of common mutations for treatment response and survival in patients with metastatic colorectal cancer.  Br J Cancer 101(3):465-72

Lupien M; Eeckhoute J; Meyer CA; Wang Q; Zhang Y; Li W; Carroll JS; Liu XS; Brown M, 2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.  Cell 132(6):958-70

Shipitsin M; Polyak K, 2008. The cancer stem cell hypothesis: in search of definitions, markers, and relevance.  Lab Invest 88(5):459-63

Choi MY; Romer AI; Wang Y; Wu MP; Ito S; Leiter AB; Shivdasani RA, 2008. Requirement of the tissue-restricted homeodomain transcription factor Nkx6.3 in differentiation of gastrin-producing G cells in the stomach antrum.  Mol Cell Biol 28(10):3208-18

Kulke MH; Freed E; Chiang DY; Philips J; Zahrieh D; Glickman JN; Shivdasani RA, 2008. High-resolution analysis of genetic alterations in small bowel carcinoid tumors reveals areas of recurrent amplification and loss.  Genes Chromosomes Cancer 47(7):591-603

Schulze H; Dose M; Korpal M; Meyer I; Italiano JE Jr; Shivdasani RA, 2008. RanBP10 is a cytoplasmic guanine nucleotide exchange factor that modulates noncentrosomal microtubules.  J Biol Chem 283(20):14109-19

Song JS; Liu X; Liu XS; He X, 2008. A high-resolution map of nucleosome positioning on a fission yeast centromere.  Genome Res 18(7):1064-72

Krum SA; Brown M, 2008. Unraveling estrogen action in osteoporosis.  Cell Cycle 7(10):1348-52

Li W; Carroll JS; Brown M; Liu xS, 2008. xMAN: extreme MApping of OligoNucleotides.  BMC Genomics 9 Suppl 1:S20

Leleu X; Eeckhoute J; Jia X; Roccaro AM; Moreau AS; Farag M; Sacco A; Ngo HT; Runnels J; Melhem MR; Burwick N; Azab A; Azab F; Hunter Z; Hatjiharissi E; Carrasco DR; Treon SP; Witzig TE; Hideshima T; Brown M; Anderson KC; Ghobrial IM, 2008. Targeting NF-kappaB in Waldenstrom macroglobulinemia.  Blood 111(10):5068-77

Qiu W; Hu M; Sridhar A; Opeskin K; Fox S; Shipitsin M; Trivett M; Thompson ER; Ramakrishna M; Gorringe KL; Polyak K; Haviv I; Campbell IG, 2008. No evidence of clonal somatic genetic alterations in cancer-associated fibroblasts from human breast and ovarian carcinomas.  Nat Genet 40(5):650-5

Campbell IG; Qiu W; Polyak K; Haviv I, 2008. Breast-cancer stromal cells with TP53 mutations.  N Engl J Med 358(15):1634-5; author reply 1636

Huang G; Zhang P; Hirai H; Elf S; Yan X; Chen Z; Koschmieder S; Okuno Y; Dayaram T; Growney JD; Shivdasani RA; Gilliland DG; Speck NA; Nimer SD; Tenen DG, 2008. PU.1 is a major downstream target of AML1 (RUNX1) in adult mouse hematopoiesis.  Nat Genet 40(1):51-60

Polyak K, 2008. Is breast tumor progression really linear?  Clin Cancer Res 14(2):339-41

Zhao X; Goswami M; Pokhriyal N; Ma H; Du H; Yao J; Victor TA; Polyak K; Sturgis CD; Band H; Band V, 2008. Cyclooxygenase-2 expression during immortalization and breast cancer progression.  Cancer Res 68(2):467-75

Napierala D; Sam K; Morello R; Zheng Q; Munivez E; Shivdasani RA; Lee B, 2008. Uncoupling of chondrocyte differentiation and perichondrial mineralization underlies the skeletal dysplasia in tricho-rhino-phalangeal syndrome.  Hum Mol Genet 17(14):2244-54

Gottardo R; Li W; Johnson WE; Liu XS, 2008. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments.  Biometrics 64(2):468-78

Patel-Hett S; Richardson JL; Schulze H; Drabek K; Isaac NA; Hoffmeister K; Shivdasani RA; Bulinski JC; Galjart N; Hartwig JH; Italiano JE Jr, 2008. Visualization of microtubule growth in living platelets reveals a dynamic marginal band with multiple microtubules.  Blood 111(9):4605-16

Johnson DS; Li W; Gordon DB; Bhattacharjee A; Curry B; Ghosh J; Brizuela L; Carroll JS; Brown M; Flicek P; Koch CM; Dunham I; Bieda M; Xu X; Farnham PJ; Kapranov P; Nix DA; Gingeras TR; Zhang X; Holster H; Jiang N; Green RD; Song JS; McCuine SA; Anton E; Nguyen L; Trinklein ND; Ye Z; Ching K; Hawkins D; Ren B; Scacheri PC; Rozowsky J; Karpikov A; Euskirchen G; Weissman S; Gerstein M; Snyder M; Yang A; Moqtaderi Z; Hirsch H; Shulha HP; Fu Y; Weng Z; Struhl K; Myers RM; Lieb JD; Liu XS, 2008. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.  Genome Res 18(3):393-403

Bao BY; Chuang BF; Wang Q; Sartor O; Balk SP; Brown M; Kantoff PW; Lee GS, 2008. Androgen receptor mediates the expression of UDP-glucuronosyltransferase 2 B15 and B17 genes.  Prostate 68(8):839-48

Nguyen PQ; Liu S; Thompson JC; Silberg JJ, 2008. Thermostability promotes the cooperative function of split adenylate kinases.  Protein Eng Des Sel 21(5):303-10

Hu M; Polyak K, 2008. Microenvironmental regulation of cancer development.  Curr Opin Genet Dev 18(1):27-34

Paruchuri V; Prasad A; McHugh K; Bhat HK; Polyak K; Ganju RK, 2008. S100A7-downregulation inhibits epidermal growth factor-induced signaling in breast cancer cells and blocks osteoclast formation.  PLoS One 3(3):e1741

Krum SA; Miranda-Carboni GA; Hauschka PV; Carroll JS; Lane TF; Freedman LP; Brown M, 2008. Estrogen protects bone by inducing Fas ligand in osteoblasts to regulate osteoclast survival.  EMBO J 27(3):535-45

Kantaputra P; Miletich I; Lüdecke HJ; Suzuki EY; Praphanphoj V; Shivdasani R; Wuelling M; Vortkamp A; Napierala D; Sharpe PT, 2008. Tricho-rhino-phalangeal syndrome with supernumerary teeth.  J Dent Res 87(11):1027-31

Krum SA; Miranda-Carboni GA; Lupien M; Eeckhoute J; Carroll JS; Brown M, 2008. Unique ERalpha cistromes control cell type-specific gene regulation.  Mol Endocrinol 22(11):2393-406

Zhang Y; Liu T; Meyer CA; Eeckhoute J; Johnson DS; Bernstein BE; Nusbaum C; Myers RM; Brown M; Li W; Liu XS, 2008. Model-based analysis of ChIP-Seq (MACS).  Genome Biol 9(9):R137

Firestein R; Bass AJ; Kim SY; Dunn IF; Silver SJ; Guney I; Freed E; Ligon AH; Vena N; Ogino S; Chheda MG; Tamayo P; Finn S; Shrestha Y; Boehm JS; Jain S; Bojarski E; Mermel C; Barretina J; Chan JA; Baselga J; Tabernero J; Root DE; Fuchs CS; Loda M; Shivdasani RA; Meyerson M; Hahn WC, 2008. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity.  Nature 455(7212):547-51

Cao D; Polyak K; Halushka MK; Nassar H; Kouprina N; Iacobuzio-Donahue C; Wu X; Sukumar S; Hicks J; De Marzo A; Argani P, 2008. Serial analysis of gene expression of lobular carcinoma in situ identifies down regulation of claudin 4 and overexpression of matrix metalloproteinase 9.  Breast Cancer Res 10(5):R91

Lefterova MI; Zhang Y; Steger DJ; Schupp M; Schug J; Cristancho A; Feng D; Zhuo D; Stoeckert CJ Jr; Liu XS; Lazar MA, 2008. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale.  Genes Dev 22(21):2941-52

Ozsolak F; Poling LL; Wang Z; Liu H; Liu XS; Roeder RG; Zhang X; Song JS; Fisher DE, 2008. Chromatin structure analyses identify miRNA promoters.  Genes Dev 22(22):3172-83

Hu M; Polyak K, 2008. Molecular characterisation of the tumour microenvironment in breast cancer.  Eur J Cancer 44(18):2760-5

Zhang Y; Shin H; Song JS; Lei Y; Liu XS, 2008. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.  BMC Genomics 9:537

Nikolsky Y; Sviridov E; Yao J; Dosymbekov D; Ustyansky V; Kaznacheev V; Dezso Z; Mulvey L; Macconaill LE; Winckler W; Serebryiskaya T; Nikolskaya T; Polyak K, 2008. Genome-wide functional synergy between amplified and mutated genes in human breast cancer.  Cancer Res 68(22):9532-40

Agoulnik IU; Bingman WE 3rd; Nakka M; Li W; Wang Q; Liu XS; Brown M; Weigel NL, 2008. Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase.  Mol Endocrinol 22(11):2420-32

Yagi S; Hirabayashi K; Sato S; Li W; Takahashi Y; Hirakawa T; Wu G; Hattori N; Hattori N; Ohgane J; Tanaka S; Liu XS; Shiota K, 2008. DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression.  Genome Res 18(12):1969-78

Mani SA; Guo W; Liao MJ; Eaton EN; Ayyanan A; Zhou AY; Brooks M; Reinhard F; Zhang CC; Shipitsin M; Campbell LL; Polyak K; Brisken C; Yang J; Weinberg RA, 2008. The epithelial-mesenchymal transition generates cells with properties of stem cells.  Cell 133(4):704-15

Hu M; Yao J; Carroll DK; Weremowicz S; Chen H; Carrasco D; Richardson A; Violette S; Nikolskaya T; Nikolsky Y; Bauerlein EL; Hahn WC; Gelman RS; Allred C; Bissell MJ; Schnitt S; Polyak K, 2008. Regulation of in situ to invasive breast carcinoma transition.  Cancer Cell 13(5):394-406

Bloushtain-Qimron N; Yao J; Snyder EL; Shipitsin M; Campbell LL; Mani SA; Hu M; Chen H; Ustyansky V; Antosiewicz JE; Argani P; Halushka MK; Thomson JA; Pharoah P; Porgador A; Sukumar S; Parsons R; Richardson AL; Stampfer MR; Gelman RS; Nikolskaya T; Nikolsky Y; Polyak K, 2008. Cell type-specific DNA methylation patterns in the human breast.  Proc Natl Acad Sci U S A 105(37):14076-81

Verzi MP; Shivdasani RA, 2008. Wnt signaling in gut organogenesis.  Organogenesis 4(2):87-91

Verzi MP; Khan AH; Ito S; Shivdasani RA, 2008. Transcription factor foxq1 controls mucin gene expression and granule content in mouse stomach surface mucous cells.  Gastroenterology 135(2):591-600

Yang XH; Richardson AL; Torres-Arzayus MI; Zhou P; Sharma C; Kazarov AR; Andzelm MM; Strominger JL; Brown M; Hemler ME, 2008. CD151 accelerates breast cancer by regulating alpha 6 integrin function, signaling, and molecular organization.  Cancer Res 68(9):3204-13

Zhai P; Stanworth C; Liu S; Silberg JJ, 2008. The human escort protein Hep binds to the ATPase domain of mitochondrial hsp70 and regulates ATP hydrolysis.  J Biol Chem 283(38):26098-106

2008. Moving AHEAD with an international human epigenome project.  Nature 454(7205):711-5

Hafler BP; Choi MY; Shivdasani RA; Rowitch DH, 2008. Expression and function of Nkx6.3 in vertebrate hindbrain.  Brain Res 1222:42-50

Kleer CG; Bloushtain-Qimron N; Chen YH; Carrasco D; Hu M; Yao J; Kraeft SK; Collins LC; Sabel MS; Argani P; Gelman R; Schnitt SJ; Krop IE; Polyak K, 2008. Epithelial and stromal cathepsin K and CXCL14 expression in breast tumor progression.  Clin Cancer Res 14(17):5357-67

Kim RJ; Kerns JM; Liu S; Nagel T; Zaszczurynski P; Lin DL; Damaser MS, 2007. Striated muscle and nerve fascicle distribution in the female rat urethral sphincter.  Anat Rec (Hoboken) 290(2):145-54

De Plaen IG; Liu SX; Tian R; Neequaye I; May MJ; Han XB; Hsueh W; Jilling T; Lu J; Caplan MS, 2007. Inhibition of nuclear factor-kappaB ameliorates bowel injury and prolongs survival in a neonatal rat model of necrotizing enterocolitis.  Pediatr Res 61(6):716-21

Blackshaw S; St Croix B; Polyak K; Kim JB; Cai L, 2007. Serial analysis of gene expression (SAGE): experimental method and data analysis.  Curr Protoc Hum Genet Chapter 11:Unit 11.7

Pomerantz MM; Freedman ML; Kantoff PW, 2007. Genetic determinants of prostate cancer risk.  BJU Int 100(2):241-3

Eeckhoute J; Keeton EK; Lupien M; Krum SA; Carroll JS; Brown M, 2007. Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer.  Cancer Res 67(13):6477-83

Boehm JS; Zhao JJ; Yao J; Kim SY; Firestein R; Dunn IF; Sjostrom SK; Garraway LA; Weremowicz S; Richardson AL; Greulich H; Stewart CJ; Mulvey LA; Shen RR; Ambrogio L; Hirozane-Kishikawa T; Hill DE; Vidal M; Meyerson M; Grenier JK; Hinkle G; Root DE; Roberts TM; Lander ES; Polyak K; Hahn WC, 2007. Integrative genomic approaches identify IKBKE as a breast cancer oncogene.  Cell 129(6):1065-79

Chen Z; Naveiras O; Balduini A; Mammoto A; Conti MA; Adelstein RS; Ingber D; Daley GQ; Shivdasani RA, 2007. The May-Hegglin anomaly gene MYH9 is a negative regulator of platelet biogenesis modulated by the Rho-ROCK pathway.  Blood 110(1):171-9

Liu SY; Lee JF; Ng SS; Li JC; Yiu RY, 2007. Rectal stump lavage: simple procedure resulting in life-threatening complication.  Asian J Surg 30(1):72-4

Chen Z; Hu M; Shivdasani RA, 2007. Expression analysis of primary mouse megakaryocyte differentiation and its application in identifying stage-specific molecular markers and a novel transcriptional target of NF-E2.  Blood 109(4):1451-9

Liu SY; Ng CF; Lai FM; Cheng CW, 2007. Undifferentiated sex cord-stromal tumor in a young adult.  Int Urol Nephrol 39(2):561-4

Leung WW; Lee JF; Liu SY; Mou JW; Ng SS; Yiu RY; Li JC, 2007. Critical appraisal on the role and outcome of emergency colectomy for uncomplicated right-sided colonic diverticulitis.  World J Surg 31(2):383-7

Ozsolak F; Song JS; Liu XS; Fisher DE, 2007. High-throughput mapping of the chromatin structure of human promoters.  Nat Biotechnol 25(2):244-8

Wang Q; Li W; Liu XS; Carroll JS; Jänne OA; Keeton EK; Chinnaiyan AM; Pienta KJ; Brown M, 2007. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.  Mol Cell 27(3):380-92

Song JS; Maghsoudi K; Li W; Fox E; Quackenbush J; Shirley Liu X, 2007. Microarray blob-defect removal improves array analysis.  Bioinformatics 23(8):966-71

Shipitsin M; Campbell LL; Argani P; Weremowicz S; Bloushtain-Qimron N; Yao J; Nikolskaya T; Serebryiskaya T; Beroukhim R; Hu M; Halushka MK; Sukumar S; Parker LM; Anderson KS; Harris LN; Garber JE; Richardson AL; Schnitt SJ; Nikolsky Y; Gelman RS; Polyak K, 2007. Molecular definition of breast tumor heterogeneity.  Cancer Cell 11(3):259-73

Litovchick L; Sadasivam S; Florens L; Zhu X; Swanson SK; Velmurugan S; Chen R; Washburn MP; Liu XS; DeCaprio JA, 2007. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence.  Mol Cell 26(4):539-51

Liu XS, 2007. Getting started in tiling microarray analysis.  PLoS Comput Biol 3(10):1842-4

Wood LD; Parsons DW; Jones S; Lin J; Sjöblom T; Leary RJ; Shen D; Boca SM; Barber T; Ptak J; Silliman N; Szabo S; Dezso Z; Ustyanksky V; Nikolskaya T; Nikolsky Y; Karchin R; Wilson PA; Kaminker JS; Zhang Z; Croshaw R; Willis J; Dawson D; Shipitsin M; Willson JK; Sukumar S; Polyak K; Park BH; Pethiyagoda CL; Pant PV; Ballinger DG; Sparks AB; Hartigan J; Smith DR; Suh E; Papadopoulos N; Buckhaults P; Markowitz SD; Parmigiani G; Kinzler KW; Velculescu VE; Vogelstein B, 2007. The genomic landscapes of human breast and colorectal cancers.  Science 318(5853):1108-13

Van Dyck F; Braem CV; Chen Z; Declercq J; Deckers R; Kim BM; Ito S; Wu MK; Cohen DE; Dewerchin M; Derua R; Waelkens E; Fiette L; Roebroek A; Schuit F; Van de Ven WJ; Shivdasani RA, 2007. Loss of the PlagL2 transcription factor affects lacteal uptake of chylomicrons.  Cell Metab 6(5):406-13

O'Neil J; Tchinda J; Gutierrez A; Moreau L; Maser RS; Wong KK; Li W; McKenna K; Liu XS; Feng B; Neuberg D; Silverman L; DeAngelo DJ; Kutok JL; Rothstein R; DePinho RA; Chin L; Lee C; Look AT, 2007. Alu elements mediate MYB gene tandem duplication in human T-ALL.  J Exp Med 204(13):3059-66

Kim BM; Mao J; Taketo MM; Shivdasani RA, 2007. Phases of canonical Wnt signaling during the development of mouse intestinal epithelium.  Gastroenterology 133(2):529-38

Blackshaw S; Croix BS; Polyak K; Kim JB; Cai L, 2007. Serial analysis of gene expression (SAGE): experimental method and data analysis.  Curr Protoc Mol Biol Chapter 25:Unit 25B.6

Karnoub AE; Dash AB; Vo AP; Sullivan A; Brooks MW; Bell GW; Richardson AL; Polyak K; Tubo R; Weinberg RA, 2007. Mesenchymal stem cells within tumour stroma promote breast cancer metastasis.  Nature 449(7162):557-63

Polyak K, 2007. Breast cancer: origins and evolution.  J Clin Invest 117(11):3155-63

Campbell LL; Polyak K, 2007. Breast tumor heterogeneity: cancer stem cells or clonal evolution?  Cell Cycle 6(19):2332-8

He H; Wang J; Liu T; Liu XS; Li T; Wang Y; Qian Z; Zheng H; Zhu X; Wu T; Shi B; Deng W; Zhou W; Skogerbø G; Chen R, 2007. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.  Genome Res 17(10):1471-7

Kim BM; Miletich I; Mao J; McMahon AP; Sharpe PA; Shivdasani RA, 2007. Independent functions and mechanisms for homeobox gene Barx1 in patterning mouse stomach and spleen.  Development 134(20):3603-13

Song JS; Johnson WE; Zhu X; Zhang X; Li W; Manrai AK; Liu JS; Chen R; Liu XS, 2007. Model-based analysis of two-color arrays (MA2C).  Genome Biol 8(8):R178

Junt T; Schulze H; Chen Z; Massberg S; Goerge T; Krueger A; Wagner DD; Graf T; Italiano JE Jr; Shivdasani RA; von Andrian UH, 2007. Dynamic visualization of thrombopoiesis within bone marrow.  Science 317(5845):1767-70

Polyak K, 2007. Breast cancer stem cells: a case of mistaken identity?  Stem Cell Rev 3(2):107-9

Ng SS; Ng NC; Liu SY; Lee JF, 2006. Radiology for the surgeon. Soft-tissue case 58: incarcerated Grynfeltt hernia.  Can J Surg 49(2):129-30

Swinburne IA; Meyer CA; Liu XS; Silver PA; Brodsky AS, 2006. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.  Genome Res 16(7):912-21

Nelson EA; Walker SR; Li W; Liu XS; Frank DA, 2006. Identification of human STAT5-dependent gene regulatory elements based on interspecies homology.  J Biol Chem 281(36):26216-24

Palomero T; Odom DT; O'Neil J; Ferrando AA; Margolin A; Neuberg DS; Winter SS; Larson RS; Li W; Liu XS; Young RA; Look AT, 2006. Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia.  Blood 108(3):986-92

Polyak K, 2006. Pregnancy and breast cancer: the other side of the coin.  Cancer Cell 9(3):151-3

Ji X; Li W; Song J; Wei L; Liu XS, 2006. CEAS: cis-regulatory element annotation system.  Nucleic Acids Res 34(Web Server issue):W551-4

Carroll JS; Brown M, 2006. Estrogen receptor target gene: an evolving concept.  Mol Endocrinol 20(8):1707-14

Polyak K; Hahn WC, 2006. Roots and stems: stem cells in cancer.  Nat Med 12(3):296-300

Schulze H; Korpal M; Hurov J; Kim SW; Zhang J; Cantley LC; Graf T; Shivdasani RA, 2006. Characterization of the megakaryocyte demarcation membrane system and its role in thrombopoiesis.  Blood 107(10):3868-75

Porter D; Yao J; Polyak K, 2006. SAGE and related approaches for cancer target identification.  Drug Discov Today 11(3-4):110-8

Yao J; Weremowicz S; Feng B; Gentleman RC; Marks JR; Gelman R; Brennan C; Polyak K, 2006. Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression.  Cancer Res 66(8):4065-78

Johnson WE; Li W; Meyer CA; Gottardo R; Carroll JS; Brown M; Liu XS, 2006. Model-based analysis of tiling-arrays for ChIP-chip.  Proc Natl Acad Sci U S A 103(33):12457-62

Polyak K, 2006. The p27Kip1 tumor suppressor gene: Still a suspect or proven guilty?  Cancer Cell 10(5):352-4

Carroll JS; Meyer CA; Song J; Li W; Geistlinger TR; Eeckhoute J; Brodsky AS; Keeton EK; Fertuck KC; Hall GF; Wang Q; Bekiranov S; Sementchenko V; Fox EA; Silver PA; Gingeras TR; Liu XS; Brown M, 2006. Genome-wide analysis of estrogen receptor binding sites.  Nat Genet 38(11):1289-97

Zhang Y; Liu XS; Liu QR; Wei L, 2006. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.  Nucleic Acids Res 34(12):3465-75

Hu M; Yao J; Polyak K, 2006. Methylation-specific digital karyotyping.  Nat Protoc 1(3):1621-36

Hu M; Polyak K, 2006. Serial analysis of gene expression.  Nat Protoc 1(4):1743-60

Eeckhoute J; Carroll JS; Geistlinger TR; Torres-Arzayus MI; Brown M, 2006. A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer.  Genes Dev 20(18):2513-26

Torres-Arzayus MI; Yuan J; DellaGatta JL; Lane H; Kung AL; Brown M, 2006. Targeting the AIB1 oncogene through mammalian target of rapamycin inhibition in the mammary gland.  Cancer Res 66(23):11381-8

Choi MY; Romer AI; Hu M; Lepourcelet M; Mechoor A; Yesilaltay A; Krieger M; Gray PA; Shivdasani RA, 2006. A dynamic expression survey identifies transcription factors relevant in mouse digestive tract development.  Development 133(20):4119-29

Shivdasani RA, 2006. MicroRNAs: regulators of gene expression and cell differentiation.  Blood 108(12):3646-53

Liu SY; Ng SS; Lee JF, 2006. Multi-limb necrotizing fasciitis in a patient with rectal cancer.  World J Gastroenterol 12(32):5256-8

Freedman ML; Haiman CA; Patterson N; McDonald GJ; Tandon A; Waliszewska A; Penney K; Steen RG; Ardlie K; John EM; Oakley-Girvan I; Whittemore AS; Cooney KA; Ingles SA; Altshuler D; Henderson BE; Reich D, 2006. Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men.  Proc Natl Acad Sci U S A 103(38):14068-73

Kim BM; Buchner G; Miletich I; Sharpe PT; Shivdasani RA, 2005. The stomach mesenchymal transcription factor Barx1 specifies gastric epithelial identity through inhibition of transient Wnt signaling.  Dev Cell 8(4):611-22

Hong P; Liu XS; Zhou Q; Lu X; Liu JS; Wong WH, 2005. A boosting approach for motif modeling using ChIP-chip data.  Bioinformatics 21(11):2636-43

Li W; Meyer CA; Liu XS, 2005. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.  Bioinformatics 21 Suppl 1:i274-82

Febbo PG; Lowenberg M; Thorner AR; Brown M; Loda M; Golub TR, 2005. Androgen mediated regulation and functional implications of fkbp51 expression in prostate cancer.  J Urol 173(5):1772-7

Keeton EK; Brown M, 2005. Cell cycle progression stimulated by tamoxifen-bound estrogen receptor-alpha and promoter-specific effects in breast cancer cells deficient in N-CoR and SMRT.  Mol Endocrinol 19(6):1543-54

Lepourcelet M; Tou L; Cai L; Sawada J; Lazar AJ; Glickman JN; Williamson JA; Everett AD; Redston M; Fox EA; Nakatani Y; Shivdasani RA, 2005. Insights into developmental mechanisms and cancers in the mammalian intestine derived from serial analysis of gene expression and study of the hepatoma-derived growth factor (HDGF).  Development 132(2):415-27

Hu M; Yao J; Cai L; Bachman KE; van den Brûle F; Velculescu V; Polyak K, 2005. Distinct epigenetic changes in the stromal cells of breast cancers.  Nat Genet 37(8):899-905

Lu L; Hope BT; Dempsey J; Liu SY; Bossert JM; Shaham Y, 2005. Central amygdala ERK signaling pathway is critical to incubation of cocaine craving.  Nat Neurosci 8(2):212-9

Peters BA; Diaz LA; Polyak K; Meszler L; Romans K; Guinan EC; Antin JH; Myerson D; Hamilton SR; Vogelstein B; Kinzler KW; Lengauer C, 2005. Contribution of bone marrow-derived endothelial cells to human tumor vasculature.  Nat Med 11(3):261-2

Hlavay J; Polyák K, 2005. Determination of surface properties of iron hydroxide-coated alumina adsorbent prepared for removal of arsenic from drinking water.  J Colloid Interface Sci 284(1):71-7

Drori S; Girnun GD; Tou L; Szwaya JD; Mueller E; Xia K; Shivdasani RA; Spiegelman BM, 2005. Hic-5 regulates an epithelial program mediated by PPARgamma.  Genes Dev 19(3):362-75

Krop I; Parker MT; Bloushtain-Qimron N; Porter D; Gelman R; Sasaki H; Maurer M; Terry MB; Parsons R; Polyak K, 2005. HIN-1, an inhibitor of cell growth, invasion, and AKT activation.  Cancer Res 65(21):9659-69

Krop I; März A; Carlsson H; Li X; Bloushtain-Qimron N; Hu M; Gelman R; Sabel MS; Schnitt S; Ramaswamy S; Kleer CG; Enerbäck C; Polyak K, 2005. A putative role for psoriasin in breast tumor progression.  Cancer Res 65(24):11326-34

Polyak K; Hu M, 2005. Do myoepithelial cells hold the key for breast tumor progression?  J Mammary Gland Biol Neoplasia 10(3):231-47

Carroll JS; Liu XS; Brodsky AS; Li W; Meyer CA; Szary AJ; Eeckhoute J; Shao W; Hestermann EV; Geistlinger TR; Fox EA; Silver PA; Brown M, 2005. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.  Cell 122(1):33-43

Hu M; Shivdasani RA, 2005. Overlapping gene expression in fetal mouse intestine development and human colorectal cancer.  Cancer Res 65(19):8715-22

Shivdasani RA; Schulze H, 2005. Culture, expansion, and differentiation of murine megakaryocytes.  Curr Protoc Immunol Chapter 22:Unit 22F.6

Carlsson H; Yhr M; Petersson S; Collins N; Polyak K; Enerbäck C, 2005. Psoriasin (S100A7) and calgranulin-B (S100A9) induction is dependent on reactive oxygen species and is downregulated by Bcl-2 and antioxidants.  Cancer Biol Ther 4(9):998-1005

Wang Q; Carroll JS; Brown M, 2005. Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking.  Mol Cell 19(5):631-42

Schulze H; Shivdasani RA, 2005. Mechanisms of thrombopoiesis.  J Thromb Haemost 3(8):1717-24

Patel SR; Richardson JL; Schulze H; Kahle E; Galjart N; Drabek K; Shivdasani RA; Hartwig JH; Italiano JE Jr, 2005. Differential roles of microtubule assembly and sliding in proplatelet formation by megakaryocytes.  Blood 106(13):4076-85

Richardson JL; Shivdasani RA; Boers C; Hartwig JH; Italiano JE Jr, 2005. Mechanisms of organelle transport and capture along proplatelets during platelet production.  Blood 106(13):4066-75

Derjuga A; Gourley TS; Holm TM; Heng HH; Shivdasani RA; Ahmed R; Andrews NC; Blank V, 2004. Complexity of CNC transcription factors as revealed by gene targeting of the Nrf3 locus.  Mol Cell Biol 24(8):3286-94

Tou L; Liu Q; Shivdasani RA, 2004. Regulation of mammalian epithelial differentiation and intestine development by class I histone deacetylases.  Mol Cell Biol 24(8):3132-9

Mehrotra J; Vali M; McVeigh M; Kominsky SL; Fackler MJ; Lahti-Domenici J; Polyak K; Sacchi N; Garrett-Mayer E; Argani P; Sukumar S, 2004. Very high frequency of hypermethylated genes in breast cancer metastasis to the bone, brain, and lung.  Clin Cancer Res 10(9):3104-9

Mehrotra J; Ganpat MM; Kanaan Y; Fackler MJ; McVeigh M; Lahti-Domenici J; Polyak K; Argani P; Naab T; Garrett E; Parmigiani G; Broome C; Sukumar S, 2004. Estrogen receptor/progesterone receptor-negative breast cancers of young African-American women have a higher frequency of methylation of multiple genes than those of Caucasian women.  Clin Cancer Res 10(6):2052-7

Burstein HJ; Polyak K; Wong JS; Lester SC; Kaelin CM, 2004. Ductal carcinoma in situ of the breast.  N Engl J Med 350(14):1430-41

Lepourcelet M; Chen YN; France DS; Wang H; Crews P; Petersen F; Bruseo C; Wood AW; Shivdasani RA, 2004. Small-molecule antagonists of the oncogenic Tcf/beta-catenin protein complex.  Cancer Cell 5(1):91-102

Shepard JD; Bossert JM; Liu SY; Shaham Y, 2004. The anxiogenic drug yohimbine reinstates methamphetamine seeking in a rat model of drug relapse.  Biol Psychiatry 55(11):1082-9

Shao W; Brown M, 2004. Advances in estrogen receptor biology: prospects for improvements in targeted breast cancer therapy.  Breast Cancer Res 6(1):39-52

Lu L; Dempsey J; Liu SY; Bossert JM; Shaham Y, 2004. A single infusion of brain-derived neurotrophic factor into the ventral tegmental area induces long-lasting potentiation of cocaine seeking after withdrawal.  J Neurosci 24(7):1604-11

Liu Y; Liu XS; Wei L; Altman RB; Batzoglou S, 2004. Eukaryotic regulatory element conservation analysis and identification using comparative genomics.  Genome Res 14(3):451-8

Kacena MA; Shivdasani RA; Wilson K; Xi Y; Troiano N; Nazarian A; Gundberg CM; Bouxsein ML; Lorenzo JA; Horowitz MC, 2004. Megakaryocyte-osteoblast interaction revealed in mice deficient in transcription factors GATA-1 and NF-E2.  J Bone Miner Res 19(4):652-60

Allinen M; Beroukhim R; Cai L; Brennan C; Lahti-Domenici J; Huang H; Porter D; Hu M; Chin L; Richardson A; Schnitt S; Sellers WR; Polyak K, 2004. Molecular characterization of the tumor microenvironment in breast cancer.  Cancer Cell 6(1):17-32

Liu Y; Wei L; Batzoglou S; Brutlag DL; Liu JS; Liu XS, 2004. A suite of web-based programs to search for transcriptional regulatory motifs.  Nucleic Acids Res 32(Web Server issue):W204-7

Torres-Arzayus MI; Font de Mora J; Yuan J; Vazquez F; Bronson R; Rue M; Sellers WR; Brown M, 2004. High tumor incidence and activation of the PI3K/AKT pathway in transgenic mice define AIB1 as an oncogene.  Cancer Cell 6(3):263-74

Krop I; Player A; Tablante A; Taylor-Parker M; Lahti-Domenici J; Fukuoka J; Batra SK; Papadopoulos N; Richards WG; Sugarbaker DJ; Wright RL; Shim J; Stamey TA; Sellers WR; Loda M; Meyerson M; Hruban R; Jen J; Polyak K, 2004. Frequent HIN-1 promoter methylation and lack of expression in multiple human tumor types.  Mol Cancer Res 2(9):489-94

Bossert JM; Liu SY; Lu L; Shaham Y, 2004. A role of ventral tegmental area glutamate in contextual cue-induced relapse to heroin seeking.  J Neurosci 24(47):10726-30

DePinho RA; Polyak K, 2004. Cancer chromosomes in crisis.  Nat Genet 36(9):932-4

Schulze H; Shivdasani RA, 2004. Molecular mechanisms of megakaryocyte differentiation.  Semin Thromb Hemost 30(4):389-98

Shivdasani RA, 2004. Lonely in Paris: when one gene copy isn't enough.  J Clin Invest 114(1):17-9

Yao J; Polyak K, 2004. EMSY links breast cancer gene 2 to the 'Royal Family'.  Breast Cancer Res 6(5):201-3

Shao W; Keeton EK; McDonnell DP; Brown M, 2004. Coactivator AIB1 links estrogen receptor transcriptional activity and stability.  Proc Natl Acad Sci U S A 101(32):11599-604

Schulze H; Korpal M; Bergmeier W; Italiano JE Jr; Wahl SM; Shivdasani RA, 2004. Interactions between the megakaryocyte/platelet-specific beta1 tubulin and the secretory leukocyte protease inhibitor SLPI suggest a role for regulated proteolysis in platelet functions.  Blood 104(13):3949-57

Italiano JE Jr; Shivdasani RA, 2003. Megakaryocytes and beyond: the birth of platelets.  J Thromb Haemost 1(6):1174-82

Krop I; Maguire P; Lahti-Domenici J; Lodeiro G; Richardson A; Johannsdottir HK; Nevanlinna H; Borg A; Gelman R; Barkardottir RB; Lindblom A; Polyak K, 2003. Lack of HIN-1 methylation in BRCA1-linked and "BRCA1-like" breast tumors.  Cancer Res 63(9):2024-7

Porter D; Lahti-Domenici J; Keshaviah A; Bae YK; Argani P; Marks J; Richardson A; Cooper A; Strausberg R; Riggins GJ; Schnitt S; Gabrielson E; Gelman R; Polyak K, 2003. Molecular markers in ductal carcinoma in situ of the breast.  Mol Cancer Res 1(5):362-75

Italiano JE Jr; Bergmeier W; Tiwari S; Falet H; Hartwig JH; Hoffmeister KM; André P; Wagner DD; Shivdasani RA, 2003. Mechanisms and implications of platelet discoid shape.  Blood 101(12):4789-96

Young MR; Liu SW; Meisinger J, 2003. Protein phosphatase-2A restricts migration of Lewis lung carcinoma cells by modulating the phosphorylation of focal adhesion proteins.  Int J Cancer 103(1):38-44

Buckhaults P; Zhang Z; Chen YC; Wang TL; St Croix B; Saha S; Bardelli A; Morin PJ; Polyak K; Hruban RH; Velculescu VE; Shih IeM, 2003. Identifying tumor origin using a gene expression-based classification map.  Cancer Res 63(14):4144-9

Conlon EM; Liu XS; Lieb JD; Liu JS, 2003. Integrating regulatory motif discovery and genome-wide expression analysis.  Proc Natl Acad Sci U S A 100(6):3339-44

Polyak K, 2003. The hairy powers of oncogenes: from biological function to cancer therapy.  Cancer Biol Ther 2(5):592-4

Porter D; Polyak K, 2003. Cancer target discovery using SAGE.  Expert Opin Ther Targets 7(6):759-69

Tiwari S; Italiano JE Jr; Barral DC; Mules EH; Novak EK; Swank RT; Seabra MC; Shivdasani RA, 2003. A role for Rab27b in NF-E2-dependent pathways of platelet formation.  Blood 102(12):3970-9

Yamada K; Lim J; Dale JM; Chen H; Shinn P; Palm CJ; Southwick AM; Wu HC; Kim C; Nguyen M; Pham P; Cheuk R; Karlin-Newmann G; Liu SX; Lam B; Sakano H; Wu T; Yu G; Miranda M; Quach HL; Tripp M; Chang CH; Lee JM; Toriumi M; Chan MM; Tang CC; Onodera CS; Deng JM; Akiyama K; Ansari Y; Arakawa T; Banh J; Banno F; Bowser L; Brooks S; Carninci P; Chao Q; Choy N; Enju A; Goldsmith AD; Gurjal M; Hansen NF; Hayashizaki Y; Johnson-Hopson C; Hsuan VW; Iida K; Karnes M; Khan S; Koesema E; Ishida J; Jiang PX; Jones T; Kawai J; Kamiya A; Meyers C; Nakajima M; Narusaka M; Seki M; Sakurai T; Satou M; Tamse R; Vaysberg M; Wallender EK; Wong C; Yamamura Y; Yuan S; Shinozaki K; Davis RW; Theologis A; Ecker JR, 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome.  Science 302(5646):842-6

Fackler MJ; McVeigh M; Evron E; Garrett E; Mehrotra J; Polyak K; Sukumar S; Argani P, 2003. DNA methylation of RASSF1A, HIN-1, RAR-beta, Cyclin D2 and Twist in in situ and invasive lobular breast carcinoma.  Int J Cancer 107(6):970-5

Porter D; Weremowicz S; Chin K; Seth P; Keshaviah A; Lahti-Domenici J; Bae YK; Monitto CL; Merlos-Suarez A; Chan J; Hulette CM; Richardson A; Morton CC; Marks J; Duyao M; Hruban R; Gabrielson E; Gelman R; Polyak K, 2003. A neural survival factor is a candidate oncogene in breast cancer.  Proc Natl Acad Sci U S A 100(19):10931-6

Hestermann EV; Brown M, 2003. Agonist and chemopreventative ligands induce differential transcriptional cofactor recruitment by aryl hydrocarbon receptor.  Mol Cell Biol 23(21):7920-5

Shao W; Halachmi S; Brown M, 2002. ERAP140, a conserved tissue-specific nuclear receptor coactivator.  Mol Cell Biol 22(10):3358-72

Shang Y; Myers M; Brown M, 2002. Formation of the androgen receptor transcription complex.  Mol Cell 9(3):601-10

Liu XS; Brutlag DL; Liu JS, 2002. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.  Nat Biotechnol 20(8):835-9

Shang Y; Brown M, 2002. Molecular determinants for the tissue specificity of SERMs.  Science 295(5564):2465-8

DiRenzo J; Signoretti S; Nakamura N; Rivera-Gonzalez R; Sellers W; Loda M; Brown M, 2002. Growth factor requirements and basal phenotype of an immortalized mammary epithelial cell line.  Cancer Res 62(1):89-98

Enerbäck C; Porter DA; Seth P; Sgroi D; Gaudet J; Weremowicz S; Morton CC; Schnitt S; Pitts RL; Stampl J; Barnhart K; Polyak K, 2002. Psoriasin expression in mammary epithelial cells in vitro and in vivo.  Cancer Res 62(1):43-7

Polyak K, 2002. Molecular alterations in ductal carcinoma in situ of the breast.  Curr Opin Oncol 14(1):92-6

Ryan DP; Kulke MH; Fuchs CS; Grossbard ML; Grossman SR; Morgan JA; Earle CC; Shivdasani R; Kim H; Mayer RJ; Clark JW, 2002. A Phase II study of gemcitabine and docetaxel in patients with metastatic pancreatic carcinoma.  Cancer 94(1):97-103

Seth P; Krop I; Porter D; Polyak K, 2002. Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression).  Oncogene 21(5):836-43

Boon K; Osorio EC; Greenhut SF; Schaefer CF; Shoemaker J; Polyak K; Morin PJ; Buetow KH; Strausberg RL; De Souza SJ; Riggins GJ, 2002. An anatomy of normal and malignant gene expression.  Proc Natl Acad Sci U S A 99(17):11287-92

Kulke MH; Demetri GD; Sharpless NE; Ryan DP; Shivdasani R; Clark JS; Spiegelman BM; Kim H; Mayer RJ; Fuchs CS, 2002. A phase II study of troglitazone, an activator of the PPARgamma receptor, in patients with chemotherapy-resistant metastatic colorectal cancer.  Cancer J 8(5):395-9

Shivdasani R, 2002. An animal model for myelofibrosis.  Blood 100(4):1109

Polyak K, 2002. Breast cancer gene discovery.  Expert Rev Mol Med 4(18):1-18

Lepourcelet M; Shivdasani RA, 2002. Characterization of a novel mammalian Groucho isoform and its role in transcriptional regulation.  J Biol Chem 277(49):47732-40

Malik TH; Von Stechow D; Bronson RT; Shivdasani RA, 2002. Deletion of the GATA domain of TRPS1 causes an absence of facial hair and provides new insights into the bone disorder in inherited tricho-rhino-phalangeal syndromes.  Mol Cell Biol 22(24):8592-600

Shivdasani RA, 2002. Molecular regulation of vertebrate early endoderm development.  Dev Biol 249(2):191-203

Seth P; Porter D; Lahti-Domenici J; Geng Y; Richardson A; Polyak K, 2002. Cellular and molecular targets of estrogen in normal human breast tissue.  Cancer Res 62(16):4540-4

Porter D; Lahti-Domenici J; Torres-Arzayus M; Chin L; Polyak K, 2002. Expression of high in normal-1 (HIN-1) and uteroglobin related protein-1 (UGRP-1) in adult and developing tissues.  Mech Dev 114(1-2):201-4

Polyak K, 2002. Is p53 a breast cancer gene?  Cancer Biol Ther 1(1):37-8

Malik TH; Shoichet SA; Latham P; Kroll TG; Peters LL; Shivdasani RA, 2001. Transcriptional repression and developmental functions of the atypical vertebrate GATA protein TRPS1.  EMBO J 20(7):1715-25

Schwer HD; Lecine P; Tiwari S; Italiano JE Jr; Hartwig JH; Shivdasani RA, 2001. A lineage-restricted and divergent beta-tubulin isoform is essential for the biogenesis, structure and function of blood platelets.  Curr Biol 11(8):579-86

Hlavay J; Polyák K; Weisz M, 2001. Monitoring of the natural environment by chemical speciation of elements in aerosol and sediment samples.  J Environ Monit 3(1):74-80

Li YJ; Higgins RR; Pak BJ; Shivdasani RA; Ney PA; Archer M; Ben-David Y, 2001. p45(NFE2) is a negative regulator of erythroid proliferation which contributes to the progression of Friend virus-induced erythroleukemias.  Mol Cell Biol 21(1):73-80

Zhang J; Rosenthal A; de Sauvage FJ; Shivdasani RA, 2001. Downregulation of Hedgehog signaling is required for organogenesis of the small intestine in Xenopus.  Dev Biol 229(1):188-202

Livingston DM; Shivdasani R, 2001. Toward mechanism-based cancer care.  JAMA 285(5):588-93

Polyak K; Riggins GJ, 2001. Gene discovery using the serial analysis of gene expression technique: implications for cancer research.  J Clin Oncol 19(11):2948-58

Polyák K; Hlavay J, 2001. Chemical fractionation of a fly ash sample by a sequential leaching method.  Fresenius J Anal Chem 371(6):838-42

Polyak K, 2001. On the birth of breast cancer.  Biochim Biophys Acta 1552(1):1-13

Poy F; Lepourcelet M; Shivdasani RA; Eck MJ, 2001. Structure of a human Tcf4-beta-catenin complex.  Nat Struct Biol 8(12):1053-7

Porter DA; Krop IE; Nasser S; Sgroi D; Kaelin CM; Marks JR; Riggins G; Polyak K, 2001. A SAGE (serial analysis of gene expression) view of breast tumor progression.  Cancer Res 61(15):5697-702

Shivdasani RA, 2001. Molecular and transcriptional regulation of megakaryocyte differentiation.  Stem Cells 19(5):397-407

Krop IE; Sgroi D; Porter DA; Lunetta KL; LeVangie R; Seth P; Kaelin CM; Rhei E; Bosenberg M; Schnitt S; Marks JR; Pagon Z; Belina D; Razumovic J; Polyak K, 2001. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells.  Proc Natl Acad Sci U S A 98(17):9796-801

Flatt PM; Polyak K; Tang LJ; Scatena CD; Westfall MD; Rubinstein LA; Yu J; Kinzler KW; Vogelstein B; Hill DE; Pietenpol JA, 2000. p53-dependent expression of PIG3 during proliferation, genotoxic stress, and reversible growth arrest.  Cancer Lett 156(1):63-72

Shoichet SA; Malik TH; Rothman JH; Shivdasani RA, 2000. Action of the Caenorhabditis elegans GATA factor END-1 in Xenopus suggests that similar mechanisms initiate endoderm development in ecdysozoa and vertebrates.  Proc Natl Acad Sci U S A 97(8):4076-81

Malik TH; Shivdasani RA, 2000. Structure and expression of a novel frizzled gene isolated from the developing mouse gut.  Biochem J 349 Pt 3:829-34

Lecine P; Italiano JE Jr; Kim SW; Villeval JL; Shivdasani RA, 2000. Hematopoietic-specific beta 1 tubulin participates in a pathway of platelet biogenesis dependent on the transcription factor NF-E2.  Blood 96(4):1366-73

Seth P; Lunetta KL; Bell DW; Gray H; Nasser SM; Rhei E; Kaelin CM; Iglehart DJ; Marks JR; Garber JE; Haber DA; Polyak K, 2000. Phenol sulfotransferases: hormonal regulation, polymorphism, and age of onset of breast cancer.  Cancer Res 60(24):6859-63

Levin J; Peng JP; Baker GR; Villeval JL; Lecine P; Burstein SA; Shivdasani RA, 1999. Pathophysiology of thrombocytopenia and anemia in mice lacking transcription factor NF-E2.  Blood 94(9):3037-47

da Costa LT; He TC; Yu J; Sparks AB; Morin PJ; Polyak K; Laken S; Vogelstein B; Kinzler KW, 1999. CDX2 is mutated in a colorectal cancer with normal APC/beta-catenin signaling.  Oncogene 18(35):5010-4

Hlavay J; Polyák K; Molnár A; Mészáros E, 1999. Development of a monitoring network for the analysis of elements in aerosol samples collected at Lake Balaton.  Acta Biol Hung 50(1-3):89-98

Lee YJ; Swencki B; Shoichet S; Shivdasani RA, 1999. A possible role for the high mobility group box transcription factor Tcf-4 in vertebrate gut epithelial cell differentiation.  J Biol Chem 274(3):1566-72

Vyas P; Ault K; Jackson CW; Orkin SH; Shivdasani RA, 1999. Consequences of GATA-1 deficiency in megakaryocytes and platelets.  Blood 93(9):2867-75

Velculescu VE; Madden SL; Zhang L; Lash AE; Yu J; Rago C; Lal A; Wang CJ; Beaudry GA; Ciriello KM; Cook BP; Dufault MR; Ferguson AT; Gao Y; He TC; Hermeking H; Hiraldo SK; Hwang PM; Lopez MA; Luderer HF; Mathews B; Petroziello JM; Polyak K; Zawel L; Kinzler KW, 1999. Analysis of human transcriptomes.  Nat Genet 23(4):387-8

Lal A; Lash AE; Altschul SF; Velculescu V; Zhang L; McLendon RE; Marra MA; Prange C; Morin PJ; Polyak K; Papadopoulos N; Vogelstein B; Kinzler KW; Strausberg RL; Riggins GJ, 1999. A public database for gene expression in human cancers.  Cancer Res 59(21):5403-7

Italiano JE Jr; Lecine P; Shivdasani RA; Hartwig JH, 1999. Blood platelets are assembled principally at the ends of proplatelet processes produced by differentiated megakaryocytes.  J Cell Biol 147(6):1299-312

Herman JG; Umar A; Polyak K; Graff JR; Ahuja N; Issa JP; Markowitz S; Willson JK; Hamilton SR; Kinzler KW; Kane MF; Kolodner RD; Vogelstein B; Kunkel TA; Baylin SB, 1998. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma.  Proc Natl Acad Sci U S A 95(12):6870-5

Martin F; van Deursen JM; Shivdasani RA; Jackson CW; Troutman AG; Ney PA, 1998. Erythroid maturation and globin gene expression in mice with combined deficiency of NF-E2 and nrf-2.  Blood 91(9):3459-66

Lecine P; Blank V; Shivdasani R, 1998. Characterization of the hematopoietic transcription factor NF-E2 in primary murine megakaryocytes.  J Biol Chem 273(13):7572-8

de Sauvage FJ; Villeval JL; Shivdasani RA, 1998. Regulation of megakaryocytopoiesis and platelet production: lessons from animal models.  J Lab Clin Med 131(6):496-501

Lecine P; Shivdasani RA, 1998. Cellular and molecular biology of megakaryocyte differentiation in the absence of lineage-restricted transcription factors.  Stem Cells 16 Suppl 2:91-5

Polyak K; Li Y; Zhu H; Lengauer C; Willson JK; Markowitz SD; Trush MA; Kinzler KW; Vogelstein B, 1998. Somatic mutations of the mitochondrial genome in human colorectal tumours.  Nat Genet 20(3):291-3

Orkin SH; Shivdasani RA; Fujiwara Y; McDevitt MA, 1998. Transcription factor GATA-1 in megakaryocyte development.  Stem Cells 16 Suppl 2:79-83

Lecine P; Villeval JL; Vyas P; Swencki B; Xu Y; Shivdasani RA, 1998. Mice lacking transcription factor NF-E2 provide in vivo validation of the proplatelet model of thrombocytopoiesis and show a platelet production defect that is intrinsic to megakaryocytes.  Blood 92(5):1608-16

Shivdasani RA; Fujiwara Y; McDevitt MA; Orkin SH, 1997. A lineage-selective knockout establishes the critical role of transcription factor GATA-1 in megakaryocyte growth and platelet development.  EMBO J 16(13):3965-73

McDevitt MA; Shivdasani RA; Fujiwara Y; Yang H; Orkin SH, 1997. A "knockdown" mutation created by cis-element gene targeting reveals the dependence of erythroid cell maturation on the level of transcription factor GATA-1.  Proc Natl Acad Sci U S A 94(13):6781-5

Polyak K; Wu TT; Hamilton SR; Kinzler KW; Vogelstein B, 1997. Less death in the dying.  Cell Death Differ 4(3):242-6

McDevitt MA; Fujiwara Y; Shivdasani RA; Orkin SH, 1997. An upstream, DNase I hypersensitive region of the hematopoietic-expressed transcription factor GATA-1 gene confers developmental specificity in transgenic mice.  Proc Natl Acad Sci U S A 94(15):7976-81

Chan FY; Robinson J; Brownlie A; Shivdasani RA; Donovan A; Brugnara C; Kim J; Lau BC; Witkowska HE; Zon LI, 1997. Characterization of adult alpha- and beta-globin genes in the zebrafish.  Blood 89(2):688-700

Shivdasani RA; Fielder P; Keller GA; Orkin SH; de Sauvage FJ, 1997. Regulation of the serum concentration of thrombopoietin in thrombocytopenic NF-E2 knockout mice.  Blood 90(5):1821-7

Shivdasani RA, 1997. Stem cell transcription factors.  Hematol Oncol Clin North Am 11(6):1199-206

Hermeking H; Lengauer C; Polyak K; He TC; Zhang L; Thiagalingam S; Kinzler KW; Vogelstein B, 1997. 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression.  Mol Cell 1(1):3-11

Deveaux S; Cohen-Kaminsky S; Shivdasani RA; Andrews NC; Filipe A; Kuzniak I; Orkin SH; Roméo PH; Mignotte V, 1997. p45 NF-E2 regulates expression of thromboxane synthase in megakaryocytes.  EMBO J 16(18):5654-61

Polyak K; Xia Y; Zweier JL; Kinzler KW; Vogelstein B, 1997. A model for p53-induced apoptosis.  Nature 389(6648):300-5

Polyak K, 1996. Negative regulation of cell growth by TGF beta.  Biochim Biophys Acta 1242(3):185-99

Leach FS; Polyak K; Burrell M; Johnson KA; Hill D; Dunlop MG; Wyllie AH; Peltomaki P; de la Chapelle A; Hamilton SR; Kinzler KW; Vogelstein B, 1996. Expression of the human mismatch repair gene hMSH2 in normal and neoplastic tissues.  Cancer Res 56(2):235-40

Shivdasani RA, 1996. The role of transcription factor NF-E2 in megakaryocyte maturation and platelet production.  Stem Cells 14 Suppl 1:112-5

Shivdasani RA; Orkin SH, 1996. The transcriptional control of hematopoiesis.  Blood 87(10):4025-39

Polyak K; Hamilton SR; Vogelstein B; Kinzler KW, 1996. Early alteration of cell-cycle-regulated gene expression in colorectal neoplasia.  Am J Pathol 149(2):381-7

Peters LL; Shivdasani RA; Liu SC; Hanspal M; John KM; Gonzalez JM; Brugnara C; Gwynn B; Mohandas N; Alper SL; Orkin SH; Lux SE, 1996. Anion exchanger 1 (band 3) is required to prevent erythrocyte membrane surface loss but not to form the membrane skeleton.  Cell 86(6):917-27

Fero ML; Rivkin M; Tasch M; Porter P; Carow CE; Firpo E; Polyak K; Tsai LH; Broudy V; Perlmutter RM; Kaushansky K; Roberts JM, 1996. A syndrome of multiorgan hyperplasia with features of gigantism, tumorigenesis, and female sterility in p27(Kip1)-deficient mice.  Cell 85(5):733-44

Polyak K; Waldman T; He TC; Kinzler KW; Vogelstein B, 1996. Genetic determinants of p53-induced apoptosis and growth arrest.  Genes Dev 10(15):1945-52

Shivdasani RA; Mayer EL; Orkin SH, 1995. Absence of blood formation in mice lacking the T-cell leukaemia oncoprotein tal-1/SCL.  Nature 373(6513):432-4

Massagué J; Polyak K, 1995. Mammalian antiproliferative signals and their targets.  Curr Opin Genet Dev 5(1):91-6

Ponce-Castañeda MV; Lee MH; Latres E; Polyak K; Lacombe L; Montgomery K; Mathew S; Krauter K; Sheinfeld J; Massague J, 1995. p27Kip1: chromosomal mapping to 12p12-12p13.1 and absence of mutations in human tumors.  Cancer Res 55(6):1211-4

Koff A; Polyak K, 1995. p27KIP1, an inhibitor of cyclin-dependent kinases.  Prog Cell Cycle Res 1:141-7

Shivdasani RA; Rosenblatt MF; Zucker-Franklin D; Jackson CW; Hunt P; Saris CJ; Orkin SH, 1995. Transcription factor NF-E2 is required for platelet formation independent of the actions of thrombopoietin/MGDF in megakaryocyte development.  Cell 81(5):695-704

Reynisdóttir I; Polyak K; Iavarone A; Massagué J, 1995. Kip/Cip and Ink4 Cdk inhibitors cooperate to induce cell cycle arrest in response to TGF-beta.  Genes Dev 9(15):1831-45

Shivdasani RA; Orkin SH, 1995. Erythropoiesis and globin gene expression in mice lacking the transcription factor NF-E2.  Proc Natl Acad Sci U S A 92(19):8690-4

Jeffrey PD; Russo AA; Polyak K; Gibbs E; Hurwitz J; Massagué J; Pavletich NP, 1995. Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex.  Nature 376(6538):313-20

Polyak K; Kato JY; Solomon MJ; Sherr CJ; Massague J; Roberts JM; Koff A, 1994. p27Kip1, a cyclin-Cdk inhibitor, links transforming growth factor-beta and contact inhibition to cell cycle arrest.  Genes Dev 8(1):9-22

Roberts JM; Koff A; Polyak K; Firpo E; Collins S; Ohtsubo M; Massagué J, 1994. Cyclins, Cdks, and cyclin kinase inhibitors.  Cold Spring Harb Symp Quant Biol 59:31-8

Polyák K; Bódog I; Hlavay J, 1994. Determination of chemical species of selected trace elements in fly ash.  Talanta 41(7):1151-9

Shivdasani RA; Anderson KC, 1994. HLA homozygosity and shared HLA haplotypes in the development of transfusion-associated graft-versus-host disease.  Leuk Lymphoma 15(3-4):227-34

Nourse J; Firpo E; Flanagan WM; Coats S; Polyak K; Lee MH; Massague J; Crabtree GR; Roberts JM, 1994. Interleukin-2-mediated elimination of the p27Kip1 cyclin-dependent kinase inhibitor prevented by rapamycin.  Nature 372(6506):570-3

Polyak K; Lee MH; Erdjument-Bromage H; Koff A; Roberts JM; Tempst P; Massagué J, 1994. Cloning of p27Kip1, a cyclin-dependent kinase inhibitor and a potential mediator of extracellular antimitogenic signals.  Cell 78(1):59-66

Kato JY; Matsuoka M; Polyak K; Massagué J; Sherr CJ, 1994. Cyclic AMP-induced G1 phase arrest mediated by an inhibitor (p27Kip1) of cyclin-dependent kinase 4 activation.  Cell 79(3):487-96

Shivdasani RA; Haluska FG; Dock NL; Dover JS; Kineke EJ; Anderson KC, 1993. Brief report: graft-versus-host disease associated with transfusion of blood from unrelated HLA-homozygous donors.  N Engl J Med 328(11):766-70

Shivdasani RA; Hess JL; Skarin AT; Pinkus GS, 1993. Intermediate lymphocytic lymphoma: clinical and pathologic features of a recently characterized subtype of non-Hodgkin's lymphoma.  J Clin Oncol 11(4):802-111

Shivdasani RA; Anderson KC, 1993. Transfusion-associated graft-versus-host disease: scratching the surface.  Transfusion 33(9):696-7

Koff A; Ohtsuki M; Polyak K; Roberts JM; Massagué J, 1993. Negative regulation of G1 in mammalian cells: inhibition of cyclin E-dependent kinase by TGF-beta.  Science 260(5107):536-9

Gyuris J; Dencsö L; Polyák K; Duda E, 1991. Complex interaction of yeast nuclear proteins with the enhancer/promoter region of SV40.  Curr Genet 20(5):359-63

Shivdasani RA; Esch TR; Chen GH; Thomas DW, 1990. Monoclonal antibodies define the characteristics and cellular distribution of an Ia-associated protein.  Hybridoma 9(1):17-30

Bielinska A; Shivdasani RA; Zhang LQ; Nabel GJ, 1990. Regulation of gene expression with double-stranded phosphorothioate oligonucleotides.  Science 250(4983):997-1000

Shivdasani RA, 1989. Science, another culture: an essay after C. P. Snow.  Pharos Alpha Omega Alpha Honor Med Soc 52(4):21-4

Shivdasani RA; Thomas DW, 1988. Molecular associations of IA antigens after T-B cell interactions. I. Identification of new molecular associations.  J Immunol 141(4):1252-60

Kim KH; Shivdasani RA; Thomas DW, 1986. Two roles for Ia in antigen-specific T lymphocyte activation.  J Immunol 137(11):3393-400

Galgóczy J; Polyák K; Novák EK, 1976. The macroconidial septum of some dermatophyton species.  Acta Microbiol Acad Sci Hung 23(1):7-13

Halász A; Pungor E; Polyák K, 1971. Properties and analytical applications of the heteropolymolybdates of phosphorus, arsenic, silicon and germanium-III Examination of two- and three-component systems without separation.  Talanta 18(6):577-86

Halász A; Polyák K; Pungor E, 1971. Properties and analytical applications of the heteropolymolybdates of phosphorus, arsenic, silicon and germanium-IV Determination of phosphomolybdic and silicomolybdic acids via the molybdenum content, with phenylfluorone.  Talanta 18(7):691-6

Publication list retrieved from NCBI using ImpactPubs

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Bailey ST; Westerling T; Brown M, 2015. Loss of Estrogen-Regulated microRNA Expression Increases HER2 Signaling and Is Prognostic of Poor Outcome in Luminal Breast Cancer.  Cancer Res 75(2):436-45

van Kruchten M; de Vries EG; Glaudemans AW; van Lanschot MC; van Faassen M; Kema IP; Brown M; Schröder CP; de Vries EF; Hospers GA, 2015. Measuring Residual Estrogen Receptor Availability during Fulvestrant Therapy in Patients with Metastatic Breast Cancer.  Cancer Discov 5(1):72-81

Chen X; Iliopoulos D; Zhang Q; Tang Q; Greenblatt MB; Hatziapostolou M; Lim E; Tam WL; Ni M; Chen Y; Mai J; Shen H; Hu DZ; Adoro S; Hu B; Song M; Tan C; Landis MD; Ferrari M; Shin SJ; Brown M; Chang JC; Liu XS; Glimcher LH, 2014. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway.  Nature 508(7494):103-7

Hsieh CL; Fei T; Chen Y; Li T; Gao Y; Wang X; Sun T; Sweeney CJ; Lee GS; Chen S; Balk SP; Liu XS; Brown M; Kantoff PW, 2014. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation.  Proc Natl Acad Sci U S A 111(20):7319-24

Jehle K; Cato L; Neeb A; Muhle-Goll C; Jung N; Smith EW; Buzon V; Carbó LR; Estébanez-Perpiñá E; Schmitz K; Fruk L; Luy B; Chen Y; Cox MB; Bräse S; Brown M; Cato AC, 2014. Coregulator control of androgen receptor action by a novel nuclear receptor-binding motif.  J Biol Chem 289(13):8839-51

Jeselsohn R; Yelensky R; Buchwalter G; Frampton G; Meric-Bernstam F; Gonzalez-Angulo AM; Ferrer-Lozano J; Perez-Fidalgo JA; Cristofanilli M; Gómez H; Arteaga CL; Giltnane J; Balko JM; Cronin MT; Jarosz M; Sun J; Hawryluk M; Lipson D; Otto G; Ross JS; Dvir A; Soussan-Gutman L; Wolf I; Rubinek T; Gilmore L; Schnitt S; Come SE; Pusztai L; Stephens P; Brown M; Miller VA, 2014. Emergence of constitutively active estrogen receptor-α mutations in pretreated advanced estrogen receptor-positive breast cancer.  Clin Cancer Res 20(7):1757-67

Cai C; He HH; Gao S; Chen S; Yu Z; Gao Y; Chen S; Chen MW; Zhang J; Ahmed M; Wang Y; Metzger E; Schüle R; Liu XS; Brown M; Balk SP, 2014. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity.  Cell Rep 9(5):1618-27

Lim E; Ni M; Cao S; Hazra A; Tamimi RM; Brown M, 2014. Importance of Breast Cancer Subtype in the Development of Androgen Receptor Directed Therapy.  Curr Breast Cancer Rep 6(2):71-78

Bailey ST; Miron PL; Choi YJ; Kochupurakkal B; Maulik G; Rodig SJ; Tian R; Foley KM; Bowman T; Miron A; Brown M; Iglehart JD; Biswas DK, 2014. NF-κB activation-induced anti-apoptosis renders HER2-positive cells drug resistant and accelerates tumor growth.  Mol Cancer Res 12(3):408-20

He HH; Meyer CA; Hu SS; Chen MW; Zang C; Liu Y; Rao PK; Fei T; Xu H; Long H; Liu XS; Brown M, 2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.  Nat Methods 11(1):73-8

Cato L; Neeb A; Brown M; Cato AC, 2014. Control of steroid receptor dynamics and function by genomic actions of the cochaperones p23 and Bag-1L.  Nucl Recept Signal 12:e005

Yoo S; Pettersson A; Jordahl KM; Lis RT; Lindstrom S; Meisner A; Nuttall EJ; Stack EC; Stampfer MJ; Kraft P; Brown M; Loda M; Giovannucci EL; Kantoff PW; Mucci LA, 2014. Androgen receptor CAG repeat polymorphism and risk of TMPRSS2:ERG-positive prostate cancer.  Cancer Epidemiol Biomarkers Prev 23(10):2027-31

Hu Y; Petit SA; Ficarro SB; Toomire KJ; Xie A; Lim E; Cao SA; Park E; Eck MJ; Scully R; Brown M; Marto JA; Livingston DM, 2014. PARP1-driven poly-ADP-ribosylation regulates BRCA1 function in homologous recombination-mediated DNA repair.  Cancer Discov 4(12):1430-47

Li W; Xu H; Xiao T; Cong L; Love MI; Zhang F; Irizarry RA; Liu JS; Brown M; Liu X, 2014. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.  Genome Biol 15(12):554

Dreijerink KM; Goudet P; Burgess JR; Valk GD, 2014. Breast-cancer predisposition in multiple endocrine neoplasia type 1.  N Engl J Med 371(6):583-4

Gordon FK; Vallaster CS; Westerling T; Iyer LK; Brown M; Schnitzler GR, 2014. Research resource: Aorta- and liver-specific ERα-binding patterns and gene regulation by estrogen.  Mol Endocrinol 28(8):1337-51

Du Z; Fei T; Verhaak RG; Su Z; Zhang Y; Brown M; Chen Y; Liu XS, 2013. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.  Nat Struct Mol Biol 20(7):908-13

Ni M; Chen Y; Fei T; Li D; Lim E; Liu XS; Brown M, 2013. Amplitude modulation of androgen signaling by c-MYC.  Genes Dev 27(7):734-48

Cai C; Wang H; He HH; Chen S; He L; Ma F; Mucci L; Wang Q; Fiore C; Sowalsky AG; Loda M; Liu XS; Brown M; Balk SP; Yuan X, 2013. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.  J Clin Invest 123(3):1109-22

Jeselsohn RM; Werner L; Regan MM; Fatima A; Gilmore L; Collins LC; Beck AH; Bailey ST; He HH; Buchwalter G; Brown M; Iglehart JD; Richardson A; Come SE, 2013. Digital quantification of gene expression in sequential breast cancer biopsies reveals activation of an immune response.  PLoS One 8(5):e64225

Li Q; Seo JH; Stranger B; McKenna A; Pe'er I; Laframboise T; Brown M; Tyekucheva S; Freedman ML, 2013. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.  Cell 152(3):633-41

Sun H; Qin B; Liu T; Wang Q; Liu J; Wang J; Lin X; Yang Y; Taing L; Rao PK; Brown M; Zhang Y; Long HW; Liu XS, 2013. CistromeFinder for ChIP-seq and DNase-seq data reuse.  Bioinformatics 29(10):1352-4

Tam WL; Lu H; Buikhuisen J; Soh BS; Lim E; Reinhardt F; Wu ZJ; Krall JA; Bierie B; Guo W; Chen X; Liu XS; Brown M; Lim B; Weinberg RA, 2013. Protein kinase C α is a central signaling node and therapeutic target for breast cancer stem cells.  Cancer Cell 24(3):347-64

Merenbakh-Lamin K; Ben-Baruch N; Yeheskel A; Dvir A; Soussan-Gutman L; Jeselsohn R; Yelensky R; Brown M; Miller VA; Sarid D; Rizel S; Klein B; Rubinek T; Wolf I, 2013. D538G mutation in estrogen receptor-α: A novel mechanism for acquired endocrine resistance in breast cancer.  Cancer Res 73(23):6856-64

Pfefferle AD; Herschkowitz JI; Usary J; Harrell JC; Spike BT; Adams JR; Torres-Arzayus MI; Brown M; Egan SE; Wahl GM; Rosen JM; Perou CM, 2013. Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts.  Genome Biol 14(11):R125

Bhat-Nakshatri P; Song EK; Collins NR; Uversky VN; Dunker AK; O'Malley BW; Geistlinger TR; Carroll JS; Brown M; Nakshatri H, 2013. Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing.  BMC Med Genomics 6:21

van Kruchten M; de Vries EG; Brown M; de Vries EF; Glaudemans AW; Dierckx RA; Schröder CP; Hospers GA, 2013. PET imaging of oestrogen receptors in patients with breast cancer.  Lancet Oncol 14(11):e465-75

McLaughlin SK; Olsen SN; Dake B; De Raedt T; Lim E; Bronson RT; Beroukhim R; Polyak K; Brown M; Kuperwasser C; Cichowski K, 2013. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor.  Cancer Cell 24(3):365-78

Buchwalter G; Hickey MM; Cromer A; Selfors LM; Gunawardane RN; Frishman J; Jeselsohn R; Lim E; Chi D; Fu X; Schiff R; Brown M; Brugge JS, 2013. PDEF promotes luminal differentiation and acts as a survival factor for ER-positive breast cancer cells.  Cancer Cell 23(6):753-67

Sun T; Yang M; Chen S; Balk S; Pomerantz M; Hsieh CL; Brown M; Lee GS; Kantoff PW, 2012. The altered expression of MiR-221/-222 and MiR-23b/-27b is associated with the development of human castration resistant prostate cancer.  Prostate 72(10):1093-103

He HH; Meyer CA; Chen MW; Jordan VC; Brown M; Liu XS, 2012. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.  Genome Res 22(6):1015-25

Villa A; Della Torre S; Stell A; Cook J; Brown M; Maggi A, 2012. Tetradian oscillation of estrogen receptor α is necessary to prevent liver lipid deposition.  Proc Natl Acad Sci U S A 109(29):11806-11

Bailey ST; Shin H; Westerling T; Liu XS; Brown M, 2012. Estrogen receptor prevents p53-dependent apoptosis in breast cancer.  Proc Natl Acad Sci U S A 109(44):18060-5

Xu K; Wu ZJ; Groner AC; He HH; Cai C; Lis RT; Wu X; Stack EC; Loda M; Liu T; Xu H; Cato L; Thornton JE; Gregory RI; Morrissey C; Vessella RL; Montironi R; Magi-Galluzzi C; Kantoff PW; Balk SP; Liu XS; Brown M, 2012. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.  Science 338(6113):1465-9

Meyer CA; He HH; Brown M; Liu XS, 2011. BINOCh: binding inference from nucleosome occupancy changes.  Bioinformatics 27(13):1867-8

Yang M; Xie W; Mostaghel E; Nakabayashi M; Werner L; Sun T; Pomerantz M; Freedman M; Ross R; Regan M; Sharifi N; Figg WD; Balk S; Brown M; Taplin ME; Oh WK; Lee GS; Kantoff PW, 2011. SLCO2B1 and SLCO1B3 may determine time to progression for patients receiving androgen deprivation therapy for prostate cancer.  J Clin Oncol 29(18):2565-73

Baba A; Ohtake F; Okuno Y; Yokota K; Okada M; Imai Y; Ni M; Meyer CA; Igarashi K; Kanno J; Brown M; Kato S, 2011. PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B.  Nat Cell Biol 13(6):668-75

Sérandour AA; Avner S; Percevault F; Demay F; Bizot M; Lucchetti-Miganeh C; Barloy-Hubler F; Brown M; Lupien M; Métivier R; Salbert G; Eeckhoute J, 2011. Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.  Genome Res 21(4):555-65

Madak-Erdogan Z; Lupien M; Stossi F; Brown M; Katzenellenbogen BS, 2011. Genomic collaboration of estrogen receptor alpha and extracellular signal-regulated kinase 2 in regulating gene and proliferation programs.  Mol Cell Biol 31(1):226-36

Scott SM; Brown M; Come SE, 2011. Emerging data on the efficacy and safety of fulvestrant, a unique antiestrogen therapy for advanced breast cancer.  Expert Opin Drug Saf 10(5):819-26

Flavin RJ; Cook J; Fiorentino M; Bailey D; Brown M; Loda MF, 2011. β-Catenin is a useful adjunct immunohistochemical marker for the diagnosis of pulmonary lymphangioleiomyomatosis.  Am J Clin Pathol 135(5):776-82

Frigo DE; Howe MK; Wittmann BM; Brunner AM; Cushman I; Wang Q; Brown M; Means AR; McDonnell DP, 2011. CaM kinase kinase beta-mediated activation of the growth regulatory kinase AMPK is required for androgen-dependent migration of prostate cancer cells.  Cancer Res 71(2):528-37

Cai C; He HH; Chen S; Coleman I; Wang H; Fang Z; Chen S; Nelson PS; Liu XS; Brown M; Balk SP, 2011. Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1.  Cancer Cell 20(4):457-71

Ni M; Chen Y; Lim E; Wimberly H; Bailey ST; Imai Y; Rimm DL; Liu XS; Brown M, 2011. Targeting androgen receptor in estrogen receptor-negative breast cancer.  Cancer Cell 20(1):119-31

Tang Q; Chen Y; Meyer C; Geistlinger T; Lupien M; Wang Q; Liu T; Zhang Y; Brown M; Liu XS, 2011. A comprehensive view of nuclear receptor cancer cistromes.  Cancer Res 71(22):6940-7

Fujiki R; Hashiba W; Sekine H; Yokoyama A; Chikanishi T; Ito S; Imai Y; Kim J; He HH; Igarashi K; Kanno J; Ohtake F; Kitagawa H; Roeder RG; Brown M; Kato S, 2011. GlcNAcylation of histone H2B facilitates its monoubiquitination.  Nature 480(7378):557-60

Wang C; Mayer JA; Mazumdar A; Fertuck K; Kim H; Brown M; Brown PH, 2011. Estrogen induces c-myc gene expression via an upstream enhancer activated by the estrogen receptor and the AP-1 transcription factor.  Mol Endocrinol 25(9):1527-38

Zhang C; Wang L; Wu D; Chen H; Chen Z; Thomas-Ahner JM; Zynger DL; Eeckhoute J; Yu J; Luo J; Brown M; Clinton SK; Nephew KP; Huang TH; Li W; Wang Q, 2011. Definition of a FoxA1 Cistrome that is crucial for G1 to S-phase cell-cycle transit in castration-resistant prostate cancer.  Cancer Res 71(21):6738-48

Liu T; Ortiz JA; Taing L; Meyer CA; Lee B; Zhang Y; Shin H; Wong SS; Ma J; Lei Y; Pape UJ; Poidinger M; Chen Y; Yeung K; Brown M; Turpaz Y; Liu XS, 2011. Cistrome: an integrative platform for transcriptional regulation studies.  Genome Biol 12(8):R83

Badve S; Collins NR; Bhat-Nakshatri P; Turbin D; Leung S; Thorat M; Dunn SE; Geistlinger TR; Carroll JS; Brown M; Bose S; Teitell MA; Nakshatri H, 2010. Subcellular localization of activated AKT in estrogen receptor- and progesterone receptor-expressing breast cancers: potential clinical implications.  Am J Pathol 176(5):2139-49

He HH; Meyer CA; Shin H; Bailey ST; Wei G; Wang Q; Zhang Y; Xu K; Ni M; Lupien M; Mieczkowski P; Lieb JD; Zhao K; Brown M; Liu XS, 2010. Nucleosome dynamics define transcriptional enhancers.  Nat Genet 42(4):343-7

Wolfer A; Wittner BS; Irimia D; Flavin RJ; Lupien M; Gunawardane RN; Meyer CA; Lightcap ES; Tamayo P; Mesirov JP; Liu XS; Shioda T; Toner M; Loda M; Brown M; Brugge JS; Ramaswamy S, 2010. MYC regulation of a "poor-prognosis" metastatic cancer cell state.  Proc Natl Acad Sci U S A 107(8):3698-703

Wade HE; Kobayashi S; Eaton ML; Jansen MS; Lobenhofer EK; Lupien M; Geistlinger TR; Zhu W; Nevins JR; Brown M; Otteson DC; McDonnell DP, 2010. Multimodal regulation of E2F1 gene expression by progestins.  Mol Cell Biol 30(8):1866-77

Ahmadiyeh N; Pomerantz MM; Grisanzio C; Herman P; Jia L; Almendro V; He HH; Brown M; Liu XS; Davis M; Caswell JL; Beckwith CA; Hills A; Macconaill L; Coetzee GA; Regan MM; Freedman ML, 2010. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC.  Proc Natl Acad Sci U S A 107(21):9742-6

Torres-Arzayus MI; Zhao J; Bronson R; Brown M, 2010. Estrogen-dependent and estrogen-independent mechanisms contribute to AIB1-mediated tumor formation.  Cancer Res 70(10):4102-11

Lupien M; Meyer CA; Bailey ST; Eeckhoute J; Cook J; Westerling T; Zhang X; Carroll JS; Rhodes DR; Liu XS; Brown M, 2010. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.  Genes Dev 24(19):2219-27

Verzi MP; Shin H; He HH; Sulahian R; Meyer CA; Montgomery RK; Fleet JC; Brown M; Liu XS; Shivdasani RA, 2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26

Verzi MP; Hatzis P; Sulahian R; Philips J; Schuijers J; Shin H; Freed E; Lynch JP; Dang DT; Brown M; Clevers H; Liu XS; Shivdasani RA, 2010. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions.  Proc Natl Acad Sci U S A 107(34):15157-62

Sun T; Wang Q; Balk S; Brown M; Lee GS; Kantoff P, 2009. The role of microRNA-221 and microRNA-222 in androgen-independent prostate cancer cell lines.  Cancer Res 69(8):3356-63

Lupien M; Eeckhoute J; Meyer CA; Krum SA; Rhodes DR; Liu XS; Brown M, 2009. Coactivator function defines the active estrogen receptor alpha cistrome.  Mol Cell Biol 29(12):3413-23

Nwachukwu JC; Mita P; Ruoff R; Ha S; Wang Q; Huang SJ; Taneja SS; Brown M; Gerald WL; Garabedian MJ; Logan SK, 2009. Genome-wide impact of androgen receptor trapped clone-27 loss on androgen-regulated transcription in prostate cancer cells.  Cancer Res 69(7):3140-7

Lupien M; Brown M, 2009. Cistromics of hormone-dependent cancer.  Endocr Relat Cancer 16(2):381-9

Eeckhoute J; Lupien M; Meyer CA; Verzi MP; Shivdasani RA; Liu XS; Brown M, 2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.  Genome Res 19(3):372-80

Xia X; Lemieux ME; Li W; Carroll JS; Brown M; Liu XS; Kung AL, 2009. Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis.  Proc Natl Acad Sci U S A 106(11):4260-5

Zhang Q; Gu J; Li L; Liu J; Luo B; Cheung HW; Boehm JS; Ni M; Geisen C; Root DE; Polyak K; Brown M; Richardson AL; Hahn WC; Kaelin WG Jr; Bommi-Reddy A, 2009. Control of cyclin D1 and breast tumorigenesis by the EglN2 prolyl hydroxylase.  Cancer Cell 16(5):413-24

Wang Q; Li W; Zhang Y; Yuan X; Xu K; Yu J; Chen Z; Beroukhim R; Wang H; Lupien M; Wu T; Regan MM; Meyer CA; Carroll JS; Manrai AK; Jänne OA; Balk SP; Mehra R; Han B; Chinnaiyan AM; Rubin MA; True L; Fiorentino M; Fiore C; Loda M; Kantoff PW; Liu XS; Brown M, 2009. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer.  Cell 138(2):245-56

Boros J; Donaldson IJ; O'Donnell A; Odrowaz ZA; Zeef L; Lupien M; Meyer CA; Liu XS; Brown M; Sharrocks AD, 2009. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery.  Genome Res 19(11):1963-73

Bhat-Nakshatri P; Wang G; Collins NR; Thomson MJ; Geistlinger TR; Carroll JS; Brown M; Hammond S; Srour EF; Liu Y; Nakshatri H, 2009. Estradiol-regulated microRNAs control estradiol response in breast cancer cells.  Nucleic Acids Res 37(14):4850-61

Frigo DE; Sherk AB; Wittmann BM; Norris JD; Wang Q; Joseph JD; Toner AP; Brown M; McDonnell DP, 2009. Induction of Kruppel-like factor 5 expression by androgens results in increased CXCR4-dependent migration of prostate cancer cells in vitro.  Mol Endocrinol 23(9):1385-96

Eeckhoute J; Lupien M; Brown M, 2009. Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies.  Methods Mol Biol 556:155-64

Nucera C; Eeckhoute J; Finn S; Carroll JS; Ligon AH; Priolo C; Fadda G; Toner M; Sheils O; Attard M; Pontecorvi A; Nose V; Loda M; Brown M, 2009. FOXA1 is a potential oncogene in anaplastic thyroid carcinoma.  Clin Cancer Res 15(11):3680-9

Leleu X; Eeckhoute J; Jia X; Roccaro AM; Moreau AS; Farag M; Sacco A; Ngo HT; Runnels J; Melhem MR; Burwick N; Azab A; Azab F; Hunter Z; Hatjiharissi E; Carrasco DR; Treon SP; Witzig TE; Hideshima T; Brown M; Anderson KC; Ghobrial IM, 2008. Targeting NF-kappaB in Waldenstrom macroglobulinemia.  Blood 111(10):5068-77

Lupien M; Eeckhoute J; Meyer CA; Wang Q; Zhang Y; Li W; Carroll JS; Liu XS; Brown M, 2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.  Cell 132(6):958-70

Bao BY; Chuang BF; Wang Q; Sartor O; Balk SP; Brown M; Kantoff PW; Lee GS, 2008. Androgen receptor mediates the expression of UDP-glucuronosyltransferase 2 B15 and B17 genes.  Prostate 68(8):839-48

Krum SA; Miranda-Carboni GA; Hauschka PV; Carroll JS; Lane TF; Freedman LP; Brown M, 2008. Estrogen protects bone by inducing Fas ligand in osteoblasts to regulate osteoclast survival.  EMBO J 27(3):535-45

Li W; Carroll JS; Brown M; Liu xS, 2008. xMAN: extreme MApping of OligoNucleotides.  BMC Genomics 9 Suppl 1:S20

Frietze S; Lupien M; Silver PA; Brown M, 2008. CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1.  Cancer Res 68(1):301-6

Johnson DS; Li W; Gordon DB; Bhattacharjee A; Curry B; Ghosh J; Brizuela L; Carroll JS; Brown M; Flicek P; Koch CM; Dunham I; Bieda M; Xu X; Farnham PJ; Kapranov P; Nix DA; Gingeras TR; Zhang X; Holster H; Jiang N; Green RD; Song JS; McCuine SA; Anton E; Nguyen L; Trinklein ND; Ye Z; Ching K; Hawkins D; Ren B; Scacheri PC; Rozowsky J; Karpikov A; Euskirchen G; Weissman S; Gerstein M; Snyder M; Yang A; Moqtaderi Z; Hirsch H; Shulha HP; Fu Y; Weng Z; Struhl K; Myers RM; Lieb JD; Liu XS, 2008. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.  Genome Res 18(3):393-403

Krum SA; Brown M, 2008. Unraveling estrogen action in osteoporosis.  Cell Cycle 7(10):1348-52

Zhang Y; Liu T; Meyer CA; Eeckhoute J; Johnson DS; Bernstein BE; Nusbaum C; Myers RM; Brown M; Li W; Liu XS, 2008. Model-based analysis of ChIP-Seq (MACS).  Genome Biol 9(9):R137

Krum SA; Miranda-Carboni GA; Lupien M; Eeckhoute J; Carroll JS; Brown M, 2008. Unique ERalpha cistromes control cell type-specific gene regulation.  Mol Endocrinol 22(11):2393-406

Hurtado A; Holmes KA; Geistlinger TR; Hutcheson IR; Nicholson RI; Brown M; Jiang J; Howat WJ; Ali S; Carroll JS, 2008. Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen.  Nature 456(7222):663-6

Holmes KA; Song JS; Liu XS; Brown M; Carroll JS, 2008. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity.  Cancer Res 68(18):7380-5

Bhat-Nakshatri P; Wang G; Appaiah H; Luktuke N; Carroll JS; Geistlinger TR; Brown M; Badve S; Liu Y; Nakshatri H, 2008. AKT alters genome-wide estrogen receptor alpha binding and impacts estrogen signaling in breast cancer.  Mol Cell Biol 28(24):7487-503

Agoulnik IU; Bingman WE 3rd; Nakka M; Li W; Wang Q; Liu XS; Brown M; Weigel NL, 2008. Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase.  Mol Endocrinol 22(11):2420-32

Yang XH; Richardson AL; Torres-Arzayus MI; Zhou P; Sharma C; Kazarov AR; Andzelm MM; Strominger JL; Brown M; Hemler ME, 2008. CD151 accelerates breast cancer by regulating alpha 6 integrin function, signaling, and molecular organization.  Cancer Res 68(9):3204-13

Setlur SR; Mertz KD; Hoshida Y; Demichelis F; Lupien M; Perner S; Sboner A; Pawitan Y; Andrén O; Johnson LA; Tang J; Adami HO; Calza S; Chinnaiyan AM; Rhodes D; Tomlins S; Fall K; Mucci LA; Kantoff PW; Stampfer MJ; Andersson SO; Varenhorst E; Johansson JE; Brown M; Golub TR; Rubin MA, 2008. Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer.  J Natl Cancer Inst 100(11):815-25

Eeckhoute J; Keeton EK; Lupien M; Krum SA; Carroll JS; Brown M, 2007. Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer.  Cancer Res 67(13):6477-83

Durand M; Kolpak A; Farrell T; Elliott NA; Shao W; Brown M; Volkert MR, 2007. The OXR domain defines a conserved family of eukaryotic oxidation resistance proteins.  BMC Cell Biol 8:13

Wang Q; Li W; Liu XS; Carroll JS; Jänne OA; Keeton EK; Chinnaiyan AM; Pienta KJ; Brown M, 2007. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.  Mol Cell 27(3):380-92

Richardson AL; Wang ZC; De Nicolo A; Lu X; Brown M; Miron A; Liao X; Iglehart JD; Livingston DM; Ganesan S, 2006. X chromosomal abnormalities in basal-like human breast cancer.  Cancer Cell 9(2):121-32

Come SE; Buzdar AU; Ingle JN; Arteaga CL; Brown M; Dowsett M; Hilsenbeck SG; Kumar R; Johnston SR; Lee AV; Paik S; Pritchard KI; Winer EP; Hart C, 2006. Proceedings of the Fifth International Conference on Recent Advances and Future Directions in Endocrine Therapy for Breast Cancer: conference summary statement.  Clin Cancer Res 12(3 Pt 2):997s-1000s

Carroll DK; Carroll JS; Leong CO; Cheng F; Brown M; Mills AA; Brugge JS; Ellisen LW, 2006. p63 regulates an adhesion programme and cell survival in epithelial cells.  Nat Cell Biol 8(6):551-61

Colilla S; Kantoff PW; Neuhausen SL; Godwin AK; Daly MB; Narod SA; Garber JE; Lynch HT; Brown M; Weber BL; Rebbeck TR, 2006. The joint effect of smoking and AIB1 on breast cancer risk in BRCA1 mutation carriers.  Carcinogenesis 27(3):599-605

Carroll JS; Brown M, 2006. Estrogen receptor target gene: an evolving concept.  Mol Endocrinol 20(8):1707-14

Carroll JS; Meyer CA; Song J; Li W; Geistlinger TR; Eeckhoute J; Brodsky AS; Keeton EK; Fertuck KC; Hall GF; Wang Q; Bekiranov S; Sementchenko V; Fox EA; Silver PA; Gingeras TR; Liu XS; Brown M, 2006. Genome-wide analysis of estrogen receptor binding sites.  Nat Genet 38(11):1289-97

Wang QF; Prabhakar S; Wang Q; Moses AM; Chanan S; Brown M; Eisen MB; Cheng JF; Rubin EM; Boffelli D, 2006. Primate-specific evolution of an LDLR enhancer.  Genome Biol 7(8):R68

Torres-Arzayus MI; Yuan J; DellaGatta JL; Lane H; Kung AL; Brown M, 2006. Targeting the AIB1 oncogene through mammalian target of rapamycin inhibition in the mammary gland.  Cancer Res 66(23):11381-8

Eeckhoute J; Carroll JS; Geistlinger TR; Torres-Arzayus MI; Brown M, 2006. A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer.  Genes Dev 20(18):2513-26

Johnson WE; Li W; Meyer CA; Gottardo R; Carroll JS; Brown M; Liu XS, 2006. Model-based analysis of tiling-arrays for ChIP-chip.  Proc Natl Acad Sci U S A 103(33):12457-62

Keeton EK; Brown M, 2005. Cell cycle progression stimulated by tamoxifen-bound estrogen receptor-alpha and promoter-specific effects in breast cancer cells deficient in N-CoR and SMRT.  Mol Endocrinol 19(6):1543-54

Febbo PG; Lowenberg M; Thorner AR; Brown M; Loda M; Golub TR, 2005. Androgen mediated regulation and functional implications of fkbp51 expression in prostate cancer.  J Urol 173(5):1772-7

Carroll JS; Liu XS; Brodsky AS; Li W; Meyer CA; Szary AJ; Eeckhoute J; Shao W; Hestermann EV; Geistlinger TR; Fox EA; Silver PA; Brown M, 2005. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.  Cell 122(1):33-43

Georgescu SP; Li JH; Lu Q; Karas RH; Brown M; Mendelsohn ME, 2005. Modulator recognition factor 1, an AT-rich interaction domain family member, is a novel corepressor for estrogen receptor alpha.  Mol Endocrinol 19(10):2491-501

Wang Q; Carroll JS; Brown M, 2005. Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking.  Mol Cell 19(5):631-42

Come SE; Buzdar AU; Arteaga CL; Bissell MJ; Brown MA; Ellis MJ; Goss PE; Green JE; Ingle JN; Lee AV; Medina D; Nicholson RI; Santen RJ; Schiff R; Hart CS, 2004. Proceedings of the Third International Conference on Recent Advances and Future Directions in Endocrine Manipulation of Breast Cancer: conference summary statement.  Clin Cancer Res 10(1 Pt 2):327S-330S

Shao W; Brown M, 2004. Advances in estrogen receptor biology: prospects for improvements in targeted breast cancer therapy.  Breast Cancer Res 6(1):39-52

Shao W; Keeton EK; McDonnell DP; Brown M, 2004. Coactivator AIB1 links estrogen receptor transcriptional activity and stability.  Proc Natl Acad Sci U S A 101(32):11599-604

Torres-Arzayus MI; Font de Mora J; Yuan J; Vazquez F; Bronson R; Rue M; Sellers WR; Brown M, 2004. High tumor incidence and activation of the PI3K/AKT pathway in transgenic mice define AIB1 as an oncogene.  Cancer Cell 6(3):263-74

Keeton EK; Brown M, 2003. Coregulator expression and breast cancer: improving the predictive power of estrogen receptor alpha.  Clin Cancer Res 9(4):1229-30

Hestermann EV; Brown M, 2003. Agonist and chemopreventative ligands induce differential transcriptional cofactor recruitment by aryl hydrocarbon receptor.  Mol Cell Biol 23(21):7920-5

Haiman CA; Brown M; Hankinson SE; Spiegelman D; Colditz GA; Willett WC; Kantoff PW; Hunter DJ, 2002. The androgen receptor CAG repeat polymorphism and risk of breast cancer in the Nurses' Health Study.  Cancer Res 62(4):1045-9

DiRenzo J; Signoretti S; Nakamura N; Rivera-Gonzalez R; Sellers W; Loda M; Brown M, 2002. Growth factor requirements and basal phenotype of an immortalized mammary epithelial cell line.  Cancer Res 62(1):89-98

Haiman CA; Hankinson SE; Spiegelman D; Brown M; Hunter DJ, 2002. No association between a single nucleotide polymorphism in CYP19 and breast cancer risk.  Cancer Epidemiol Biomarkers Prev 11(2):215-6

Shao W; Halachmi S; Brown M, 2002. ERAP140, a conserved tissue-specific nuclear receptor coactivator.  Mol Cell Biol 22(10):3358-72

Carroll PR; Kantoff PW; Balk SP; Brown MA; D'amico AV; George DJ; Grossfeld GD; Johnson CS; Kelly WK; Klotz L; Lee WR; Lubeck DP; Mcleod DG; Oh WK; Pollack A; Sartor O; Smith MR; Hart C, 2002. Overview consensus statement. Newer approaches to androgen deprivation therapy in prostate cancer.  Urology 60(3 Suppl 1):1-6

Shang Y; Myers M; Brown M, 2002. Formation of the androgen receptor transcription complex.  Mol Cell 9(3):601-10

Shang Y; Brown M, 2002. Molecular determinants for the tissue specificity of SERMs.  Science 295(5564):2465-8

Publication list retrieved from NCBI using ImpactPubs

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Jiang P; Liu XS, 2015. Big data mining yields novel insights on cancer.  Nat Genet 47(2):103-4

Chu R; Liu SY; Vlantis AC; van Hasselt CA; Ng EK; Fan MD; Ng SK; Chan AB; Du J; Wei W; Liu X; Liu Z; Chen GG, 2015. Inhibition of Foxp3 in cancer cells induces apoptosis of thyroid cancer cells.  Mol Cell Endocrinol 399:228-34

Wang H; Zang C; Liu XS; Aster JC, 2015. The role of notch receptors in transcriptional regulation.  J Cell Physiol 230(5):982-8

Verzi MP; Shin H; San Roman AK; Liu XS; Shivdasani RA, 2015. Erratum for Verzi et al., Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding.  Mol Cell Biol 35(2):496

Fan D; Liu SY; van Hasselt CA; Vlantis AC; Ng EK; Zhang H; Dong Y; Ng SK; Chu R; Chan AB; Du J; Wei W; Liu X; Liu Z; Xing M; Chen GG, 2015. Estrogen receptor alpha induces pro-survival autophagy in papillary thyroid cancer via stimulating reactive oxygen species and extracellular-signal-regulated kinases.  J Clin Endocrinol Metab.

He HH; Meyer CA; Hu SS; Chen MW; Zang C; Liu Y; Rao PK; Fei T; Xu H; Long H; Liu XS; Brown M, 2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.  Nat Methods 11(1):73-8

Wang H; Zang C; Taing L; Arnett KL; Wong YJ; Pear WS; Blacklow SC; Liu XS; Aster JC, 2014. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers.  Proc Natl Acad Sci U S A 111(2):705-10

Watanabe H; Ma Q; Peng S; Adelmant G; Swain D; Song W; Fox C; Francis JM; Pedamallu CS; DeLuca DS; Brooks AN; Wang S; Que J; Rustgi AK; Wong KK; Ligon KL; Liu XS; Marto JA; Meyerson M; Bass AJ, 2014. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.  J Clin Invest 124(4):1636-45

Zhang Y; Vastenhouw NL; Feng J; Fu K; Wang C; Ge Y; Pauli A; van Hummelen P; Schier AF; Liu XS, 2014. Canonical nucleosome organization at promoters forms during genome activation.  Genome Res 24(2):260-6

Wang Q; Huang J; Sun H; Liu J; Wang J; Wang Q; Qin Q; Mei S; Zhao C; Yang X; Liu XS; Zhang Y, 2014. CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse.  Nucleic Acids Res 42(Database issue):D450-8

Marrus N; Veenstra-Vanderweele J; Hellings JA; Stigler KA; Szymanski L; King BH; Carlisle LL; Cook EH Jr; Pruett JR Jr, 2014. Training of child and adolescent psychiatry fellows in autism and intellectual disability.  Autism 18(4):471-5

Chu R; van Hasselt A; Vlantis AC; Ng EK; Liu SY; Fan MD; Ng SK; Chan AB; Liu Z; Li XY; Chen GG, 2014. The cross-talk between estrogen receptor and peroxisome proliferator-activated receptor gamma in thyroid cancer.  Cancer 120(1):142-53

Lu T; Aron L; Zullo J; Pan Y; Kim H; Chen Y; Yang TH; Kim HM; Drake D; Liu XS; Bennett DA; Colaiácovo MP; Yankner BA, 2014. REST and stress resistance in ageing and Alzheimer's disease.  Nature 507(7493):448-54

Lee RK; Liu SY; Tong CS; Lee PS; Ng EK; Ahuja AT, 2014. Morphologic change in computed tomography of aldosterone-producing adenoma after radiofrequency ablation.  Can Assoc Radiol J 65(1):86-90

Chen X; Iliopoulos D; Zhang Q; Tang Q; Greenblatt MB; Hatziapostolou M; Lim E; Tam WL; Ni M; Chen Y; Mai J; Shen H; Hu DZ; Adoro S; Hu B; Song M; Tan C; Landis MD; Ferrari M; Shin SJ; Brown M; Chang JC; Liu XS; Glimcher LH, 2014. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway.  Nature 508(7494):103-7

Cai C; He HH; Gao S; Chen S; Yu Z; Gao Y; Chen S; Chen MW; Zhang J; Ahmed M; Wang Y; Metzger E; Schüle R; Liu XS; Brown M; Balk SP, 2014. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity.  Cell Rep 9(5):1618-27

Meng FL; Du Z; Federation A; Hu J; Wang Q; Kieffer-Kwon KR; Meyers RM; Amor C; Wasserman CR; Neuberg D; Casellas R; Nussenzweig MC; Bradner JE; Liu XS; Alt FW, 2014. Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability.  Cell 159(7):1538-48

Liu SY; Wong SK; Ng EK, 2014. Novel oesophago-gastro-duodenal stenting for gastric leaks after laparoscopic sleeve gastrectomy.  Obes Res Clin Pract.

Luyten A; Zang C; Liu XS; Shivdasani RA, 2014. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells.  Genes Dev 28(16):1827-39

Meyer CA; Liu XS, 2014. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.  Nat Rev Genet 15(11):709-21

Stoeck A; Lejnine S; Truong A; Pan L; Wang H; Zang C; Yuan J; Ware C; MacLean J; Garrett-Engele PW; Kluk M; Laskey J; Haines BB; Moskaluk C; Zawel L; Fawell S; Gilliland G; Zhang T; Kremer BE; Knoechel B; Bernstein BE; Pear WS; Liu XS; Aster JC; Sathyanarayanan S, 2014. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma.  Cancer Discov 4(10):1154-67

Hu CY; Mohtat D; Yu Y; Ko YA; Shenoy N; Bhattacharya S; Izquierdo MC; Park AS; Giricz O; Vallumsetla N; Gundabolu K; Ware K; Bhagat TD; Suzuki M; Pullman J; Liu XS; Greally JM; Susztak K; Verma A, 2014. Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival.  Clin Cancer Res 20(16):4349-60

Yamamoto S; Wu Z; Russnes HG; Takagi S; Peluffo G; Vaske C; Zhao X; Moen Vollan HK; Maruyama R; Ekram MB; Sun H; Kim JH; Carver K; Zucca M; Feng J; Almendro V; Bessarabova M; Rueda OM; Nikolsky Y; Caldas C; Liu XS; Polyak K, 2014. JARID1B is a luminal lineage-driving oncogene in breast cancer.  Cancer Cell 25(6):762-77

Wang J; Lin X; Wang S; Wang C; Wang Q; Duan X; Lu P; Wang Q; Wang C; Liu XS; Huang J, 2014. PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression.  Sci Rep 4:5008

Cai C; Wang H; He HH; Chen S; He L; Ma F; Mucci L; Wang Q; Fiore C; Sowalsky AG; Loda M; Liu XS; Brown M; Balk SP; Yuan X, 2013. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.  J Clin Invest 123(3):1109-22

Bergmann KR; Liu SX; Tian R; Kushnir A; Turner JR; Li HL; Chou PM; Weber CR; De Plaen IG, 2013. Bifidobacteria stabilize claudins at tight junctions and prevent intestinal barrier dysfunction in mouse necrotizing enterocolitis.  Am J Pathol 182(5):1595-606

Mahdavi A; Segall-Shapiro TH; Kou S; Jindal GA; Hoff KG; Liu S; Chitsaz M; Ismagilov RF; Silberg JJ; Tirrell DA, 2013. A genetically encoded and gate for cell-targeted metabolic labeling of proteins.  J Am Chem Soc 135(8):2979-82

Trynka G; Sandor C; Han B; Xu H; Stranger BE; Liu XS; Raychaudhuri S, 2013. Chromatin marks identify critical cell types for fine mapping complex trait variants.  Nat Genet 45(2):124-30

Verzi MP; Shin H; San Roman AK; Liu XS; Shivdasani RA, 2013. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.  Mol Cell Biol 33(2):281-92

Zhang X; Peterson KA; Liu XS; McMahon AP; Ohba S, 2013. Gene regulatory networks mediating canonical Wnt signal-directed control of pluripotency and differentiation in embryo stem cells.  Stem Cells 31(12):2667-79

Du Z; Li H; Wei Q; Zhao X; Wang C; Zhu Q; Yi X; Xu W; Liu XS; Jin W; Su Z, 2013. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.  Mol Plant 6(5):1463-72

Chiu PW; Wu JC; Teoh AY; Chan Y; Wong SK; Liu SY; Yung MY; Lam CC; Sung JJ; Chan FK; Lau JY; Ng EK, 2013. Peroral endoscopic myotomy for treatment of achalasia: from bench to bedside (with video).  Gastrointest Endosc 77(1):29-38

Catic A; Suh CY; Hill CT; Daheron L; Henkel T; Orford KW; Dombkowski DM; Liu T; Liu XS; Scadden DT, 2013. Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation.  Cell 155(6):1380-95

Wang S; Sun H; Ma J; Zang C; Wang C; Wang J; Tang Q; Meyer CA; Zhang Y; Liu XS, 2013. Target analysis by integration of transcriptome and ChIP-seq data with BETA.  Nat Protoc 8(12):2502-15

Sun H; Qin B; Liu T; Wang Q; Liu J; Wang J; Lin X; Yang Y; Taing L; Rao PK; Brown M; Zhang Y; Long HW; Liu XS, 2013. CistromeFinder for ChIP-seq and DNase-seq data reuse.  Bioinformatics 29(10):1352-4

Masiello CA; Chen Y; Gao X; Liu S; Cheng HY; Bennett MR; Rudgers JA; Wagner DS; Zygourakis K; Silberg JJ, 2013. Biochar and microbial signaling: production conditions determine effects on microbial communication.  Environ Sci Technol 47(20):11496-503

Wang H; Meyer CA; Fei T; Wang G; Zhang F; Liu XS, 2013. A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer.  BMC Genomics 14:680

Ni M; Chen Y; Fei T; Li D; Lim E; Liu XS; Brown M, 2013. Amplitude modulation of androgen signaling by c-MYC.  Genes Dev 27(7):734-48

Du Z; Fei T; Verhaak RG; Su Z; Zhang Y; Brown M; Chen Y; Liu XS, 2013. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.  Nat Struct Mol Biol 20(7):908-13

Choudhury S; Almendro V; Merino VF; Wu Z; Maruyama R; Su Y; Martins FC; Fackler MJ; Bessarabova M; Kowalczyk A; Conway T; Beresford-Smith B; Macintyre G; Cheng YK; Lopez-Bujanda Z; Kaspi A; Hu R; Robens J; Nikolskaya T; Haakensen VD; Schnitt SJ; Argani P; Ethington G; Panos L; Grant M; Clark J; Herlihy W; Lin SJ; Chew G; Thompson EW; Greene-Colozzi A; Richardson AL; Rosson GD; Pike M; Garber JE; Nikolsky Y; Blum JL; Au A; Hwang ES; Tamimi RM; Michor F; Haviv I; Liu XS; Sukumar S; Polyak K, 2013. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics.  Cell Stem Cell 13(1):117-30

Wang C; Tian R; Zhao Q; Xu H; Meyer CA; Li C; Zhang Y; Liu XS, 2012. Computational inference of mRNA stability from histone modification and transcriptome profiles.  Nucleic Acids Res 40(14):6414-23

Qin B; Zhou M; Ge Y; Taing L; Liu T; Wang Q; Wang S; Chen J; Shen L; Duan X; Hu S; Li W; Long H; Zhang Y; Liu XS, 2012. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.  Bioinformatics 28(10):1411-2

Liu SH; Heiland F, 2012. Should we get married? The effect of parents' marriage on out-of-wedlock children.  Econ Inq 50(1):17-38

He HH; Meyer CA; Chen MW; Jordan VC; Brown M; Liu XS, 2012. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.  Genome Res 22(6):1015-25

Maruyama R; Shipitsin M; Choudhury S; Wu Z; Protopopov A; Yao J; Lo PK; Bessarabova M; Ishkin A; Nikolsky Y; Liu XS; Sukumar S; Polyak K, 2012. Altered antisense-to-sense transcript ratios in breast cancer.  Proc Natl Acad Sci U S A 109(8):2820-4

Chen Y; Negre N; Li Q; Mieczkowska JO; Slattery M; Liu T; Zhang Y; Kim TK; He HH; Zieba J; Ruan Y; Bickel PJ; Myers RM; Wold BJ; White KP; Lieb JD; Liu XS, 2012. Systematic evaluation of factors influencing ChIP-seq fidelity.  Nat Methods 9(6):609-14

Li JC; Leung KL; Ng SS; Liu SY; Lee JF; Hon SS, 2012. Laparoscopic-assisted versus open resection of right-sided colonic cancer--a prospective randomized controlled trial.  Int J Colorectal Dis 27(1):95-102

Mehta MM; Liu S; Silberg JJ, 2012. A transposase strategy for creating libraries of circularly permuted proteins.  Nucleic Acids Res 40(9):e71

Vu MT; Zhai P; Lee J; Guerra C; Liu S; Gustin MC; Silberg JJ, 2012. The DNLZ/HEP zinc-binding subdomain is critical for regulation of the mitochondrial chaperone HSPA9.  Protein Sci 21(2):258-67

Benson MJ; Aijö T; Chang X; Gagnon J; Pape UJ; Anantharaman V; Aravind L; Pursiheimo JP; Oberdoerffer S; Liu XS; Lahesmaa R; Lähdesmäki H; Rao A, 2012. Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells.  Proc Natl Acad Sci U S A 109(40):16252-7

Xu Y; Xu C; Kato A; Tempel W; Abreu JG; Bian C; Hu Y; Hu D; Zhao B; Cerovina T; Diao J; Wu F; He HH; Cui Q; Clark E; Ma C; Barbara A; Veenstra GJ; Xu G; Kaiser UB; Liu XS; Sugrue SP; He X; Min J; Kato Y; Shi YG, 2012. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.  Cell 151(6):1200-13

Chiu PW; Wong TC; Teoh AY; To KF; Liu SY; Wong SK; Chan FK; Ng EK, 2012. Recognition of changes in microvascular and microstructural patterns upon magnifying endoscopy predicted the presence of extranodal gastric MALToma.  J Interv Gastroenterol 2(1):3-7

Landt SG; Marinov GK; Kundaje A; Kheradpour P; Pauli F; Batzoglou S; Bernstein BE; Bickel P; Brown JB; Cayting P; Chen Y; DeSalvo G; Epstein C; Fisher-Aylor KI; Euskirchen G; Gerstein M; Gertz J; Hartemink AJ; Hoffman MM; Iyer VR; Jung YL; Karmakar S; Kellis M; Kharchenko PV; Li Q; Liu T; Liu XS; Ma L; Milosavljevic A; Myers RM; Park PJ; Pazin MJ; Perry MD; Raha D; Reddy TE; Rozowsky J; Shoresh N; Sidow A; Slattery M; Stamatoyannopoulos JA; Tolstorukov MY; White KP; Xi S; Farnham PJ; Lieb JD; Wold BJ; Snyder M, 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.  Genome Res 22(9):1813-31

Xu K; Wu ZJ; Groner AC; He HH; Cai C; Lis RT; Wu X; Stack EC; Loda M; Liu T; Xu H; Cato L; Thornton JE; Gregory RI; Morrissey C; Vessella RL; Montironi R; Magi-Galluzzi C; Kantoff PW; Balk SP; Liu XS; Brown M, 2012. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.  Science 338(6113):1465-9

Meyer CA; Tang Q; Liu XS, 2012. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.  Mol Endocrinol 26(10):1651-9

Chiu PW; Teoh AY; To KF; Wong SK; Liu SY; Lam CC; Yung MY; Chan FK; Lau JY; Ng EK, 2012. Endoscopic submucosal dissection (ESD) compared with gastrectomy for treatment of early gastric neoplasia: a retrospective cohort study.  Surg Endosc 26(12):3584-91

Feng J; Meyer CA; Wang Q; Liu JS; Shirley Liu X; Zhang Y, 2012. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.  Bioinformatics 28(21):2782-8

Fu K; Tang Q; Feng J; Liu XS; Zhang Y, 2012. DiNuP: a systematic approach to identify regions of differential nucleosome positioning.  Bioinformatics 28(15):1965-71

Feng D; Liu T; Sun Z; Bugge A; Mullican SE; Alenghat T; Liu XS; Lazar MA, 2011. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism.  Science 331(6022):1315-9

Verzi MP; Shin H; Ho LL; Liu XS; Shivdasani RA, 2011. Essential and redundant functions of caudal family proteins in activating adult intestinal genes.  Mol Cell Biol 31(10):2026-39

Wang X; Laurie JD; Liu T; Wentz J; Liu XS, 2011. Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites.  Genomics 97(4):235-43

Liu T; Rechtsteiner A; Egelhofer TA; Vielle A; Latorre I; Cheung MS; Ercan S; Ikegami K; Jensen M; Kolasinska-Zwierz P; Rosenbaum H; Shin H; Taing S; Takasaki T; Iniguez AL; Desai A; Dernburg AF; Kimura H; Lieb JD; Ahringer J; Strome S; Liu XS, 2011. Broad chromosomal domains of histone modification patterns in C. elegans.  Genome Res 21(2):227-36

Cao Q; Zhou M; Wang X; Meyer CA; Zhang Y; Chen Z; Li C; Liu XS, 2011. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.  Nucleic Acids Res 39(Database issue):D968-74

Meyer CA; He HH; Brown M; Liu XS, 2011. BINOCh: binding inference from nucleosome occupancy changes.  Bioinformatics 27(13):1867-8

Teoh AY; Yan Chiu PW; Wong TC; Liu SY; Hung Wong SK; Ng EK, 2011. Functional performance and quality of life in patients with squamous esophageal carcinoma receiving surgery or chemoradiation: results from a randomized trial.  Ann Surg 253(1):1-5

Maruyama R; Choudhury S; Kowalczyk A; Bessarabova M; Beresford-Smith B; Conway T; Kaspi A; Wu Z; Nikolskaya T; Merino VF; Lo PK; Liu XS; Nikolsky Y; Sukumar S; Haviv I; Polyak K, 2011. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.  PLoS Genet 7(4):e1001369

Pastor WA; Pape UJ; Huang Y; Henderson HR; Lister R; Ko M; McLoughlin EM; Brudno Y; Mahapatra S; Kapranov P; Tahiliani M; Daley GQ; Liu XS; Ecker JR; Milos PM; Agarwal S; Rao A, 2011. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.  Nature 473(7347):394-7

Adams DJ; Berger B; Harismendy O; Huttenhower C; Liu XS; Myers CL; Oshlack A; Rinn JL; Walhout AJ, 2011. Genomics in 2011: challenges and opportunities.  Genome Biol 12(12):137

Wang X; Liu XS, 2011. Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.  Front Genet 2:25

Xu J; Liu S; Chen M; Ma J; Matthews KS, 2011. Altering residues N125 and D149 impacts sugar effector binding and allosteric parameters in Escherichia coli lactose repressor.  Biochemistry 50(42):9002-13

Cai C; He HH; Chen S; Coleman I; Wang H; Fang Z; Chen S; Nelson PS; Liu XS; Brown M; Balk SP, 2011. Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1.  Cancer Cell 20(4):457-71

Marotta LL; Almendro V; Marusyk A; Shipitsin M; Schemme J; Walker SR; Bloushtain-Qimron N; Kim JJ; Choudhury SA; Maruyama R; Wu Z; Gönen M; Mulvey LA; Bessarabova MO; Huh SJ; Silver SJ; Kim SY; Park SY; Lee HE; Anderson KS; Richardson AL; Nikolskaya T; Nikolsky Y; Liu XS; Root DE; Hahn WC; Frank DA; Polyak K, 2011. The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors.  J Clin Invest 121(7):2723-35

Liu T; Ortiz JA; Taing L; Meyer CA; Lee B; Zhang Y; Shin H; Wong SS; Ma J; Lei Y; Pape UJ; Poidinger M; Chen Y; Yeung K; Brown M; Turpaz Y; Liu XS, 2011. Cistrome: an integrative platform for transcriptional regulation studies.  Genome Biol 12(8):R83

Ni M; Chen Y; Lim E; Wimberly H; Bailey ST; Imai Y; Rimm DL; Liu XS; Brown M, 2011. Targeting androgen receptor in estrogen receptor-negative breast cancer.  Cancer Cell 20(1):119-31

Hirsch HA; Iliopoulos D; Joshi A; Zhang Y; Jaeger SA; Bulyk M; Tsichlis PN; Shirley Liu X; Struhl K, 2010. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.  Cancer Cell 17(4):348-61

Wong YS; Liu SY; Ng SS; Wong VW; Mak OS; Li JC; Lee JF, 2010. Giant Meckel's diverticulitis: a rare condition complicating pregnancy.  Am J Surg 200(1):184-5

Ahmadiyeh N; Pomerantz MM; Grisanzio C; Herman P; Jia L; Almendro V; He HH; Brown M; Liu XS; Davis M; Caswell JL; Beckwith CA; Hills A; Macconaill L; Coetzee GA; Regan MM; Freedman ML, 2010. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC.  Proc Natl Acad Sci U S A 107(21):9742-6

Li JC; Liu SY; Lo AW; Hon SS; Ng SS; Lee JF; Leung KL, 2010. The learning curve for endorectal ultrasonography in rectal cancer staging.  Surg Endosc 24(12):3054-9

Kamata M; Liu S; Liang M; Nagaoka Y; Chen IS, 2010. Generation of human induced pluripotent stem cells bearing an anti-HIV transgene by a lentiviral vector carrying an internal murine leukemia virus promoter.  Hum Gene Ther 21(11):1555-67

Ji H; Liu XS, 2010. Analyzing 'omics data using hierarchical models.  Nat Biotechnol 28(4):337-40

He HH; Meyer CA; Shin H; Bailey ST; Wei G; Wang Q; Zhang Y; Xu K; Ni M; Lupien M; Mieczkowski P; Lieb JD; Zhao K; Brown M; Liu XS, 2010. Nucleosome dynamics define transcriptional enhancers.  Nat Genet 42(4):343-7

Vastenhouw NL; Zhang Y; Woods IG; Imam F; Regev A; Liu XS; Rinn J; Schier AF, 2010. Chromatin signature of embryonic pluripotency is established during genome activation.  Nature 464(7290):922-6

Bienvenu F; Jirawatnotai S; Elias JE; Meyer CA; Mizeracka K; Marson A; Frampton GM; Cole MF; Odom DT; Odajima J; Geng Y; Zagozdzon A; Jecrois M; Young RA; Liu XS; Cepko CL; Gygi SP; Sicinski P, 2010. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.  Nature 463(7279):374-8

Wolfer A; Wittner BS; Irimia D; Flavin RJ; Lupien M; Gunawardane RN; Meyer CA; Lightcap ES; Tamayo P; Mesirov JP; Liu XS; Shioda T; Toner M; Loda M; Brown M; Brugge JS; Ramaswamy S, 2010. MYC regulation of a "poor-prognosis" metastatic cancer cell state.  Proc Natl Acad Sci U S A 107(8):3698-703

Ko M; Huang Y; Jankowska AM; Pape UJ; Tahiliani M; Bandukwala HS; An J; Lamperti ED; Koh KP; Ganetzky R; Liu XS; Aravind L; Agarwal S; Maciejewski JP; Rao A, 2010. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2.  Nature 468(7325):839-43

Verzi MP; Shin H; He HH; Sulahian R; Meyer CA; Montgomery RK; Fleet JC; Brown M; Liu XS; Shivdasani RA, 2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26

Gerstein MB; Lu ZJ; Van Nostrand EL; Cheng C; Arshinoff BI; Liu T; Yip KY; Robilotto R; Rechtsteiner A; Ikegami K; Alves P; Chateigner A; Perry M; Morris M; Auerbach RK; Feng X; Leng J; Vielle A; Niu W; Rhrissorrakrai K; Agarwal A; Alexander RP; Barber G; Brdlik CM; Brennan J; Brouillet JJ; Carr A; Cheung MS; Clawson H; Contrino S; Dannenberg LO; Dernburg AF; Desai A; Dick L; Dosé AC; Du J; Egelhofer T; Ercan S; Euskirchen G; Ewing B; Feingold EA; Gassmann R; Good PJ; Green P; Gullier F; Gutwein M; Guyer MS; Habegger L; Han T; Henikoff JG; Henz SR; Hinrichs A; Holster H; Hyman T; Iniguez AL; Janette J; Jensen M; Kato M; Kent WJ; Kephart E; Khivansara V; Khurana E; Kim JK; Kolasinska-Zwierz P; Lai EC; Latorre I; Leahey A; Lewis S; Lloyd P; Lochovsky L; Lowdon RF; Lubling Y; Lyne R; MacCoss M; Mackowiak SD; Mangone M; McKay S; Mecenas D; Merrihew G; Miller DM 3rd; Muroyama A; Murray JI; Ooi SL; Pham H; Phippen T; Preston EA; Rajewsky N; Rätsch G; Rosenbaum H; Rozowsky J; Rutherford K; Ruzanov P; Sarov M; Sasidharan R; Sboner A; Scheid P; Segal E; Shin H; Shou C; Slack FJ; Slightam C; Smith R; Spencer WC; Stinson EO; Taing S; Takasaki T; Vafeados D; Voronina K; Wang G; Washington NL; Whittle CM; Wu B; Yan KK; Zeller G; Zha Z; Zhong M; Zhou X; Ahringer J; Strome S; Gunsalus KC; Micklem G; Liu XS; Reinke V; Kim SK; Hillier LW; Henikoff S; Piano F; Snyder M; Stein L; Lieb JD; Waterston RH, 2010. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.  Science 330(6012):1775-87

Kamata M; Liang M; Liu S; Nagaoka Y; Chen IS, 2010. Live cell monitoring of hiPSC generation and differentiation using differential expression of endogenous microRNAs.  PLoS One 5(7):e11834

Tian R; Liu SX; Williams C; Soltau TD; Dimmitt R; Zheng X; De Plaen IG, 2010. Characterization of a necrotizing enterocolitis model in newborn mice.  Int J Clin Exp Med 3(4):293-302

Liu SY; Ng EK; Lee PS; Wong SK; Chiu PW; Mui WL; So WY; Chow FC, 2010. Radiofrequency ablation for benign aldosterone-producing adenoma: a scarless technique to an old disease.  Ann Surg 252(6):1058-64

Wu ZJ; Meyer CA; Choudhury S; Shipitsin M; Maruyama R; Bessarabova M; Nikolskaya T; Sukumar S; Schwartzman A; Liu JS; Polyak K; Liu XS, 2010. Gene expression profiling of human breast tissue samples using SAGE-Seq.  Genome Res 20(12):1730-9

Lupien M; Meyer CA; Bailey ST; Eeckhoute J; Cook J; Westerling T; Zhang X; Carroll JS; Rhodes DR; Liu XS; Brown M, 2010. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.  Genes Dev 24(19):2219-27

Verzi MP; Hatzis P; Sulahian R; Philips J; Schuijers J; Shin H; Freed E; Lynch JP; Dang DT; Brown M; Clevers H; Liu XS; Shivdasani RA, 2010. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions.  Proc Natl Acad Sci U S A 107(34):15157-62

Fan X; Moqtaderi Z; Jin Y; Zhang Y; Liu XS; Struhl K, 2010. Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.  Proc Natl Acad Sci U S A 107(42):17945-50

Lupien M; Eeckhoute J; Meyer CA; Krum SA; Rhodes DR; Liu XS; Brown M, 2009. Coactivator function defines the active estrogen receptor alpha cistrome.  Mol Cell Biol 29(12):3413-23

Wang X; Elling AA; Li X; Li N; Peng Z; He G; Sun H; Qi Y; Liu XS; Deng XW, 2009. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize.  Plant Cell 21(4):1053-69

Liu SY; Lee KF; Lai PB, 2009. Needle track seeding: a real hazard after percutaneous radiofrequency ablation for colorectal liver metastasis.  World J Gastroenterol 15(13):1653-5

Xia X; Lemieux ME; Li W; Carroll JS; Brown M; Liu XS; Kung AL, 2009. Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis.  Proc Natl Acad Sci U S A 106(11):4260-5

Eeckhoute J; Lupien M; Meyer CA; Verzi MP; Shivdasani RA; Liu XS; Brown M, 2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.  Genome Res 19(3):372-80

Liu SX; Tian R; Baskind H; Hsueh W; De Plaen IG, 2009. Platelet-activating factor induces the processing of nuclear factor-kappaB p105 into p50, which mediates acute bowel injury in mice.  Am J Physiol Gastrointest Liver Physiol 297(1):G76-81

Kolasinska-Zwierz P; Down T; Latorre I; Liu T; Liu XS; Ahringer J, 2009. Differential chromatin marking of introns and expressed exons by H3K36me3.  Nat Genet 41(3):376-81

Liu XS; Meyer CA, 2009. ChIP-Chip: algorithms for calling binding sites.  Methods Mol Biol 556:165-75

Huang J; Chen T; Liu X; Jiang J; Li J; Li D; Liu XS; Li W; Kang J; Pei G, 2009. More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells.  Cell Res 19(10):1127-38

Boros J; Donaldson IJ; O'Donnell A; Odrowaz ZA; Zeef L; Lupien M; Meyer CA; Liu XS; Brown M; Sharrocks AD, 2009. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery.  Genome Res 19(11):1963-73

Shin H; Liu T; Manrai AK; Liu XS, 2009. CEAS: cis-regulatory element annotation system.  Bioinformatics 25(19):2605-6

Wang Q; Li W; Zhang Y; Yuan X; Xu K; Yu J; Chen Z; Beroukhim R; Wang H; Lupien M; Wu T; Regan MM; Meyer CA; Carroll JS; Manrai AK; Jänne OA; Balk SP; Mehra R; Han B; Chinnaiyan AM; Rubin MA; True L; Fiorentino M; Fiore C; Loda M; Kantoff PW; Liu XS; Brown M, 2009. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer.  Cell 138(2):245-56

Zhang Y; Moqtaderi Z; Rattner BP; Euskirchen G; Snyder M; Kadonaga JT; Liu XS; Struhl K, 2009. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.  Nat Struct Mol Biol 16(8):847-52

Song JS; Liu X; Liu XS; He X, 2008. A high-resolution map of nucleosome positioning on a fission yeast centromere.  Genome Res 18(7):1064-72

Li W; Carroll JS; Brown M; Liu xS, 2008. xMAN: extreme MApping of OligoNucleotides.  BMC Genomics 9 Suppl 1:S20

Lupien M; Eeckhoute J; Meyer CA; Wang Q; Zhang Y; Li W; Carroll JS; Liu XS; Brown M, 2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.  Cell 132(6):958-70

Johnson DS; Li W; Gordon DB; Bhattacharjee A; Curry B; Ghosh J; Brizuela L; Carroll JS; Brown M; Flicek P; Koch CM; Dunham I; Bieda M; Xu X; Farnham PJ; Kapranov P; Nix DA; Gingeras TR; Zhang X; Holster H; Jiang N; Green RD; Song JS; McCuine SA; Anton E; Nguyen L; Trinklein ND; Ye Z; Ching K; Hawkins D; Ren B; Scacheri PC; Rozowsky J; Karpikov A; Euskirchen G; Weissman S; Gerstein M; Snyder M; Yang A; Moqtaderi Z; Hirsch H; Shulha HP; Fu Y; Weng Z; Struhl K; Myers RM; Lieb JD; Liu XS, 2008. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.  Genome Res 18(3):393-403

Gottardo R; Li W; Johnson WE; Liu XS, 2008. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments.  Biometrics 64(2):468-78

Nguyen PQ; Liu S; Thompson JC; Silberg JJ, 2008. Thermostability promotes the cooperative function of split adenylate kinases.  Protein Eng Des Sel 21(5):303-10

Zhai P; Stanworth C; Liu S; Silberg JJ, 2008. The human escort protein Hep binds to the ATPase domain of mitochondrial hsp70 and regulates ATP hydrolysis.  J Biol Chem 283(38):26098-106

Zhang Y; Shin H; Song JS; Lei Y; Liu XS, 2008. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.  BMC Genomics 9:537

Agoulnik IU; Bingman WE 3rd; Nakka M; Li W; Wang Q; Liu XS; Brown M; Weigel NL, 2008. Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase.  Mol Endocrinol 22(11):2420-32

Lefterova MI; Zhang Y; Steger DJ; Schupp M; Schug J; Cristancho A; Feng D; Zhuo D; Stoeckert CJ Jr; Liu XS; Lazar MA, 2008. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale.  Genes Dev 22(21):2941-52

Ozsolak F; Poling LL; Wang Z; Liu H; Liu XS; Roeder RG; Zhang X; Song JS; Fisher DE, 2008. Chromatin structure analyses identify miRNA promoters.  Genes Dev 22(22):3172-83

Yagi S; Hirabayashi K; Sato S; Li W; Takahashi Y; Hirakawa T; Wu G; Hattori N; Hattori N; Ohgane J; Tanaka S; Liu XS; Shiota K, 2008. DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression.  Genome Res 18(12):1969-78

Zhang Y; Liu T; Meyer CA; Eeckhoute J; Johnson DS; Bernstein BE; Nusbaum C; Myers RM; Brown M; Li W; Liu XS, 2008. Model-based analysis of ChIP-Seq (MACS).  Genome Biol 9(9):R137

Song JS; Maghsoudi K; Li W; Fox E; Quackenbush J; Shirley Liu X, 2007. Microarray blob-defect removal improves array analysis.  Bioinformatics 23(8):966-71

Liu SY; Lee JF; Ng SS; Li JC; Yiu RY, 2007. Rectal stump lavage: simple procedure resulting in life-threatening complication.  Asian J Surg 30(1):72-4

Ozsolak F; Song JS; Liu XS; Fisher DE, 2007. High-throughput mapping of the chromatin structure of human promoters.  Nat Biotechnol 25(2):244-8

De Plaen IG; Liu SX; Tian R; Neequaye I; May MJ; Han XB; Hsueh W; Jilling T; Lu J; Caplan MS, 2007. Inhibition of nuclear factor-kappaB ameliorates bowel injury and prolongs survival in a neonatal rat model of necrotizing enterocolitis.  Pediatr Res 61(6):716-21

Liu SY; Ng CF; Lai FM; Cheng CW, 2007. Undifferentiated sex cord-stromal tumor in a young adult.  Int Urol Nephrol 39(2):561-4

Leung WW; Lee JF; Liu SY; Mou JW; Ng SS; Yiu RY; Li JC, 2007. Critical appraisal on the role and outcome of emergency colectomy for uncomplicated right-sided colonic diverticulitis.  World J Surg 31(2):383-7

O'Neil J; Tchinda J; Gutierrez A; Moreau L; Maser RS; Wong KK; Li W; McKenna K; Liu XS; Feng B; Neuberg D; Silverman L; DeAngelo DJ; Kutok JL; Rothstein R; DePinho RA; Chin L; Lee C; Look AT, 2007. Alu elements mediate MYB gene tandem duplication in human T-ALL.  J Exp Med 204(13):3059-66

Kim RJ; Kerns JM; Liu S; Nagel T; Zaszczurynski P; Lin DL; Damaser MS, 2007. Striated muscle and nerve fascicle distribution in the female rat urethral sphincter.  Anat Rec (Hoboken) 290(2):145-54

Liu XS, 2007. Getting started in tiling microarray analysis.  PLoS Comput Biol 3(10):1842-4

Song JS; Johnson WE; Zhu X; Zhang X; Li W; Manrai AK; Liu JS; Chen R; Liu XS, 2007. Model-based analysis of two-color arrays (MA2C).  Genome Biol 8(8):R178

He H; Wang J; Liu T; Liu XS; Li T; Wang Y; Qian Z; Zheng H; Zhu X; Wu T; Shi B; Deng W; Zhou W; Skogerbø G; Chen R, 2007. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.  Genome Res 17(10):1471-7

Litovchick L; Sadasivam S; Florens L; Zhu X; Swanson SK; Velmurugan S; Chen R; Washburn MP; Liu XS; DeCaprio JA, 2007. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence.  Mol Cell 26(4):539-51

Wang Q; Li W; Liu XS; Carroll JS; Jänne OA; Keeton EK; Chinnaiyan AM; Pienta KJ; Brown M, 2007. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.  Mol Cell 27(3):380-92

Palomero T; Odom DT; O'Neil J; Ferrando AA; Margolin A; Neuberg DS; Winter SS; Larson RS; Li W; Liu XS; Young RA; Look AT, 2006. Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia.  Blood 108(3):986-92

Swinburne IA; Meyer CA; Liu XS; Silver PA; Brodsky AS, 2006. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.  Genome Res 16(7):912-21

Nelson EA; Walker SR; Li W; Liu XS; Frank DA, 2006. Identification of human STAT5-dependent gene regulatory elements based on interspecies homology.  J Biol Chem 281(36):26216-24

Ng SS; Ng NC; Liu SY; Lee JF, 2006. Radiology for the surgeon. Soft-tissue case 58: incarcerated Grynfeltt hernia.  Can J Surg 49(2):129-30

Carroll JS; Meyer CA; Song J; Li W; Geistlinger TR; Eeckhoute J; Brodsky AS; Keeton EK; Fertuck KC; Hall GF; Wang Q; Bekiranov S; Sementchenko V; Fox EA; Silver PA; Gingeras TR; Liu XS; Brown M, 2006. Genome-wide analysis of estrogen receptor binding sites.  Nat Genet 38(11):1289-97

Ji X; Li W; Song J; Wei L; Liu XS, 2006. CEAS: cis-regulatory element annotation system.  Nucleic Acids Res 34(Web Server issue):W551-4

Liu SY; Ng SS; Lee JF, 2006. Multi-limb necrotizing fasciitis in a patient with rectal cancer.  World J Gastroenterol 12(32):5256-8

Johnson WE; Li W; Meyer CA; Gottardo R; Carroll JS; Brown M; Liu XS, 2006. Model-based analysis of tiling-arrays for ChIP-chip.  Proc Natl Acad Sci U S A 103(33):12457-62

Zhang Y; Liu XS; Liu QR; Wei L, 2006. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.  Nucleic Acids Res 34(12):3465-75

Hong P; Liu XS; Zhou Q; Lu X; Liu JS; Wong WH, 2005. A boosting approach for motif modeling using ChIP-chip data.  Bioinformatics 21(11):2636-43

Lu L; Hope BT; Dempsey J; Liu SY; Bossert JM; Shaham Y, 2005. Central amygdala ERK signaling pathway is critical to incubation of cocaine craving.  Nat Neurosci 8(2):212-9

Li W; Meyer CA; Liu XS, 2005. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.  Bioinformatics 21 Suppl 1:i274-82

Carroll JS; Liu XS; Brodsky AS; Li W; Meyer CA; Szary AJ; Eeckhoute J; Shao W; Hestermann EV; Geistlinger TR; Fox EA; Silver PA; Brown M, 2005. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.  Cell 122(1):33-43

Shepard JD; Bossert JM; Liu SY; Shaham Y, 2004. The anxiogenic drug yohimbine reinstates methamphetamine seeking in a rat model of drug relapse.  Biol Psychiatry 55(11):1082-9

Lu L; Dempsey J; Liu SY; Bossert JM; Shaham Y, 2004. A single infusion of brain-derived neurotrophic factor into the ventral tegmental area induces long-lasting potentiation of cocaine seeking after withdrawal.  J Neurosci 24(7):1604-11

Liu Y; Liu XS; Wei L; Altman RB; Batzoglou S, 2004. Eukaryotic regulatory element conservation analysis and identification using comparative genomics.  Genome Res 14(3):451-8

Liu Y; Wei L; Batzoglou S; Brutlag DL; Liu JS; Liu XS, 2004. A suite of web-based programs to search for transcriptional regulatory motifs.  Nucleic Acids Res 32(Web Server issue):W204-7

Bossert JM; Liu SY; Lu L; Shaham Y, 2004. A role of ventral tegmental area glutamate in contextual cue-induced relapse to heroin seeking.  J Neurosci 24(47):10726-30

Young MR; Liu SW; Meisinger J, 2003. Protein phosphatase-2A restricts migration of Lewis lung carcinoma cells by modulating the phosphorylation of focal adhesion proteins.  Int J Cancer 103(1):38-44

Yamada K; Lim J; Dale JM; Chen H; Shinn P; Palm CJ; Southwick AM; Wu HC; Kim C; Nguyen M; Pham P; Cheuk R; Karlin-Newmann G; Liu SX; Lam B; Sakano H; Wu T; Yu G; Miranda M; Quach HL; Tripp M; Chang CH; Lee JM; Toriumi M; Chan MM; Tang CC; Onodera CS; Deng JM; Akiyama K; Ansari Y; Arakawa T; Banh J; Banno F; Bowser L; Brooks S; Carninci P; Chao Q; Choy N; Enju A; Goldsmith AD; Gurjal M; Hansen NF; Hayashizaki Y; Johnson-Hopson C; Hsuan VW; Iida K; Karnes M; Khan S; Koesema E; Ishida J; Jiang PX; Jones T; Kawai J; Kamiya A; Meyers C; Nakajima M; Narusaka M; Seki M; Sakurai T; Satou M; Tamse R; Vaysberg M; Wallender EK; Wong C; Yamamura Y; Yuan S; Shinozaki K; Davis RW; Theologis A; Ecker JR, 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome.  Science 302(5646):842-6

Conlon EM; Liu XS; Lieb JD; Liu JS, 2003. Integrating regulatory motif discovery and genome-wide expression analysis.  Proc Natl Acad Sci U S A 100(6):3339-44

Liu XS; Brutlag DL; Liu JS, 2002. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.  Nat Biotechnol 20(8):835-9

Publication list retrieved from NCBI using ImpactPubs

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Schumacher MA; Aihara E; Feng R; Engevik A; Shroyer NF; Ottemann KM; Worrell RT; Montrose MH; Shivdasani RA; Zavros Y, 2015. The use of murine-derived fundic organoids in studies of gastric physiology.  J Physiol.

San Roman AK; Aronson BE; Krasinski SD; Shivdasani RA; Verzi MP, 2015. Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction with Transcription Factor CDX2.  J Biol Chem 290(3):1850-60

Verzi MP; Shin H; San Roman AK; Liu XS; Shivdasani RA, 2015. Erratum for Verzi et al., Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding.  Mol Cell Biol 35(2):496

Kim TH; Li F; Ferreiro-Neira I; Ho LL; Luyten A; Nalapareddy K; Long H; Verzi M; Shivdasani RA, 2014. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity.  Nature 506(7489):511-5

Sulahian R; Casey F; Shen J; Qian ZR; Shin H; Ogino S; Weir BA; Vazquez F; Liu XS; Hahn WC; Bass AJ; Chan V; Shivdasani RA, 2014. An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer.  Oncogene 33(49):5637-48

Shivdasani RA, 2014. Radiation redux: reserve intestinal stem cells miss the call to duty.  Cell Stem Cell 14(2):135-6

Feng R; Aihara E; Kenny S; Yang L; Li J; Varro A; Montrose MH; Shroyer NF; Wang TC; Shivdasani RA; Zavros Y, 2014. Indian Hedgehog mediates gastrin-induced proliferation in stomach of adult mice.  Gastroenterology 147(3):655-666.e9

Luyten A; Zang C; Liu XS; Shivdasani RA, 2014. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells.  Genes Dev 28(16):1827-39

San Roman AK; Jayewickreme CD; Murtaugh LC; Shivdasani RA, 2014. Wnt secretion from epithelial cells and subepithelial myofibroblasts is not required in the mouse intestinal stem cell niche in vivo.  Stem Cell Reports 2(2):127-34

Morris SA; Cahan P; Li H; Zhao AM; San Roman AK; Shivdasani RA; Collins JJ; Daley GQ, 2014. Dissecting engineered cell types and enhancing cell fate conversion via CellNet.  Cell 158(4):889-902

Verzi MP; Shin H; San Roman AK; Liu XS; Shivdasani RA, 2013. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.  Mol Cell Biol 33(2):281-92

Ho LL; Sinha A; Verzi M; Bernt KM; Armstrong SA; Shivdasani RA, 2013. DOT1L-mediated H3K79 methylation in chromatin is dispensable for Wnt pathway-specific and other intestinal epithelial functions.  Mol Cell Biol 33(9):1735-45

Lobo GP; Amengual J; Baus D; Shivdasani RA; Taylor D; von Lintig J, 2013. Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX.  J Biol Chem 288(13):9017-27

Pignon JC; Grisanzio C; Geng Y; Song J; Shivdasani RA; Signoretti S, 2013. p63-expressing cells are the stem cells of developing prostate, bladder, and colorectal epithelia.  Proc Natl Acad Sci U S A 110(20):8105-10

Francis JM; Kiezun A; Ramos AH; Serra S; Pedamallu CS; Qian ZR; Banck MS; Kanwar R; Kulkarni AA; Karpathakis A; Manzo V; Contractor T; Philips J; Nickerson E; Pho N; Hooshmand SM; Brais LK; Lawrence MS; Pugh T; McKenna A; Sivachenko A; Cibulskis K; Carter SL; Ojesina AI; Freeman S; Jones RT; Voet D; Saksena G; Auclair D; Onofrio R; Shefler E; Sougnez C; Grimsby J; Green L; Lennon N; Meyer T; Caplin M; Chung DC; Beutler AS; Ogino S; Thirlwell C; Shivdasani R; Asa SL; Harris CR; Getz G; Kulke M; Meyerson M, 2013. Somatic mutation of CDKN1B in small intestine neuroendocrine tumors.  Nat Genet 45(12):1483-6

Ho Sui SJ; Begley K; Reilly D; Chapman B; McGovern R; Rocca-Sera P; Maguire E; Altschuler GM; Hansen TA; Sompallae R; Krivtsov A; Shivdasani RA; Armstrong SA; Culhane AC; Correll M; Sansone SA; Hofmann O; Hide W, 2012. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.  Nucleic Acids Res 40(Database issue):D984-91

Kostic AD; Gevers D; Pedamallu CS; Michaud M; Duke F; Earl AM; Ojesina AI; Jung J; Bass AJ; Tabernero J; Baselga J; Liu C; Shivdasani RA; Ogino S; Birren BW; Huttenhower C; Garrett WS; Meyerson M, 2012. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.  Genome Res 22(2):292-8

Horst D; Chen J; Morikawa T; Ogino S; Kirchner T; Shivdasani RA, 2012. Differential WNT activity in colorectal cancer confers limited tumorigenic potential and is regulated by MAPK signaling.  Cancer Res 72(6):1547-56

Kim TH; Escudero S; Shivdasani RA, 2012. Intact function of Lgr5 receptor-expressing intestinal stem cells in the absence of Paneth cells.  Proc Natl Acad Sci U S A 109(10):3932-7

Takada K; Zhu D; Bird GH; Sukhdeo K; Zhao JJ; Mani M; Lemieux M; Carrasco DE; Ryan J; Horst D; Fulciniti M; Munshi NC; Xu W; Kung AL; Shivdasani RA; Walensky LD; Carrasco DR, 2012. Targeted disruption of the BCL9/β-catenin complex inhibits oncogenic Wnt signaling.  Sci Transl Med 4(148):148ra117

Dulak AM; Schumacher SE; van Lieshout J; Imamura Y; Fox C; Shim B; Ramos AH; Saksena G; Baca SC; Baselga J; Tabernero J; Barretina J; Enzinger PC; Corso G; Roviello F; Lin L; Bandla S; Luketich JD; Pennathur A; Meyerson M; Ogino S; Shivdasani RA; Beer DG; Godfrey TE; Beroukhim R; Bass AJ, 2012. Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis.  Cancer Res 72(17):4383-93

Kim TH; Shivdasani RA, 2012. Stem cell niches: famished Paneth cells, gluttonous stem cells.  Curr Biol 22(14):R579-80

Shivdasani RA, 2012. GEFs on the RhoAd to a colossal nucleus.  Dev Cell 22(3):471-2

Kim TH; Shivdasani RA, 2011. Notch signaling in stomach epithelial stem cell homeostasis.  J Exp Med 208(4):677-88

Kim BM; Woo J; Kanellopoulou C; Shivdasani RA, 2011. Regulation of mouse stomach development and Barx1 expression by specific microRNAs.  Development 138(6):1081-6

Mills JC; Shivdasani RA, 2011. Gastric epithelial stem cells.  Gastroenterology 140(2):412-24

Verzi MP; Shin H; Ho LL; Liu XS; Shivdasani RA, 2011. Essential and redundant functions of caudal family proteins in activating adult intestinal genes.  Mol Cell Biol 31(10):2026-39

Kim TH; Shivdasani RA, 2011. Genetic evidence that intestinal Notch functions vary regionally and operate through a common mechanism of Math1 repression.  J Biol Chem 286(13):11427-33

Zhang J; Roberts TM; Shivdasani RA, 2011. Targeting PI3K signaling as a therapeutic approach for colorectal cancer.  Gastroenterology 141(1):50-61

San Roman AK; Shivdasani RA, 2011. Boundaries, junctions and transitions in the gastrointestinal tract.  Exp Cell Res 317(19):2711-8

Yonesaka K; Zejnullahu K; Okamoto I; Satoh T; Cappuzzo F; Souglakos J; Ercan D; Rogers A; Roncalli M; Takeda M; Fujisaka Y; Philips J; Shimizu T; Maenishi O; Cho Y; Sun J; Destro A; Taira K; Takeda K; Okabe T; Swanson J; Itoh H; Takada M; Lifshits E; Okuno K; Engelman JA; Shivdasani RA; Nishio K; Fukuoka M; Varella-Garcia M; Nakagawa K; Jänne PA, 2011. Activation of ERBB2 signaling causes resistance to the EGFR-directed therapeutic antibody cetuximab.  Sci Transl Med 3(99):99ra86

Woo J; Miletich I; Kim BM; Sharpe PT; Shivdasani RA, 2011. Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation.  PLoS One 6(7):e22493

Kim TH; Kim BM; Mao J; Rowan S; Shivdasani RA, 2011. Endodermal Hedgehog signals modulate Notch pathway activity in the developing digestive tract mesenchyme.  Development 138(15):3225-33

Mao J; Kim BM; Rajurkar M; Shivdasani RA; McMahon AP, 2010. Hedgehog signaling controls mesenchymal growth in the developing mammalian digestive tract.  Development 137(10):1721-9

Echtler K; Stark K; Lorenz M; Kerstan S; Walch A; Jennen L; Rudelius M; Seidl S; Kremmer E; Emambokus NR; von Bruehl ML; Frampton J; Isermann B; Genzel-Boroviczény O; Schreiber C; Mehilli J; Kastrati A; Schwaiger M; Shivdasani RA; Massberg S, 2010. Platelets contribute to postnatal occlusion of the ductus arteriosus.  Nat Med 16(1):75-82

Verzi MP; Hatzis P; Sulahian R; Philips J; Schuijers J; Shin H; Freed E; Lynch JP; Dang DT; Brown M; Clevers H; Liu XS; Shivdasani RA, 2010. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions.  Proc Natl Acad Sci U S A 107(34):15157-62

Horst D; Gu X; Bhasin M; Yang Q; Verzi M; Lin D; Joseph M; Zhang X; Chen W; Li YP; Shivdasani RA; Libermann TA, 2010. Requirement of the epithelium-specific Ets transcription factor Spdef for mucous gland cell function in the gastric antrum.  J Biol Chem 285(45):35047-55

Verzi MP; Shin H; He HH; Sulahian R; Meyer CA; Montgomery RK; Fleet JC; Brown M; Liu XS; Shivdasani RA, 2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26

Verzi MP; Shivdasani RA, 2010. Stem cells: The intestinal-crypt casino.  Nature 467(7319):1055-6

Montgomery RK; Shivdasani RA, 2009. Prominin1 (CD133) as an intestinal stem cell marker: promise and nuance.  Gastroenterology 136(7):2051-4

Wuelling M; Kaiser FJ; Buelens LA; Braunholz D; Shivdasani RA; Depping R; Vortkamp A, 2009. Trps1, a regulator of chondrocyte proliferation and differentiation, interacts with the activator form of Gli3.  Dev Biol 328(1):40-53

Verzi MP; Stanfel MN; Moses KA; Kim BM; Zhang Y; Schwartz RJ; Shivdasani RA; Zimmer WE, 2009. Role of the homeodomain transcription factor Bapx1 in mouse distal stomach development.  Gastroenterology 136(5):1701-10

Eeckhoute J; Lupien M; Meyer CA; Verzi MP; Shivdasani RA; Liu XS; Brown M, 2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.  Genome Res 19(3):372-80

Baba Y; Nosho K; Shima K; Freed E; Irahara N; Philips J; Meyerhardt JA; Hornick JL; Shivdasani RA; Fuchs CS; Ogino S, 2009. Relationship of CDX2 loss with molecular features and prognosis in colorectal cancer.  Clin Cancer Res 15(14):4665-73

Pomerantz MM; Ahmadiyeh N; Jia L; Herman P; Verzi MP; Doddapaneni H; Beckwith CA; Chan JA; Hills A; Davis M; Yao K; Kehoe SM; Lenz HJ; Haiman CA; Yan C; Henderson BE; Frenkel B; Barretina J; Bass A; Tabernero J; Baselga J; Regan MM; Manak JR; Shivdasani R; Coetzee GA; Freedman ML, 2009. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer.  Nat Genet 41(8):882-4

Souglakos J; Philips J; Wang R; Marwah S; Silver M; Tzardi M; Silver J; Ogino S; Hooshmand S; Kwak E; Freed E; Meyerhardt JA; Saridaki Z; Georgoulias V; Finkelstein D; Fuchs CS; Kulke MH; Shivdasani RA, 2009. Prognostic and predictive value of common mutations for treatment response and survival in patients with metastatic colorectal cancer.  Br J Cancer 101(3):465-72

Bass AJ; Watanabe H; Mermel CH; Yu S; Perner S; Verhaak RG; Kim SY; Wardwell L; Tamayo P; Gat-Viks I; Ramos AH; Woo MS; Weir BA; Getz G; Beroukhim R; O'Kelly M; Dutt A; Rozenblatt-Rosen O; Dziunycz P; Komisarof J; Chirieac LR; Lafargue CJ; Scheble V; Wilbertz T; Ma C; Rao S; Nakagawa H; Stairs DB; Lin L; Giordano TJ; Wagner P; Minna JD; Gazdar AF; Zhu CQ; Brose MS; Cecconello I; Jr UR; Marie SK; Dahl O; Shivdasani RA; Tsao MS; Rubin MA; Wong KK; Regev A; Hahn WC; Beer DG; Rustgi AK; Meyerson M, 2009. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.  Nat Genet 41(11):1238-42

MacConaill LE; Campbell CD; Kehoe SM; Bass AJ; Hatton C; Niu L; Davis M; Yao K; Hanna M; Mondal C; Luongo L; Emery CM; Baker AC; Philips J; Goff DJ; Fiorentino M; Rubin MA; Polyak K; Chan J; Wang Y; Fletcher JA; Santagata S; Corso G; Roviello F; Shivdasani R; Kieran MW; Ligon KL; Stiles CD; Hahn WC; Meyerson ML; Garraway LA, 2009. Profiling critical cancer gene mutations in clinical tumor samples.  PLoS One 4(11):e7887

Chen Z; Shivdasani RA, 2009. Regulation of platelet biogenesis: insights from the May-Hegglin anomaly and other MYH9-related disorders.  J Thromb Haemost 7 Suppl 1:272-6

Kunert S; Meyer I; Fleischhauer S; Wannack M; Fiedler J; Shivdasani RA; Schulze H, 2009. The microtubule modulator RanBP10 plays a critical role in regulation of platelet discoid shape and degranulation.  Blood 114(27):5532-40

Choi MY; Romer AI; Wang Y; Wu MP; Ito S; Leiter AB; Shivdasani RA, 2008. Requirement of the tissue-restricted homeodomain transcription factor Nkx6.3 in differentiation of gastrin-producing G cells in the stomach antrum.  Mol Cell Biol 28(10):3208-18

Kulke MH; Freed E; Chiang DY; Philips J; Zahrieh D; Glickman JN; Shivdasani RA, 2008. High-resolution analysis of genetic alterations in small bowel carcinoid tumors reveals areas of recurrent amplification and loss.  Genes Chromosomes Cancer 47(7):591-603

Patel-Hett S; Richardson JL; Schulze H; Drabek K; Isaac NA; Hoffmeister K; Shivdasani RA; Bulinski JC; Galjart N; Hartwig JH; Italiano JE Jr, 2008. Visualization of microtubule growth in living platelets reveals a dynamic marginal band with multiple microtubules.  Blood 111(9):4605-16

Napierala D; Sam K; Morello R; Zheng Q; Munivez E; Shivdasani RA; Lee B, 2008. Uncoupling of chondrocyte differentiation and perichondrial mineralization underlies the skeletal dysplasia in tricho-rhino-phalangeal syndrome.  Hum Mol Genet 17(14):2244-54

Huang G; Zhang P; Hirai H; Elf S; Yan X; Chen Z; Koschmieder S; Okuno Y; Dayaram T; Growney JD; Shivdasani RA; Gilliland DG; Speck NA; Nimer SD; Tenen DG, 2008. PU.1 is a major downstream target of AML1 (RUNX1) in adult mouse hematopoiesis.  Nat Genet 40(1):51-60

Schulze H; Dose M; Korpal M; Meyer I; Italiano JE Jr; Shivdasani RA, 2008. RanBP10 is a cytoplasmic guanine nucleotide exchange factor that modulates noncentrosomal microtubules.  J Biol Chem 283(20):14109-19

Verzi MP; Khan AH; Ito S; Shivdasani RA, 2008. Transcription factor foxq1 controls mucin gene expression and granule content in mouse stomach surface mucous cells.  Gastroenterology 135(2):591-600

Verzi MP; Shivdasani RA, 2008. Wnt signaling in gut organogenesis.  Organogenesis 4(2):87-91

Firestein R; Bass AJ; Kim SY; Dunn IF; Silver SJ; Guney I; Freed E; Ligon AH; Vena N; Ogino S; Chheda MG; Tamayo P; Finn S; Shrestha Y; Boehm JS; Jain S; Bojarski E; Mermel C; Barretina J; Chan JA; Baselga J; Tabernero J; Root DE; Fuchs CS; Loda M; Shivdasani RA; Meyerson M; Hahn WC, 2008. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity.  Nature 455(7212):547-51

Kantaputra P; Miletich I; Lüdecke HJ; Suzuki EY; Praphanphoj V; Shivdasani R; Wuelling M; Vortkamp A; Napierala D; Sharpe PT, 2008. Tricho-rhino-phalangeal syndrome with supernumerary teeth.  J Dent Res 87(11):1027-31

Hafler BP; Choi MY; Shivdasani RA; Rowitch DH, 2008. Expression and function of Nkx6.3 in vertebrate hindbrain.  Brain Res 1222:42-50

Kim BM; Mao J; Taketo MM; Shivdasani RA, 2007. Phases of canonical Wnt signaling during the development of mouse intestinal epithelium.  Gastroenterology 133(2):529-38

Chen Z; Naveiras O; Balduini A; Mammoto A; Conti MA; Adelstein RS; Ingber D; Daley GQ; Shivdasani RA, 2007. The May-Hegglin anomaly gene MYH9 is a negative regulator of platelet biogenesis modulated by the Rho-ROCK pathway.  Blood 110(1):171-9

Kim BM; Miletich I; Mao J; McMahon AP; Sharpe PA; Shivdasani RA, 2007. Independent functions and mechanisms for homeobox gene Barx1 in patterning mouse stomach and spleen.  Development 134(20):3603-13

Chen Z; Hu M; Shivdasani RA, 2007. Expression analysis of primary mouse megakaryocyte differentiation and its application in identifying stage-specific molecular markers and a novel transcriptional target of NF-E2.  Blood 109(4):1451-9

Junt T; Schulze H; Chen Z; Massberg S; Goerge T; Krueger A; Wagner DD; Graf T; Italiano JE Jr; Shivdasani RA; von Andrian UH, 2007. Dynamic visualization of thrombopoiesis within bone marrow.  Science 317(5845):1767-70

Van Dyck F; Braem CV; Chen Z; Declercq J; Deckers R; Kim BM; Ito S; Wu MK; Cohen DE; Dewerchin M; Derua R; Waelkens E; Fiette L; Roebroek A; Schuit F; Van de Ven WJ; Shivdasani RA, 2007. Loss of the PlagL2 transcription factor affects lacteal uptake of chylomicrons.  Cell Metab 6(5):406-13

Schulze H; Korpal M; Hurov J; Kim SW; Zhang J; Cantley LC; Graf T; Shivdasani RA, 2006. Characterization of the megakaryocyte demarcation membrane system and its role in thrombopoiesis.  Blood 107(10):3868-75

Shivdasani RA, 2006. MicroRNAs: regulators of gene expression and cell differentiation.  Blood 108(12):3646-53

Choi MY; Romer AI; Hu M; Lepourcelet M; Mechoor A; Yesilaltay A; Krieger M; Gray PA; Shivdasani RA, 2006. A dynamic expression survey identifies transcription factors relevant in mouse digestive tract development.  Development 133(20):4119-29

Kim BM; Buchner G; Miletich I; Sharpe PT; Shivdasani RA, 2005. The stomach mesenchymal transcription factor Barx1 specifies gastric epithelial identity through inhibition of transient Wnt signaling.  Dev Cell 8(4):611-22

Drori S; Girnun GD; Tou L; Szwaya JD; Mueller E; Xia K; Shivdasani RA; Spiegelman BM, 2005. Hic-5 regulates an epithelial program mediated by PPARgamma.  Genes Dev 19(3):362-75

Lepourcelet M; Tou L; Cai L; Sawada J; Lazar AJ; Glickman JN; Williamson JA; Everett AD; Redston M; Fox EA; Nakatani Y; Shivdasani RA, 2005. Insights into developmental mechanisms and cancers in the mammalian intestine derived from serial analysis of gene expression and study of the hepatoma-derived growth factor (HDGF).  Development 132(2):415-27

Schulze H; Shivdasani RA, 2005. Mechanisms of thrombopoiesis.  J Thromb Haemost 3(8):1717-24

Patel SR; Richardson JL; Schulze H; Kahle E; Galjart N; Drabek K; Shivdasani RA; Hartwig JH; Italiano JE Jr, 2005. Differential roles of microtubule assembly and sliding in proplatelet formation by megakaryocytes.  Blood 106(13):4076-85

Shivdasani RA; Schulze H, 2005. Culture, expansion, and differentiation of murine megakaryocytes.  Curr Protoc Immunol Chapter 22:Unit 22F.6

Richardson JL; Shivdasani RA; Boers C; Hartwig JH; Italiano JE Jr, 2005. Mechanisms of organelle transport and capture along proplatelets during platelet production.  Blood 106(13):4066-75

Hu M; Shivdasani RA, 2005. Overlapping gene expression in fetal mouse intestine development and human colorectal cancer.  Cancer Res 65(19):8715-22

Kacena MA; Shivdasani RA; Wilson K; Xi Y; Troiano N; Nazarian A; Gundberg CM; Bouxsein ML; Lorenzo JA; Horowitz MC, 2004. Megakaryocyte-osteoblast interaction revealed in mice deficient in transcription factors GATA-1 and NF-E2.  J Bone Miner Res 19(4):652-60

Lepourcelet M; Chen YN; France DS; Wang H; Crews P; Petersen F; Bruseo C; Wood AW; Shivdasani RA, 2004. Small-molecule antagonists of the oncogenic Tcf/beta-catenin protein complex.  Cancer Cell 5(1):91-102

Tou L; Liu Q; Shivdasani RA, 2004. Regulation of mammalian epithelial differentiation and intestine development by class I histone deacetylases.  Mol Cell Biol 24(8):3132-9

Shivdasani RA, 2004. Lonely in Paris: when one gene copy isn't enough.  J Clin Invest 114(1):17-9

Derjuga A; Gourley TS; Holm TM; Heng HH; Shivdasani RA; Ahmed R; Andrews NC; Blank V, 2004. Complexity of CNC transcription factors as revealed by gene targeting of the Nrf3 locus.  Mol Cell Biol 24(8):3286-94

Schulze H; Korpal M; Bergmeier W; Italiano JE Jr; Wahl SM; Shivdasani RA, 2004. Interactions between the megakaryocyte/platelet-specific beta1 tubulin and the secretory leukocyte protease inhibitor SLPI suggest a role for regulated proteolysis in platelet functions.  Blood 104(13):3949-57

Schulze H; Shivdasani RA, 2004. Molecular mechanisms of megakaryocyte differentiation.  Semin Thromb Hemost 30(4):389-98

Italiano JE Jr; Bergmeier W; Tiwari S; Falet H; Hartwig JH; Hoffmeister KM; André P; Wagner DD; Shivdasani RA, 2003. Mechanisms and implications of platelet discoid shape.  Blood 101(12):4789-96

Italiano JE Jr; Shivdasani RA, 2003. Megakaryocytes and beyond: the birth of platelets.  J Thromb Haemost 1(6):1174-82

Tiwari S; Italiano JE Jr; Barral DC; Mules EH; Novak EK; Swank RT; Seabra MC; Shivdasani RA, 2003. A role for Rab27b in NF-E2-dependent pathways of platelet formation.  Blood 102(12):3970-9

Shivdasani R, 2002. An animal model for myelofibrosis.  Blood 100(4):1109

Ryan DP; Kulke MH; Fuchs CS; Grossbard ML; Grossman SR; Morgan JA; Earle CC; Shivdasani R; Kim H; Mayer RJ; Clark JW, 2002. A Phase II study of gemcitabine and docetaxel in patients with metastatic pancreatic carcinoma.  Cancer 94(1):97-103

Shivdasani RA, 2002. Molecular regulation of vertebrate early endoderm development.  Dev Biol 249(2):191-203

Kulke MH; Demetri GD; Sharpless NE; Ryan DP; Shivdasani R; Clark JS; Spiegelman BM; Kim H; Mayer RJ; Fuchs CS, 2002. A phase II study of troglitazone, an activator of the PPARgamma receptor, in patients with chemotherapy-resistant metastatic colorectal cancer.  Cancer J 8(5):395-9

Lepourcelet M; Shivdasani RA, 2002. Characterization of a novel mammalian Groucho isoform and its role in transcriptional regulation.  J Biol Chem 277(49):47732-40

Malik TH; Von Stechow D; Bronson RT; Shivdasani RA, 2002. Deletion of the GATA domain of TRPS1 causes an absence of facial hair and provides new insights into the bone disorder in inherited tricho-rhino-phalangeal syndromes.  Mol Cell Biol 22(24):8592-600

Livingston DM; Shivdasani R, 2001. Toward mechanism-based cancer care.  JAMA 285(5):588-93

Malik TH; Shoichet SA; Latham P; Kroll TG; Peters LL; Shivdasani RA, 2001. Transcriptional repression and developmental functions of the atypical vertebrate GATA protein TRPS1.  EMBO J 20(7):1715-25

Zhang J; Rosenthal A; de Sauvage FJ; Shivdasani RA, 2001. Downregulation of Hedgehog signaling is required for organogenesis of the small intestine in Xenopus.  Dev Biol 229(1):188-202

Li YJ; Higgins RR; Pak BJ; Shivdasani RA; Ney PA; Archer M; Ben-David Y, 2001. p45(NFE2) is a negative regulator of erythroid proliferation which contributes to the progression of Friend virus-induced erythroleukemias.  Mol Cell Biol 21(1):73-80

Poy F; Lepourcelet M; Shivdasani RA; Eck MJ, 2001. Structure of a human Tcf4-beta-catenin complex.  Nat Struct Biol 8(12):1053-7

Schwer HD; Lecine P; Tiwari S; Italiano JE Jr; Hartwig JH; Shivdasani RA, 2001. A lineage-restricted and divergent beta-tubulin isoform is essential for the biogenesis, structure and function of blood platelets.  Curr Biol 11(8):579-86

Shivdasani RA, 2001. Molecular and transcriptional regulation of megakaryocyte differentiation.  Stem Cells 19(5):397-407

Lecine P; Italiano JE Jr; Kim SW; Villeval JL; Shivdasani RA, 2000. Hematopoietic-specific beta 1 tubulin participates in a pathway of platelet biogenesis dependent on the transcription factor NF-E2.  Blood 96(4):1366-73

Shoichet SA; Malik TH; Rothman JH; Shivdasani RA, 2000. Action of the Caenorhabditis elegans GATA factor END-1 in Xenopus suggests that similar mechanisms initiate endoderm development in ecdysozoa and vertebrates.  Proc Natl Acad Sci U S A 97(8):4076-81

Malik TH; Shivdasani RA, 2000. Structure and expression of a novel frizzled gene isolated from the developing mouse gut.  Biochem J 349 Pt 3:829-34

Lee YJ; Swencki B; Shoichet S; Shivdasani RA, 1999. A possible role for the high mobility group box transcription factor Tcf-4 in vertebrate gut epithelial cell differentiation.  J Biol Chem 274(3):1566-72

Vyas P; Ault K; Jackson CW; Orkin SH; Shivdasani RA, 1999. Consequences of GATA-1 deficiency in megakaryocytes and platelets.  Blood 93(9):2867-75

Levin J; Peng JP; Baker GR; Villeval JL; Lecine P; Burstein SA; Shivdasani RA, 1999. Pathophysiology of thrombocytopenia and anemia in mice lacking transcription factor NF-E2.  Blood 94(9):3037-47

Italiano JE Jr; Lecine P; Shivdasani RA; Hartwig JH, 1999. Blood platelets are assembled principally at the ends of proplatelet processes produced by differentiated megakaryocytes.  J Cell Biol 147(6):1299-312

Lecine P; Blank V; Shivdasani R, 1998. Characterization of the hematopoietic transcription factor NF-E2 in primary murine megakaryocytes.  J Biol Chem 273(13):7572-8

Lecine P; Shivdasani RA, 1998. Cellular and molecular biology of megakaryocyte differentiation in the absence of lineage-restricted transcription factors.  Stem Cells 16 Suppl 2:91-5

Martin F; van Deursen JM; Shivdasani RA; Jackson CW; Troutman AG; Ney PA, 1998. Erythroid maturation and globin gene expression in mice with combined deficiency of NF-E2 and nrf-2.  Blood 91(9):3459-66

de Sauvage FJ; Villeval JL; Shivdasani RA, 1998. Regulation of megakaryocytopoiesis and platelet production: lessons from animal models.  J Lab Clin Med 131(6):496-501

Orkin SH; Shivdasani RA; Fujiwara Y; McDevitt MA, 1998. Transcription factor GATA-1 in megakaryocyte development.  Stem Cells 16 Suppl 2:79-83

Lecine P; Villeval JL; Vyas P; Swencki B; Xu Y; Shivdasani RA, 1998. Mice lacking transcription factor NF-E2 provide in vivo validation of the proplatelet model of thrombocytopoiesis and show a platelet production defect that is intrinsic to megakaryocytes.  Blood 92(5):1608-16

McDevitt MA; Shivdasani RA; Fujiwara Y; Yang H; Orkin SH, 1997. A "knockdown" mutation created by cis-element gene targeting reveals the dependence of erythroid cell maturation on the level of transcription factor GATA-1.  Proc Natl Acad Sci U S A 94(13):6781-5

Chan FY; Robinson J; Brownlie A; Shivdasani RA; Donovan A; Brugnara C; Kim J; Lau BC; Witkowska HE; Zon LI, 1997. Characterization of adult alpha- and beta-globin genes in the zebrafish.  Blood 89(2):688-700

Shivdasani RA; Fujiwara Y; McDevitt MA; Orkin SH, 1997. A lineage-selective knockout establishes the critical role of transcription factor GATA-1 in megakaryocyte growth and platelet development.  EMBO J 16(13):3965-73

Shivdasani RA; Fielder P; Keller GA; Orkin SH; de Sauvage FJ, 1997. Regulation of the serum concentration of thrombopoietin in thrombocytopenic NF-E2 knockout mice.  Blood 90(5):1821-7

McDevitt MA; Fujiwara Y; Shivdasani RA; Orkin SH, 1997. An upstream, DNase I hypersensitive region of the hematopoietic-expressed transcription factor GATA-1 gene confers developmental specificity in transgenic mice.  Proc Natl Acad Sci U S A 94(15):7976-81

Shivdasani RA, 1997. Stem cell transcription factors.  Hematol Oncol Clin North Am 11(6):1199-206

Deveaux S; Cohen-Kaminsky S; Shivdasani RA; Andrews NC; Filipe A; Kuzniak I; Orkin SH; Roméo PH; Mignotte V, 1997. p45 NF-E2 regulates expression of thromboxane synthase in megakaryocytes.  EMBO J 16(18):5654-61

Shivdasani RA, 1996. The role of transcription factor NF-E2 in megakaryocyte maturation and platelet production.  Stem Cells 14 Suppl 1:112-5

Peters LL; Shivdasani RA; Liu SC; Hanspal M; John KM; Gonzalez JM; Brugnara C; Gwynn B; Mohandas N; Alper SL; Orkin SH; Lux SE, 1996. Anion exchanger 1 (band 3) is required to prevent erythrocyte membrane surface loss but not to form the membrane skeleton.  Cell 86(6):917-27

Shivdasani RA; Orkin SH, 1996. The transcriptional control of hematopoiesis.  Blood 87(10):4025-39

Shivdasani RA; Rosenblatt MF; Zucker-Franklin D; Jackson CW; Hunt P; Saris CJ; Orkin SH, 1995. Transcription factor NF-E2 is required for platelet formation independent of the actions of thrombopoietin/MGDF in megakaryocyte development.  Cell 81(5):695-704

Shivdasani RA; Mayer EL; Orkin SH, 1995. Absence of blood formation in mice lacking the T-cell leukaemia oncoprotein tal-1/SCL.  Nature 373(6513):432-4

Shivdasani RA; Orkin SH, 1995. Erythropoiesis and globin gene expression in mice lacking the transcription factor NF-E2.  Proc Natl Acad Sci U S A 92(19):8690-4

Shivdasani RA; Anderson KC, 1994. HLA homozygosity and shared HLA haplotypes in the development of transfusion-associated graft-versus-host disease.  Leuk Lymphoma 15(3-4):227-34

Shivdasani RA; Hess JL; Skarin AT; Pinkus GS, 1993. Intermediate lymphocytic lymphoma: clinical and pathologic features of a recently characterized subtype of non-Hodgkin's lymphoma.  J Clin Oncol 11(4):802-111

Shivdasani RA; Haluska FG; Dock NL; Dover JS; Kineke EJ; Anderson KC, 1993. Brief report: graft-versus-host disease associated with transfusion of blood from unrelated HLA-homozygous donors.  N Engl J Med 328(11):766-70

Shivdasani RA; Anderson KC, 1993. Transfusion-associated graft-versus-host disease: scratching the surface.  Transfusion 33(9):696-7

Shivdasani RA; Esch TR; Chen GH; Thomas DW, 1990. Monoclonal antibodies define the characteristics and cellular distribution of an Ia-associated protein.  Hybridoma 9(1):17-30

Bielinska A; Shivdasani RA; Zhang LQ; Nabel GJ, 1990. Regulation of gene expression with double-stranded phosphorothioate oligonucleotides.  Science 250(4983):997-1000

Shivdasani RA, 1989. Science, another culture: an essay after C. P. Snow.  Pharos Alpha Omega Alpha Honor Med Soc 52(4):21-4

Shivdasani RA; Thomas DW, 1988. Molecular associations of IA antigens after T-B cell interactions. I. Identification of new molecular associations.  J Immunol 141(4):1252-60

Kim KH; Shivdasani RA; Thomas DW, 1986. Two roles for Ia in antigen-specific T lymphocyte activation.  J Immunol 137(11):3393-400

Publication list retrieved from NCBI using ImpactPubs

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Janiszewska M; Polyak K, 2015. Clonal evolution in cancer: a tale of twisted twines.  Cell Stem Cell 16(1):11-2

Huh SJ; Clement K; Jee D; Merlini A; Choudhury S; Maruyama R; Yoo R; Chytil A; Boyle P; Ran FA; Moses HL; Barcellos-Hoff MH; Jackson-Grusby L; Meissner A; Polyak K, 2015. Age- and Pregnancy-Associated DNA Methylation Changes in Mammary Epithelial Cells.  Stem Cell Reports.

Hines WC; Su Y; Kuhn I; Polyak K; Bissell MJ, 2014. Sorting out the FACS: a devil in the details.  Cell Rep 6(5):779-81

Polyak K; Marusyk A, 2014. Cancer: Clonal cooperation.  Nature 508(7494):52-3

Almendro V; Cheng YK; Randles A; Itzkovitz S; Marusyk A; Ametller E; Gonzalez-Farre X; Muñoz M; Russnes HG; Helland A; Rye IH; Borresen-Dale AL; Maruyama R; van Oudenaarden A; Dowsett M; Jones RL; Reis-Filho J; Gascon P; Gönen M; Michor F; Polyak K, 2014. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.  Cell Rep 6(3):514-27

Chin YR; Yoshida T; Marusyk A; Beck AH; Polyak K; Toker A, 2014. Targeting Akt3 signaling in triple-negative breast cancer.  Cancer Res 74(3):964-73

Godinho SA; Picone R; Burute M; Dagher R; Su Y; Leung CT; Polyak K; Brugge JS; Théry M; Pellman D, 2014. Oncogene-like induction of cellular invasion from centrosome amplification.  Nature 510(7503):167-71

Almendro V; Kim HJ; Cheng YK; Gönen M; Itzkovitz S; Argani P; van Oudenaarden A; Sukumar S; Michor F; Polyak K, 2014. Genetic and phenotypic diversity in breast tumor metastases.  Cancer Res 74(5):1338-48

Polyak K, 2014. Tumor heterogeneity confounds and illuminates: a case for Darwinian tumor evolution.  Nat Med 20(4):344-6

Pathania S; Bade S; Le Guillou M; Burke K; Reed R; Bowman-Colin C; Su Y; Ting DT; Polyak K; Richardson AL; Feunteun J; Garber JE; Livingston DM, 2014. BRCA1 haploinsufficiency for replication stress suppression in primary cells.  Nat Commun 5:5496

Cuiffo BG; Campagne A; Bell GW; Lembo A; Orso F; Lien EC; Bhasin MK; Raimo M; Hanson SE; Marusyk A; El-Ashry D; Hematti P; Polyak K; Mechta-Grigoriou F; Mariani O; Volinia S; Vincent-Salomon A; Taverna D; Karnoub AE, 2014. MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis.  Cell Stem Cell 15(6):762-74

Marusyk A; Tabassum DP; Altrock PM; Almendro V; Michor F; Polyak K, 2014. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity.  Nature 514(7520):54-8

Janiszewska M; Beca F; Polyak K, 2014. Tumor heterogeneity: the lernaean hydra of oncology?  Oncology (Williston Park) 28.

Yamamoto S; Wu Z; Russnes HG; Takagi S; Peluffo G; Vaske C; Zhao X; Moen Vollan HK; Maruyama R; Ekram MB; Sun H; Kim JH; Carver K; Zucca M; Feng J; Almendro V; Bessarabova M; Rueda OM; Nikolsky Y; Caldas C; Liu XS; Polyak K, 2014. JARID1B is a luminal lineage-driving oncogene in breast cancer.  Cancer Cell 25(6):762-77

Zou MR; Cao J; Liu Z; Huh SJ; Polyak K; Yan Q, 2014. Histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) controls mammary gland development by regulating key developmental and lineage specification genes.  J Biol Chem 289(25):17620-33

Eswaran J; Horvath A; Godbole S; Reddy SD; Mudvari P; Ohshiro K; Cyanam D; Nair S; Fuqua SA; Polyak K; Florea LD; Kumar R, 2013. RNA sequencing of cancer reveals novel splicing alterations.  Sci Rep 3:1689

Marusyk A; Polyak K, 2013. Cancer. Cancer cell phenotypes, in fifty shades of grey.  Science 339(6119):528-9

Almendro V; Marusyk A; Polyak K, 2013. Cellular heterogeneity and molecular evolution in cancer.  Annu Rev Pathol 8:277-302

Steenbergen RD; Ongenaert M; Snellenberg S; Trooskens G; van der Meide WF; Pandey D; Bloushtain-Qimron N; Polyak K; Meijer CJ; Snijders PJ; Van Criekinge W, 2013. Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis.  J Pathol 231(1):53-62

Seo JH; Li Q; Fatima A; Eklund A; Szallasi Z; Polyak K; Richardson AL; Freedman ML, 2013. Deconvoluting complex tissues for expression quantitative trait locus-based analyses.  Philos Trans R Soc Lond B Biol Sci 368(1620):20120363

Timmerman LA; Holton T; Yuneva M; Louie RJ; Padró M; Daemen A; Hu M; Chan DA; Ethier SP; van 't Veer LJ; Polyak K; McCormick F; Gray JW, 2013. Glutamine sensitivity analysis identifies the xCT antiporter as a common triple-negative breast tumor therapeutic target.  Cancer Cell 24(4):450-65

Choudhury S; Almendro V; Merino VF; Wu Z; Maruyama R; Su Y; Martins FC; Fackler MJ; Bessarabova M; Kowalczyk A; Conway T; Beresford-Smith B; Macintyre G; Cheng YK; Lopez-Bujanda Z; Kaspi A; Hu R; Robens J; Nikolskaya T; Haakensen VD; Schnitt SJ; Argani P; Ethington G; Panos L; Grant M; Clark J; Herlihy W; Lin SJ; Chew G; Thompson EW; Greene-Colozzi A; Richardson AL; Rosson GD; Pike M; Garber JE; Nikolsky Y; Blum JL; Au A; Hwang ES; Tamimi RM; Michor F; Haviv I; Liu XS; Sukumar S; Polyak K, 2013. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics.  Cell Stem Cell 13(1):117-30

McLaughlin SK; Olsen SN; Dake B; De Raedt T; Lim E; Bronson RT; Beroukhim R; Polyak K; Brown M; Kuperwasser C; Cichowski K, 2013. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor.  Cancer Cell 24(3):365-78

Pantel K; Diaz LA Jr; Polyak K, 2013. Tracking tumor resistance using 'liquid biopsies'.  Nat Med 19(6):676-7

Polyak K; Vogt PK, 2012. Progress in breast cancer research.  Proc Natl Acad Sci U S A 109(8):2715-7

Polyak K, 2012. On chromatin remodeling in mammary gland differentiation and breast tumorigenesis.  Cold Spring Harb Perspect Biol 4.

Jiao X; Wood LD; Lindman M; Jones S; Buckhaults P; Polyak K; Sukumar S; Carter H; Kim D; Karchin R; Sjöblom T, 2012. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers.  Genes Chromosomes Cancer 51(5):480-9

Shrestha Y; Schafer EJ; Boehm JS; Thomas SR; He F; Du J; Wang S; Barretina J; Weir BA; Zhao JJ; Polyak K; Golub TR; Beroukhim R; Hahn WC, 2012. PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling.  Oncogene 31(29):3397-408

Marusyk A; Almendro V; Polyak K, 2012. Intra-tumour heterogeneity: a looking glass for cancer?  Nat Rev Cancer 12(5):323-34

Maruyama R; Shipitsin M; Choudhury S; Wu Z; Protopopov A; Yao J; Lo PK; Bessarabova M; Ishkin A; Nikolsky Y; Liu XS; Sukumar S; Polyak K, 2012. Altered antisense-to-sense transcript ratios in breast cancer.  Proc Natl Acad Sci U S A 109(8):2820-4

Balko JM; Miller TW; Morrison MM; Hutchinson K; Young C; Rinehart C; Sánchez V; Jee D; Polyak K; Prat A; Perou CM; Arteaga CL; Cook RS, 2012. The receptor tyrosine kinase ErbB3 maintains the balance between luminal and basal breast epithelium.  Proc Natl Acad Sci U S A 109(1):221-6

Martins FC; De S; Almendro V; Gönen M; Park SY; Blum JL; Herlihy W; Ethington G; Schnitt SJ; Tung N; Garber JE; Fetten K; Michor F; Polyak K, 2012. Evolutionary pathways in BRCA1-associated breast tumors.  Cancer Discov 2(6):503-11

Beck S; Bernstein BE; Campbell RM; Costello JF; Dhanak D; Ecker JR; Greally JM; Issa JP; Laird PW; Polyak K; Tycko B; Jones PA, 2012. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.  Cancer Res 72(24):6319-24

Vegfors J; Petersson S; Kovács A; Polyak K; Enerbäck C, 2012. The expression of Psoriasin (S100A7) and CD24 is linked and related to the differentiation of mammary epithelial cells.  PLoS One 7(12):e53119

Bhatia S; Frangioni JV; Hoffman RM; Iafrate AJ; Polyak K, 2012. The challenges posed by cancer heterogeneity.  Nat Biotechnol 30(7):604-10

Polyak K; Metzger Filho O, 2012. SnapShot: breast cancer.  Cancer Cell 22(4):562-562.e1

Polyak K, 2012. On using functional genetics to understand breast cancer biology.  Cold Spring Harb Perspect Biol 4(7):a013516

Banerji S; Cibulskis K; Rangel-Escareno C; Brown KK; Carter SL; Frederick AM; Lawrence MS; Sivachenko AY; Sougnez C; Zou L; Cortes ML; Fernandez-Lopez JC; Peng S; Ardlie KG; Auclair D; Bautista-Piña V; Duke F; Francis J; Jung J; Maffuz-Aziz A; Onofrio RC; Parkin M; Pho NH; Quintanar-Jurado V; Ramos AH; Rebollar-Vega R; Rodriguez-Cuevas S; Romero-Cordoba SL; Schumacher SE; Stransky N; Thompson KM; Uribe-Figueroa L; Baselga J; Beroukhim R; Polyak K; Sgroi DC; Richardson AL; Jimenez-Sanchez G; Lander ES; Gabriel SB; Garraway LA; Golub TR; Melendez-Zajgla J; Toker A; Getz G; Hidalgo-Miranda A; Meyerson M, 2012. Sequence analysis of mutations and translocations across breast cancer subtypes.  Nature 486(7403):405-9

Bessarabova M; Pustovalova O; Shi W; Serebriyskaya T; Ishkin A; Polyak K; Velculescu VE; Nikolskaya T; Nikolsky Y, 2011. Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.  Cancer Res 71(10):3471-81

Polyak K; Garber J, 2011. Targeting the missing links for cancer therapy.  Nat Med 17(3):283-4

Chaffer CL; Brueckmann I; Scheel C; Kaestli AJ; Wiggins PA; Rodrigues LO; Brooks M; Reinhardt F; Su Y; Polyak K; Arendt LM; Kuperwasser C; Bierie B; Weinberg RA, 2011. Normal and neoplastic nonstem cells can spontaneously convert to a stem-like state.  Proc Natl Acad Sci U S A 108(19):7950-5

Polyak K, 2011. Heterogeneity in breast cancer.  J Clin Invest 121(10):3786-8

Place AE; Jin Huh S; Polyak K, 2011. The microenvironment in breast cancer progression: biology and implications for treatment.  Breast Cancer Res 13(6):227

Marotta LL; Polyak K, 2011. Unraveling the complexity of basal-like breast cancer.  Oncotarget 2(8):588-9

Maruyama R; Choudhury S; Kowalczyk A; Bessarabova M; Beresford-Smith B; Conway T; Kaspi A; Wu Z; Nikolskaya T; Merino VF; Lo PK; Liu XS; Nikolsky Y; Sukumar S; Haviv I; Polyak K, 2011. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.  PLoS Genet 7(4):e1001369

Marotta LL; Almendro V; Marusyk A; Shipitsin M; Schemme J; Walker SR; Bloushtain-Qimron N; Kim JJ; Choudhury SA; Maruyama R; Wu Z; Gönen M; Mulvey LA; Bessarabova MO; Huh SJ; Silver SJ; Kim SY; Park SY; Lee HE; Anderson KS; Richardson AL; Nikolskaya T; Nikolsky Y; Liu XS; Root DE; Hahn WC; Frank DA; Polyak K, 2011. The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors.  J Clin Invest 121(7):2723-35

Park SY; Lee HE; Li H; Shipitsin M; Gelman R; Polyak K, 2010. Heterogeneity for stem cell-related markers according to tumor subtype and histologic stage in breast cancer.  Clin Cancer Res 16(3):876-87

Lauring J; Cosgrove DP; Fontana S; Gustin JP; Konishi H; Abukhdeir AM; Garay JP; Mohseni M; Wang GM; Higgins MJ; Gorkin D; Reis M; Vogelstein B; Polyak K; Cowherd M; Buckhaults PJ; Park BH, 2010. Knock in of the AKT1 E17K mutation in human breast epithelial cells does not recapitulate oncogenic PIK3CA mutations.  Oncogene 29(16):2337-45

Marusyk A; Polyak K, 2010. Tumor heterogeneity: causes and consequences.  Biochim Biophys Acta 1805(1):105-17

Petersen OW; Polyak K, 2010. Stem cells in the human breast.  Cold Spring Harb Perspect Biol 2(5):a003160

Park SY; Gönen M; Kim HJ; Michor F; Polyak K, 2010. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype.  J Clin Invest 120(2):636-44

Miron A; Varadi M; Carrasco D; Li H; Luongo L; Kim HJ; Park SY; Cho EY; Lewis G; Kehoe S; Iglehart JD; Dillon D; Allred DC; Macconaill L; Gelman R; Polyak K, 2010. PIK3CA mutations in in situ and invasive breast carcinomas.  Cancer Res 70(14):5674-8

Polyak K, 2010. Molecular markers for the diagnosis and management of ductal carcinoma in situ.  J Natl Cancer Inst Monogr 2010(41):210-3

Wu ZJ; Meyer CA; Choudhury S; Shipitsin M; Maruyama R; Bessarabova M; Nikolskaya T; Sukumar S; Schwartzman A; Liu JS; Polyak K; Liu XS, 2010. Gene expression profiling of human breast tissue samples using SAGE-Seq.  Genome Res 20(12):1730-9

Polyak K, 2010. Going small is the new big.  Nat Methods 7(8):597, 599-600

Michor F; Polyak K, 2010. The origins and implications of intratumor heterogeneity.  Cancer Prev Res (Phila) 3(11):1361-4

Irie HY; Shrestha Y; Selfors LM; Frye F; Iida N; Wang Z; Zou L; Yao J; Lu Y; Epstein CB; Natesan S; Richardson AL; Polyak K; Mills GB; Hahn WC; Brugge JS, 2010. PTK6 regulates IGF-1-induced anchorage-independent survival.  PLoS One 5(7):e11729

Polyak K; Kalluri R, 2010. The role of the microenvironment in mammary gland development and cancer.  Cold Spring Harb Perspect Biol 2(11):a003244

Haviv I; Polyak K; Qiu W; Hu M; Campbell I, 2009. Origin of carcinoma associated fibroblasts.  Cell Cycle 8(4):589-95

Hu M; Peluffo G; Chen H; Gelman R; Schnitt S; Polyak K, 2009. Role of COX-2 in epithelial-stromal cell interactions and progression of ductal carcinoma in situ of the breast.  Proc Natl Acad Sci U S A 106(9):3372-7

Marotta LL; Polyak K, 2009. Cancer stem cells: a model in the making.  Curr Opin Genet Dev 19(1):44-50

Polyak K; Haviv I; Campbell IG, 2009. Co-evolution of tumor cells and their microenvironment.  Trends Genet 25(1):30-8

Bloushtain-Qimron N; Yao J; Shipitsin M; Maruyama R; Polyak K, 2009. Epigenetic patterns of embryonic and adult stem cells.  Cell Cycle 8(6):809-17

Anderson KS; Wong J; Polyak K; Aronzon D; Enerbäck C, 2009. Detection of psoriasin/S100A7 in the sera of patients with psoriasis.  Br J Dermatol 160(2):325-32

Zhang Q; Gu J; Li L; Liu J; Luo B; Cheung HW; Boehm JS; Ni M; Geisen C; Root DE; Polyak K; Brown M; Richardson AL; Hahn WC; Kaelin WG Jr; Bommi-Reddy A, 2009. Control of cyclin D1 and breast tumorigenesis by the EglN2 prolyl hydroxylase.  Cancer Cell 16(5):413-24

Polyak K; Weinberg RA, 2009. Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits.  Nat Rev Cancer 9(4):265-73

Behbod F; Kittrell FS; LaMarca H; Edwards D; Kerbawy S; Heestand JC; Young E; Mukhopadhyay P; Yeh HW; Allred DC; Hu M; Polyak K; Rosen JM; Medina D, 2009. An intraductal human-in-mouse transplantation model mimics the subtypes of ductal carcinoma in situ.  Breast Cancer Res 11(5):R66

MacConaill LE; Campbell CD; Kehoe SM; Bass AJ; Hatton C; Niu L; Davis M; Yao K; Hanna M; Mondal C; Luongo L; Emery CM; Baker AC; Philips J; Goff DJ; Fiorentino M; Rubin MA; Polyak K; Chan J; Wang Y; Fletcher JA; Santagata S; Corso G; Roviello F; Shivdasani R; Kieran MW; Ligon KL; Stiles CD; Hahn WC; Meyerson ML; Garraway LA, 2009. Profiling critical cancer gene mutations in clinical tumor samples.  PLoS One 4(11):e7887

Campbell I; Polyak K; Haviv I, 2009. Clonal mutations in the cancer-associated fibroblasts: the case against genetic coevolution.  Cancer Res 69(17):6765-8; discussion 6769

Snyder EL; Bailey D; Shipitsin M; Polyak K; Loda M, 2009. Identification of CD44v6(+)/CD24- breast carcinoma cells in primary human tumors by quantum dot-conjugated antibodies.  Lab Invest 89(8):857-66

Qiu W; Hu M; Sridhar A; Opeskin K; Fox S; Shipitsin M; Trivett M; Thompson ER; Ramakrishna M; Gorringe KL; Polyak K; Haviv I; Campbell IG, 2008. No evidence of clonal somatic genetic alterations in cancer-associated fibroblasts from human breast and ovarian carcinomas.  Nat Genet 40(5):650-5

Campbell IG; Qiu W; Polyak K; Haviv I, 2008. Breast-cancer stromal cells with TP53 mutations.  N Engl J Med 358(15):1634-5; author reply 1636

Shipitsin M; Polyak K, 2008. The cancer stem cell hypothesis: in search of definitions, markers, and relevance.  Lab Invest 88(5):459-63

Hu M; Yao J; Carroll DK; Weremowicz S; Chen H; Carrasco D; Richardson A; Violette S; Nikolskaya T; Nikolsky Y; Bauerlein EL; Hahn WC; Gelman RS; Allred C; Bissell MJ; Schnitt S; Polyak K, 2008. Regulation of in situ to invasive breast carcinoma transition.  Cancer Cell 13(5):394-406

Zhao X; Goswami M; Pokhriyal N; Ma H; Du H; Yao J; Victor TA; Polyak K; Sturgis CD; Band H; Band V, 2008. Cyclooxygenase-2 expression during immortalization and breast cancer progression.  Cancer Res 68(2):467-75

Polyak K, 2008. Is breast tumor progression really linear?  Clin Cancer Res 14(2):339-41

Paruchuri V; Prasad A; McHugh K; Bhat HK; Polyak K; Ganju RK, 2008. S100A7-downregulation inhibits epidermal growth factor-induced signaling in breast cancer cells and blocks osteoclast formation.  PLoS One 3(3):e1741

Hu M; Polyak K, 2008. Microenvironmental regulation of cancer development.  Curr Opin Genet Dev 18(1):27-34

Nikolsky Y; Sviridov E; Yao J; Dosymbekov D; Ustyansky V; Kaznacheev V; Dezso Z; Mulvey L; Macconaill LE; Winckler W; Serebryiskaya T; Nikolskaya T; Polyak K, 2008. Genome-wide functional synergy between amplified and mutated genes in human breast cancer.  Cancer Res 68(22):9532-40

Hu M; Polyak K, 2008. Molecular characterisation of the tumour microenvironment in breast cancer.  Eur J Cancer 44(18):2760-5

Bloushtain-Qimron N; Yao J; Snyder EL; Shipitsin M; Campbell LL; Mani SA; Hu M; Chen H; Ustyansky V; Antosiewicz JE; Argani P; Halushka MK; Thomson JA; Pharoah P; Porgador A; Sukumar S; Parsons R; Richardson AL; Stampfer MR; Gelman RS; Nikolskaya T; Nikolsky Y; Polyak K, 2008. Cell type-specific DNA methylation patterns in the human breast.  Proc Natl Acad Sci U S A 105(37):14076-81

Cao D; Polyak K; Halushka MK; Nassar H; Kouprina N; Iacobuzio-Donahue C; Wu X; Sukumar S; Hicks J; De Marzo A; Argani P, 2008. Serial analysis of gene expression of lobular carcinoma in situ identifies down regulation of claudin 4 and overexpression of matrix metalloproteinase 9.  Breast Cancer Res 10(5):R91

Mani SA; Guo W; Liao MJ; Eaton EN; Ayyanan A; Zhou AY; Brooks M; Reinhard F; Zhang CC; Shipitsin M; Campbell LL; Polyak K; Brisken C; Yang J; Weinberg RA, 2008. The epithelial-mesenchymal transition generates cells with properties of stem cells.  Cell 133(4):704-15

Kleer CG; Bloushtain-Qimron N; Chen YH; Carrasco D; Hu M; Yao J; Kraeft SK; Collins LC; Sabel MS; Argani P; Gelman R; Schnitt SJ; Krop IE; Polyak K, 2008. Epithelial and stromal cathepsin K and CXCL14 expression in breast tumor progression.  Clin Cancer Res 14(17):5357-67

2008. Moving AHEAD with an international human epigenome project.  Nature 454(7205):711-5

Boehm JS; Zhao JJ; Yao J; Kim SY; Firestein R; Dunn IF; Sjostrom SK; Garraway LA; Weremowicz S; Richardson AL; Greulich H; Stewart CJ; Mulvey LA; Shen RR; Ambrogio L; Hirozane-Kishikawa T; Hill DE; Vidal M; Meyerson M; Grenier JK; Hinkle G; Root DE; Roberts TM; Lander ES; Polyak K; Hahn WC, 2007. Integrative genomic approaches identify IKBKE as a breast cancer oncogene.  Cell 129(6):1065-79

Shipitsin M; Campbell LL; Argani P; Weremowicz S; Bloushtain-Qimron N; Yao J; Nikolskaya T; Serebryiskaya T; Beroukhim R; Hu M; Halushka MK; Sukumar S; Parker LM; Anderson KS; Harris LN; Garber JE; Richardson AL; Schnitt SJ; Nikolsky Y; Gelman RS; Polyak K, 2007. Molecular definition of breast tumor heterogeneity.  Cancer Cell 11(3):259-73

Campbell LL; Polyak K, 2007. Breast tumor heterogeneity: cancer stem cells or clonal evolution?  Cell Cycle 6(19):2332-8

Blackshaw S; St Croix B; Polyak K; Kim JB; Cai L, 2007. Serial analysis of gene expression (SAGE): experimental method and data analysis.  Curr Protoc Hum Genet Chapter 11:Unit 11.7

Polyak K, 2007. Breast cancer stem cells: a case of mistaken identity?  Stem Cell Rev 3(2):107-9

Blackshaw S; Croix BS; Polyak K; Kim JB; Cai L, 2007. Serial analysis of gene expression (SAGE): experimental method and data analysis.  Curr Protoc Mol Biol Chapter 25:Unit 25B.6

Polyak K, 2007. Breast cancer: origins and evolution.  J Clin Invest 117(11):3155-63

Wood LD; Parsons DW; Jones S; Lin J; Sjöblom T; Leary RJ; Shen D; Boca SM; Barber T; Ptak J; Silliman N; Szabo S; Dezso Z; Ustyanksky V; Nikolskaya T; Nikolsky Y; Karchin R; Wilson PA; Kaminker JS; Zhang Z; Croshaw R; Willis J; Dawson D; Shipitsin M; Willson JK; Sukumar S; Polyak K; Park BH; Pethiyagoda CL; Pant PV; Ballinger DG; Sparks AB; Hartigan J; Smith DR; Suh E; Papadopoulos N; Buckhaults P; Markowitz SD; Parmigiani G; Kinzler KW; Velculescu VE; Vogelstein B, 2007. The genomic landscapes of human breast and colorectal cancers.  Science 318(5853):1108-13

Karnoub AE; Dash AB; Vo AP; Sullivan A; Brooks MW; Bell GW; Richardson AL; Polyak K; Tubo R; Weinberg RA, 2007. Mesenchymal stem cells within tumour stroma promote breast cancer metastasis.  Nature 449(7162):557-63

Porter D; Yao J; Polyak K, 2006. SAGE and related approaches for cancer target identification.  Drug Discov Today 11(3-4):110-8

Polyak K; Hahn WC, 2006. Roots and stems: stem cells in cancer.  Nat Med 12(3):296-300

Yao J; Weremowicz S; Feng B; Gentleman RC; Marks JR; Gelman R; Brennan C; Polyak K, 2006. Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression.  Cancer Res 66(8):4065-78

Polyak K, 2006. Pregnancy and breast cancer: the other side of the coin.  Cancer Cell 9(3):151-3

Polyak K, 2006. The p27Kip1 tumor suppressor gene: Still a suspect or proven guilty?  Cancer Cell 10(5):352-4

Hu M; Yao J; Polyak K, 2006. Methylation-specific digital karyotyping.  Nat Protoc 1(3):1621-36

Hu M; Polyak K, 2006. Serial analysis of gene expression.  Nat Protoc 1(4):1743-60

Hlavay J; Polyák K, 2005. Determination of surface properties of iron hydroxide-coated alumina adsorbent prepared for removal of arsenic from drinking water.  J Colloid Interface Sci 284(1):71-7

Peters BA; Diaz LA; Polyak K; Meszler L; Romans K; Guinan EC; Antin JH; Myerson D; Hamilton SR; Vogelstein B; Kinzler KW; Lengauer C, 2005. Contribution of bone marrow-derived endothelial cells to human tumor vasculature.  Nat Med 11(3):261-2

Hu M; Yao J; Cai L; Bachman KE; van den Brûle F; Velculescu V; Polyak K, 2005. Distinct epigenetic changes in the stromal cells of breast cancers.  Nat Genet 37(8):899-905

Polyak K; Hu M, 2005. Do myoepithelial cells hold the key for breast tumor progression?  J Mammary Gland Biol Neoplasia 10(3):231-47

Carlsson H; Yhr M; Petersson S; Collins N; Polyak K; Enerbäck C, 2005. Psoriasin (S100A7) and calgranulin-B (S100A9) induction is dependent on reactive oxygen species and is downregulated by Bcl-2 and antioxidants.  Cancer Biol Ther 4(9):998-1005

Krop I; März A; Carlsson H; Li X; Bloushtain-Qimron N; Hu M; Gelman R; Sabel MS; Schnitt S; Ramaswamy S; Kleer CG; Enerbäck C; Polyak K, 2005. A putative role for psoriasin in breast tumor progression.  Cancer Res 65(24):11326-34

Krop I; Parker MT; Bloushtain-Qimron N; Porter D; Gelman R; Sasaki H; Maurer M; Terry MB; Parsons R; Polyak K, 2005. HIN-1, an inhibitor of cell growth, invasion, and AKT activation.  Cancer Res 65(21):9659-69

Mehrotra J; Vali M; McVeigh M; Kominsky SL; Fackler MJ; Lahti-Domenici J; Polyak K; Sacchi N; Garrett-Mayer E; Argani P; Sukumar S, 2004. Very high frequency of hypermethylated genes in breast cancer metastasis to the bone, brain, and lung.  Clin Cancer Res 10(9):3104-9

Mehrotra J; Ganpat MM; Kanaan Y; Fackler MJ; McVeigh M; Lahti-Domenici J; Polyak K; Argani P; Naab T; Garrett E; Parmigiani G; Broome C; Sukumar S, 2004. Estrogen receptor/progesterone receptor-negative breast cancers of young African-American women have a higher frequency of methylation of multiple genes than those of Caucasian women.  Clin Cancer Res 10(6):2052-7

Burstein HJ; Polyak K; Wong JS; Lester SC; Kaelin CM, 2004. Ductal carcinoma in situ of the breast.  N Engl J Med 350(14):1430-41

Allinen M; Beroukhim R; Cai L; Brennan C; Lahti-Domenici J; Huang H; Porter D; Hu M; Chin L; Richardson A; Schnitt S; Sellers WR; Polyak K, 2004. Molecular characterization of the tumor microenvironment in breast cancer.  Cancer Cell 6(1):17-32

Yao J; Polyak K, 2004. EMSY links breast cancer gene 2 to the 'Royal Family'.  Breast Cancer Res 6(5):201-3

Krop I; Player A; Tablante A; Taylor-Parker M; Lahti-Domenici J; Fukuoka J; Batra SK; Papadopoulos N; Richards WG; Sugarbaker DJ; Wright RL; Shim J; Stamey TA; Sellers WR; Loda M; Meyerson M; Hruban R; Jen J; Polyak K, 2004. Frequent HIN-1 promoter methylation and lack of expression in multiple human tumor types.  Mol Cancer Res 2(9):489-94

DePinho RA; Polyak K, 2004. Cancer chromosomes in crisis.  Nat Genet 36(9):932-4

Buckhaults P; Zhang Z; Chen YC; Wang TL; St Croix B; Saha S; Bardelli A; Morin PJ; Polyak K; Hruban RH; Velculescu VE; Shih IeM, 2003. Identifying tumor origin using a gene expression-based classification map.  Cancer Res 63(14):4144-9

Porter D; Weremowicz S; Chin K; Seth P; Keshaviah A; Lahti-Domenici J; Bae YK; Monitto CL; Merlos-Suarez A; Chan J; Hulette CM; Richardson A; Morton CC; Marks J; Duyao M; Hruban R; Gabrielson E; Gelman R; Polyak K, 2003. A neural survival factor is a candidate oncogene in breast cancer.  Proc Natl Acad Sci U S A 100(19):10931-6

Krop I; Maguire P; Lahti-Domenici J; Lodeiro G; Richardson A; Johannsdottir HK; Nevanlinna H; Borg A; Gelman R; Barkardottir RB; Lindblom A; Polyak K, 2003. Lack of HIN-1 methylation in BRCA1-linked and "BRCA1-like" breast tumors.  Cancer Res 63(9):2024-7

Porter D; Lahti-Domenici J; Keshaviah A; Bae YK; Argani P; Marks J; Richardson A; Cooper A; Strausberg R; Riggins GJ; Schnitt S; Gabrielson E; Gelman R; Polyak K, 2003. Molecular markers in ductal carcinoma in situ of the breast.  Mol Cancer Res 1(5):362-75

Porter D; Polyak K, 2003. Cancer target discovery using SAGE.  Expert Opin Ther Targets 7(6):759-69

Fackler MJ; McVeigh M; Evron E; Garrett E; Mehrotra J; Polyak K; Sukumar S; Argani P, 2003. DNA methylation of RASSF1A, HIN-1, RAR-beta, Cyclin D2 and Twist in in situ and invasive lobular breast carcinoma.  Int J Cancer 107(6):970-5

Polyak K, 2003. The hairy powers of oncogenes: from biological function to cancer therapy.  Cancer Biol Ther 2(5):592-4

Seth P; Krop I; Porter D; Polyak K, 2002. Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression).  Oncogene 21(5):836-43

Polyak K, 2002. Molecular alterations in ductal carcinoma in situ of the breast.  Curr Opin Oncol 14(1):92-6

Enerbäck C; Porter DA; Seth P; Sgroi D; Gaudet J; Weremowicz S; Morton CC; Schnitt S; Pitts RL; Stampl J; Barnhart K; Polyak K, 2002. Psoriasin expression in mammary epithelial cells in vitro and in vivo.  Cancer Res 62(1):43-7

Boon K; Osorio EC; Greenhut SF; Schaefer CF; Shoemaker J; Polyak K; Morin PJ; Buetow KH; Strausberg RL; De Souza SJ; Riggins GJ, 2002. An anatomy of normal and malignant gene expression.  Proc Natl Acad Sci U S A 99(17):11287-92

Porter D; Lahti-Domenici J; Torres-Arzayus M; Chin L; Polyak K, 2002. Expression of high in normal-1 (HIN-1) and uteroglobin related protein-1 (UGRP-1) in adult and developing tissues.  Mech Dev 114(1-2):201-4

Polyak K, 2002. Breast cancer gene discovery.  Expert Rev Mol Med 4(18):1-18

Polyak K, 2002. Is p53 a breast cancer gene?  Cancer Biol Ther 1(1):37-8

Seth P; Porter D; Lahti-Domenici J; Geng Y; Richardson A; Polyak K, 2002. Cellular and molecular targets of estrogen in normal human breast tissue.  Cancer Res 62(16):4540-4

Polyak K; Riggins GJ, 2001. Gene discovery using the serial analysis of gene expression technique: implications for cancer research.  J Clin Oncol 19(11):2948-58

Hlavay J; Polyák K; Weisz M, 2001. Monitoring of the natural environment by chemical speciation of elements in aerosol and sediment samples.  J Environ Monit 3(1):74-80

Porter DA; Krop IE; Nasser S; Sgroi D; Kaelin CM; Marks JR; Riggins G; Polyak K, 2001. A SAGE (serial analysis of gene expression) view of breast tumor progression.  Cancer Res 61(15):5697-702

Polyák K; Hlavay J, 2001. Chemical fractionation of a fly ash sample by a sequential leaching method.  Fresenius J Anal Chem 371(6):838-42

Krop IE; Sgroi D; Porter DA; Lunetta KL; LeVangie R; Seth P; Kaelin CM; Rhei E; Bosenberg M; Schnitt S; Marks JR; Pagon Z; Belina D; Razumovic J; Polyak K, 2001. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells.  Proc Natl Acad Sci U S A 98(17):9796-801

Polyak K, 2001. On the birth of breast cancer.  Biochim Biophys Acta 1552(1):1-13

Flatt PM; Polyak K; Tang LJ; Scatena CD; Westfall MD; Rubinstein LA; Yu J; Kinzler KW; Vogelstein B; Hill DE; Pietenpol JA, 2000. p53-dependent expression of PIG3 during proliferation, genotoxic stress, and reversible growth arrest.  Cancer Lett 156(1):63-72

Seth P; Lunetta KL; Bell DW; Gray H; Nasser SM; Rhei E; Kaelin CM; Iglehart DJ; Marks JR; Garber JE; Haber DA; Polyak K, 2000. Phenol sulfotransferases: hormonal regulation, polymorphism, and age of onset of breast cancer.  Cancer Res 60(24):6859-63

Hlavay J; Polyák K; Molnár A; Mészáros E, 1999. Development of a monitoring network for the analysis of elements in aerosol samples collected at Lake Balaton.  Acta Biol Hung 50(1-3):89-98

da Costa LT; He TC; Yu J; Sparks AB; Morin PJ; Polyak K; Laken S; Vogelstein B; Kinzler KW, 1999. CDX2 is mutated in a colorectal cancer with normal APC/beta-catenin signaling.  Oncogene 18(35):5010-4

Velculescu VE; Madden SL; Zhang L; Lash AE; Yu J; Rago C; Lal A; Wang CJ; Beaudry GA; Ciriello KM; Cook BP; Dufault MR; Ferguson AT; Gao Y; He TC; Hermeking H; Hiraldo SK; Hwang PM; Lopez MA; Luderer HF; Mathews B; Petroziello JM; Polyak K; Zawel L; Kinzler KW, 1999. Analysis of human transcriptomes.  Nat Genet 23(4):387-8

Lal A; Lash AE; Altschul SF; Velculescu V; Zhang L; McLendon RE; Marra MA; Prange C; Morin PJ; Polyak K; Papadopoulos N; Vogelstein B; Kinzler KW; Strausberg RL; Riggins GJ, 1999. A public database for gene expression in human cancers.  Cancer Res 59(21):5403-7

Herman JG; Umar A; Polyak K; Graff JR; Ahuja N; Issa JP; Markowitz S; Willson JK; Hamilton SR; Kinzler KW; Kane MF; Kolodner RD; Vogelstein B; Kunkel TA; Baylin SB, 1998. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma.  Proc Natl Acad Sci U S A 95(12):6870-5

Polyak K; Li Y; Zhu H; Lengauer C; Willson JK; Markowitz SD; Trush MA; Kinzler KW; Vogelstein B, 1998. Somatic mutations of the mitochondrial genome in human colorectal tumours.  Nat Genet 20(3):291-3

Polyak K; Wu TT; Hamilton SR; Kinzler KW; Vogelstein B, 1997. Less death in the dying.  Cell Death Differ 4(3):242-6

Hermeking H; Lengauer C; Polyak K; He TC; Zhang L; Thiagalingam S; Kinzler KW; Vogelstein B, 1997. 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression.  Mol Cell 1(1):3-11

Polyak K; Xia Y; Zweier JL; Kinzler KW; Vogelstein B, 1997. A model for p53-induced apoptosis.  Nature 389(6648):300-5

Leach FS; Polyak K; Burrell M; Johnson KA; Hill D; Dunlop MG; Wyllie AH; Peltomaki P; de la Chapelle A; Hamilton SR; Kinzler KW; Vogelstein B, 1996. Expression of the human mismatch repair gene hMSH2 in normal and neoplastic tissues.  Cancer Res 56(2):235-40

Polyak K, 1996. Negative regulation of cell growth by TGF beta.  Biochim Biophys Acta 1242(3):185-99

Fero ML; Rivkin M; Tasch M; Porter P; Carow CE; Firpo E; Polyak K; Tsai LH; Broudy V; Perlmutter RM; Kaushansky K; Roberts JM, 1996. A syndrome of multiorgan hyperplasia with features of gigantism, tumorigenesis, and female sterility in p27(Kip1)-deficient mice.  Cell 85(5):733-44

Polyak K; Waldman T; He TC; Kinzler KW; Vogelstein B, 1996. Genetic determinants of p53-induced apoptosis and growth arrest.  Genes Dev 10(15):1945-52

Polyak K; Hamilton SR; Vogelstein B; Kinzler KW, 1996. Early alteration of cell-cycle-regulated gene expression in colorectal neoplasia.  Am J Pathol 149(2):381-7

Massagué J; Polyak K, 1995. Mammalian antiproliferative signals and their targets.  Curr Opin Genet Dev 5(1):91-6

Ponce-Castañeda MV; Lee MH; Latres E; Polyak K; Lacombe L; Montgomery K; Mathew S; Krauter K; Sheinfeld J; Massague J, 1995. p27Kip1: chromosomal mapping to 12p12-12p13.1 and absence of mutations in human tumors.  Cancer Res 55(6):1211-4

Koff A; Polyak K, 1995. p27KIP1, an inhibitor of cyclin-dependent kinases.  Prog Cell Cycle Res 1:141-7

Jeffrey PD; Russo AA; Polyak K; Gibbs E; Hurwitz J; Massagué J; Pavletich NP, 1995. Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex.  Nature 376(6538):313-20

Reynisdóttir I; Polyak K; Iavarone A; Massagué J, 1995. Kip/Cip and Ink4 Cdk inhibitors cooperate to induce cell cycle arrest in response to TGF-beta.  Genes Dev 9(15):1831-45

Polyák K; Bódog I; Hlavay J, 1994. Determination of chemical species of selected trace elements in fly ash.  Talanta 41(7):1151-9

Roberts JM; Koff A; Polyak K; Firpo E; Collins S; Ohtsubo M; Massagué J, 1994. Cyclins, Cdks, and cyclin kinase inhibitors.  Cold Spring Harb Symp Quant Biol 59:31-8

Polyak K; Kato JY; Solomon MJ; Sherr CJ; Massague J; Roberts JM; Koff A, 1994. p27Kip1, a cyclin-Cdk inhibitor, links transforming growth factor-beta and contact inhibition to cell cycle arrest.  Genes Dev 8(1):9-22

Nourse J; Firpo E; Flanagan WM; Coats S; Polyak K; Lee MH; Massague J; Crabtree GR; Roberts JM, 1994. Interleukin-2-mediated elimination of the p27Kip1 cyclin-dependent kinase inhibitor prevented by rapamycin.  Nature 372(6506):570-3

Kato JY; Matsuoka M; Polyak K; Massagué J; Sherr CJ, 1994. Cyclic AMP-induced G1 phase arrest mediated by an inhibitor (p27Kip1) of cyclin-dependent kinase 4 activation.  Cell 79(3):487-96

Polyak K; Lee MH; Erdjument-Bromage H; Koff A; Roberts JM; Tempst P; Massagué J, 1994. Cloning of p27Kip1, a cyclin-dependent kinase inhibitor and a potential mediator of extracellular antimitogenic signals.  Cell 78(1):59-66

Koff A; Ohtsuki M; Polyak K; Roberts JM; Massagué J, 1993. Negative regulation of G1 in mammalian cells: inhibition of cyclin E-dependent kinase by TGF-beta.  Science 260(5107):536-9

Gyuris J; Dencsö L; Polyák K; Duda E, 1991. Complex interaction of yeast nuclear proteins with the enhancer/promoter region of SV40.  Curr Genet 20(5):359-63

Galgóczy J; Polyák K; Novák EK, 1976. The macroconidial septum of some dermatophyton species.  Acta Microbiol Acad Sci Hung 23(1):7-13

Halász A; Pungor E; Polyák K, 1971. Properties and analytical applications of the heteropolymolybdates of phosphorus, arsenic, silicon and germanium-III Examination of two- and three-component systems without separation.  Talanta 18(6):577-86

Halász A; Polyák K; Pungor E, 1971. Properties and analytical applications of the heteropolymolybdates of phosphorus, arsenic, silicon and germanium-IV Determination of phosphomolybdic and silicomolybdic acids via the molybdenum content, with phenylfluorone.  Talanta 18(7):691-6

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Penney KL; Sinnott JA; Tyekucheva S; Gerke T; Shui IM; Kraft P; Sesso HD; Freedman ML; Loda M; Mucci LA; Stampfer MJ, 2015. Association of prostate cancer risk variants with gene expression in normal and tumor tissue.  Cancer Epidemiol Biomarkers Prev 24(1):255-60

Li Q; Stram A; Chen C; Kar S; Gayther S; Pharoah P; Haiman C; Stranger B; Kraft P; Freedman ML, 2014. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.  Hum Mol Genet 23(19):5294-302

Al Olama AA; Kote-Jarai Z; Berndt SI; Conti DV; Schumacher F; Han Y; Benlloch S; Hazelett DJ; Wang Z; Saunders E; Leongamornlert D; Lindstrom S; Jugurnauth-Little S; Dadaev T; Tymrakiewicz M; Stram DO; Rand K; Wan P; Stram A; Sheng X; Pooler LC; Park K; Xia L; Tyrer J; Kolonel LN; Le Marchand L; Hoover RN; Machiela MJ; Yeager M; Burdette L; Chung CC; Hutchinson A; Yu K; Goh C; Ahmed M; Govindasami K; Guy M; Tammela TL; Auvinen A; Wahlfors T; Schleutker J; Visakorpi T; Leinonen KA; Xu J; Aly M; Donovan J; Travis RC; Key TJ; Siddiq A; Canzian F; Khaw KT; Takahashi A; Kubo M; Pharoah P; Pashayan N; Weischer M; Nordestgaard BG; Nielsen SF; Klarskov P; Røder MA; Iversen P; Thibodeau SN; McDonnell SK; Schaid DJ; Stanford JL; Kolb S; Holt S; Knudsen B; Coll AH; Gapstur SM; Diver WR; Stevens VL; Maier C; Luedeke M; Herkommer K; Rinckleb AE; Strom SS; Pettaway C; Yeboah ED; Tettey Y; Biritwum RB; Adjei AA; Tay E; Truelove A; Niwa S; Chokkalingam AP; Cannon-Albright L; Cybulski C; Wokołorczyk D; Kluźniak W; Park J; Sellers T; Lin HY; Isaacs WB; Partin AW; Brenner H; Dieffenbach AK; Stegmaier C; Chen C; Giovannucci EL; Ma J; Stampfer M; Penney KL; Mucci L; John EM; Ingles SA; Kittles RA; Murphy AB; Pandha H; Michael A; Kierzek AM; Blot W; Signorello LB; Zheng W; Albanes D; Virtamo J; Weinstein S; Nemesure B; Carpten J; Leske C; Wu SY; Hennis A; Kibel AS; Rybicki BA; Neslund-Dudas C; Hsing AW; Chu L; Goodman PJ; Klein EA; Zheng SL; Batra J; Clements J; Spurdle A; Teixeira MR; Paulo P; Maia S; Slavov C; Kaneva R; Mitev V; Witte JS; Casey G; Gillanders EM; Seminara D; Riboli E; Hamdy FC; Coetzee GA; Li Q; Freedman ML; Hunter DJ; Muir K; Gronberg H; Neal DE; Southey M; Giles GG; Severi G; Cook MB; Nakagawa H; Wiklund F; Kraft P; Chanock SJ; Henderson BE; Easton DF; Eeles RA; Haiman CA, 2014. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.  Nat Genet 46(10):1103-9

Schutz FA; Pomerantz MM; Gray KP; Atkins MB; Rosenberg JE; Hirsch MS; McDermott DF; Lampron ME; Lee GS; Signoretti S; Kantoff PW; Freedman ML; Choueiri TK, 2013. Single nucleotide polymorphisms and risk of recurrence of renal-cell carcinoma: a cohort study.  Lancet Oncol 14(1):81-7

Li Q; Seo JH; Stranger B; McKenna A; Pe'er I; Laframboise T; Brown M; Tyekucheva S; Freedman ML, 2013. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.  Cell 152(3):633-41

Seo JH; Li Q; Fatima A; Eklund A; Szallasi Z; Polyak K; Richardson AL; Freedman ML, 2013. Deconvoluting complex tissues for expression quantitative trait locus-based analyses.  Philos Trans R Soc Lond B Biol Sci 368(1620):20120363

Nan H; Morikawa T; Suuriniemi M; Imamura Y; Werner L; Kuchiba A; Yamauchi M; Hunter DJ; Kraft P; Giovannucci EL; Fuchs CS; Ogino S; Freedman ML; Chan AT, 2013. Aspirin use, 8q24 single nucleotide polymorphism rs6983267, and colorectal cancer according to CTNNB1 alterations.  J Natl Cancer Inst 105(24):1852-61

Grisanzio C; Werner L; Takeda D; Awoyemi BC; Pomerantz MM; Yamada H; Sooriakumaran P; Robinson BD; Leung R; Schinzel AC; Mills I; Ross-Adams H; Neal DE; Kido M; Yamamoto T; Petrozziello G; Stack EC; Lis R; Kantoff PW; Loda M; Sartor O; Egawa S; Tewari AK; Hahn WC; Freedman ML, 2012. Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis.  Proc Natl Acad Sci U S A 109(28):11252-7

Pomerantz MM; Werner L; Xie W; Regan MM; Lee GS; Sun T; Evan C; Petrozziello G; Nakabayashi M; Oh WK; Kantoff PW; Freedman ML, 2011. Association of prostate cancer risk Loci with disease aggressiveness and prostate cancer-specific mortality.  Cancer Prev Res (Phila) 4(5):719-28

Sun T; Mary LG; Oh WK; Freedman ML; Pomerantz M; Pienta KJ; Kantoff PW, 2011. Inherited variants in the chemokine CCL2 gene and prostate cancer aggressiveness in a Caucasian cohort.  Clin Cancer Res 17(6):1546-52

Freedman ML; Monteiro AN; Gayther SA; Coetzee GA; Risch A; Plass C; Casey G; De Biasi M; Carlson C; Duggan D; James M; Liu P; Tichelaar JW; Vikis HG; You M; Mills IG, 2011. Principles for the post-GWAS functional characterization of cancer risk loci.  Nat Genet 43(6):513-8

Sun T; Oh WK; Jacobus S; Regan M; Pomerantz M; Freedman ML; Lee GS; Kantoff PW, 2011. The impact of common genetic variations in genes of the sex hormone metabolic pathways on steroid hormone levels and prostate cancer aggressiveness.  Cancer Prev Res (Phila) 4(12):2044-50

Pomerantz MM; Freedman ML, 2011. The genetics of cancer risk.  Cancer J 17(6):416-22

Sun T; Lee GS; Werner L; Pomerantz M; Oh WK; Kantoff PW; Freedman ML, 2010. Inherited variations in AR, ESR1, and ESR2 genes are not associated with prostate cancer aggressiveness or with efficacy of androgen deprivation therapy.  Cancer Epidemiol Biomarkers Prev 19(7):1871-8

Ahmadiyeh N; Pomerantz MM; Grisanzio C; Herman P; Jia L; Almendro V; He HH; Brown M; Liu XS; Davis M; Caswell JL; Beckwith CA; Hills A; Macconaill L; Coetzee GA; Regan MM; Freedman ML, 2010. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC.  Proc Natl Acad Sci U S A 107(21):9742-6

Grisanzio C; Freedman ML, 2010. Chromosome 8q24-Associated Cancers and MYC.  Genes Cancer 1(6):555-9

Nguyen PL; Ma J; Chavarro JE; Freedman ML; Lis R; Fedele G; Fiore C; Qiu W; Fiorentino M; Finn S; Penney KL; Eisenstein A; Schumacher FR; Mucci LA; Stampfer MJ; Giovannucci E; Loda M, 2010. Fatty acid synthase polymorphisms, tumor expression, body mass index, prostate cancer risk, and survival.  J Clin Oncol 28(25):3958-64

Sun T; Lee GS; Oh WK; Pomerantz M; Yang M; Xie W; Freedman ML; Kantoff PW, 2010. Single-nucleotide polymorphisms in p53 pathway and aggressiveness of prostate cancer in a Caucasian population.  Clin Cancer Res 16(21):5244-51

Pomerantz MM; Freedman ML, 2010. Genetics of prostate cancer risk.  Mt Sinai J Med 77(6):643-54

Pomerantz MM; Shrestha Y; Flavin RJ; Regan MM; Penney KL; Mucci LA; Stampfer MJ; Hunter DJ; Chanock SJ; Schafer EJ; Chan JA; Tabernero J; Baselga J; Richardson AL; Loda M; Oh WK; Kantoff PW; Hahn WC; Freedman ML, 2010. Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis.  PLoS Genet 6(11):e1001204

Pomerantz MM; Beckwith CA; Regan MM; Wyman SK; Petrovics G; Chen Y; Hawksworth DJ; Schumacher FR; Mucci L; Penney KL; Stampfer MJ; Chan JA; Ardlie KG; Fritz BR; Parkin RK; Lin DW; Dyke M; Herman P; Lee S; Oh WK; Kantoff PW; Tewari M; McLeod DG; Srivastava S; Freedman ML, 2009. Evaluation of the 8q24 prostate cancer risk locus and MYC expression.  Cancer Res 69(13):5568-74

Pomerantz MM; Ahmadiyeh N; Jia L; Herman P; Verzi MP; Doddapaneni H; Beckwith CA; Chan JA; Hills A; Davis M; Yao K; Kehoe SM; Lenz HJ; Haiman CA; Yan C; Henderson BE; Frenkel B; Barretina J; Bass A; Tabernero J; Baselga J; Regan MM; Manak JR; Shivdasani R; Coetzee GA; Freedman ML, 2009. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer.  Nat Genet 41(8):882-4

Pomerantz MM; Freedman ML; Kantoff PW, 2007. Genetic determinants of prostate cancer risk.  BJU Int 100(2):241-3

Freedman ML; Haiman CA; Patterson N; McDonald GJ; Tandon A; Waliszewska A; Penney K; Steen RG; Ardlie K; John EM; Oakley-Girvan I; Whittemore AS; Cooney KA; Ingles SA; Altshuler D; Henderson BE; Reich D, 2006. Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men.  Proc Natl Acad Sci U S A 103(38):14068-73

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