Publications
2015. Adult body size and physical activity in relation to risk of breast cancer according to tumor androgen receptor status.  Cancer Epidemiol Biomarkers Prev.
,2015. Clonal evolution in cancer: a tale of twisted twines.  Cell Stem Cell 16(1):11-2
,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
,2015. The role of Notch receptors in transcriptional regulation.  J Cell Physiol 230(5):982-8
,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
,2015. Inhibition of Foxp3 in cancer cells induces apoptosis of thyroid cancer cells.  Mol Cell Endocrinol 399:228-34
,2015. Association of prostate cancer risk variants with gene expression in normal and tumor tissue.  Cancer Epidemiol Biomarkers Prev 24(1):255-60
,2015. Measuring residual estrogen receptor availability during fulvestrant therapy in patients with metastatic breast cancer.  Cancer Discov 5(1):72-81
,2015. The use of murine-derived fundic organoids in studies of gastric physiology.  J Physiol.
,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
,2015. Molecular mechanisms underlying the regulation of the MFG-E8 gene promoter activity in physiological and inflammatory conditions.  J Cell Biochem.
,2015. Long-term Results on Weight Loss and Diabetes Remission after Laparoscopic Sleeve Gastrectomy for A Morbidly Obese Chinese Population.  Obes Surg.
,2015. 26th pezcoller symposium: cancers driven by hormones.  Cancer Res 75(7):1177-80
,2015. PLZF, a Tumor Suppressor Genetically Lost in Metastatic Castration Resistant Prostate Cancer, is a Mediator of Resistance to Androgen Deprivation Therapy.  Cancer Res.
,2015. Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells.  Stem Cell Reports 4(2):297-311
,2015. CLK2 Is an Oncogenic Kinase and Splicing Regulator in Breast Cancer.  Cancer Res 75(7):1516-26
,2015. Intestinal vascular endothelial growth factor is decreased in necrotizing enterocolitis.  Neonatology 107(3):191-8
,2015. Big data mining yields novel insights on cancer.  Nat Genet 47(2):103-4
,2014. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.  J Clin Invest 124(4):1636-45
,2014. Radiation redux: reserve intestinal stem cells miss the call to duty.  Cell Stem Cell 14(2):135-6
,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
,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
,2014. Oncogene-like induction of cellular invasion from centrosome amplification.  Nature 510(7503):167-71
,2014. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway.  Nature 508(7494):103-7
,2014. REST and stress resistance in ageing and Alzheimer's disease.  Nature 507(7493):448-54
,2014. Tumor heterogeneity confounds and illuminates: a case for Darwinian tumor evolution.  Nat Med 20(4):344-6
,2014. Sorting out the FACS: a devil in the details.  Cell Rep 6(5):779-81
,2014. Genetic and phenotypic diversity in breast tumor metastases.  Cancer Res 74(5):1338-48
,2014. Cancer: Clonal cooperation.  Nature 508(7494):52-3
,2014. An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer.  Oncogene 33(49):5637-48
,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
,2014. The cross-talk between estrogen receptor and peroxisome proliferator-activated receptor gamma in thyroid cancer.  Cancer 120(1):142-53
,2014. Training of child and adolescent psychiatry fellows in autism and intellectual disability.  Autism 18(4):471-5
,2014. Morphologic change in computed tomography of aldosterone-producing adenoma after radiofrequency ablation.  Can Assoc Radiol J 65(1):86-90
,2014. Canonical nucleosome organization at promoters forms during genome activation.  Genome Res 24(2):260-6
,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
,2014. Emergence of constitutively active estrogen receptor-α mutations in pretreated advanced estrogen receptor-positive breast cancer.  Clin Cancer Res 20(7):1757-67
,2014. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers.  Proc Natl Acad Sci U S A 111(2):705-10
,2014. Targeting Akt3 signaling in triple-negative breast cancer.  Cancer Res 74(3):964-73
,2014. NF-κB activation-induced anti-apoptosis renders HER2-positive cells drug resistant and accelerates tumor growth.  Mol Cancer Res 12(3):408-20
,2014. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity.  Nature 506(7489):511-5
,2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.  Nat Methods 11(1):73-8
,2014. BRCA1 haploinsufficiency for replication stress suppression in primary cells.  Nat Commun 5:5496
,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
,2014. PARP1-driven poly-ADP-ribosylation regulates BRCA1 function in homologous recombination-mediated DNA repair.  Cancer Discov 4(12):1430-47
,2014. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.  Nat Rev Genet 15(11):709-21
,2014. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.  Nat Genet 46(10):1103-9
,2014. Control of steroid receptor dynamics and function by genomic actions of the cochaperones p23 and Bag-1L.  Nucl Recept Signal 12:e005
,2014. MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis.  Cell Stem Cell 15(6):762-74
,2014. Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability.  Cell 159(7):1538-48
,2014. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity.  Cell Rep 9(5):1618-27
,2014. Novel oesophago-gastro-duodenal stenting for gastric leaks after laparoscopic sleeve gastrectomy.  Obes Res Clin Pract.
,2014. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.  Genome Biol 15(12):554
,2014. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells.  Genes Dev 28(16):1827-39
,2014. Tumor heterogeneity: the Lernaean hydra of oncology?  Oncology (Williston Park) 28(9):781-2, 784
,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
,2014. Androgen receptor CAG repeat polymorphism and risk of TMPRSS2:ERG-positive prostate cancer.  Cancer Epidemiol Biomarkers Prev 23(10):2027-31
,2014. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.  Hum Mol Genet 23(19):5294-302
,2014. Indian Hedgehog mediates gastrin-induced proliferation in stomach of adult mice.  Gastroenterology 147(3):655-666.e9
,2014. PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression.  Sci Rep 4:5008
,2014. Dissecting engineered cell types and enhancing cell fate conversion via CellNet.  Cell 158(4):889-902
,2014. JARID1B is a luminal lineage-driving oncogene in breast cancer.  Cancer Cell 25(6):762-77
,2014. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma.  Cancer Discov 4(10):1154-67
,2014. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity.  Nature 514(7520):54-8
,2014. Breast-cancer predisposition in multiple endocrine neoplasia type 1.  N Engl J Med 371(6):583-4
,2014. Research resource: Aorta- and liver-specific ERα-binding patterns and gene regulation by estrogen.  Mol Endocrinol 28(8):1337-51
,2013. Computational methodology for ChIP-seq analysis.  Quant Biol 1(1):54-70
,2013. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.  J Clin Invest 123(3):1109-22
,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
,2013. A genetically encoded and gate for cell-targeted metabolic labeling of proteins.  J Am Chem Soc 135(8):2979-82
,2013. Bifidobacteria stabilize claudins at tight junctions and prevent intestinal barrier dysfunction in mouse necrotizing enterocolitis.  Am J Pathol 182(5):1595-606
,2013. Gene regulatory networks mediating canonical Wnt signal-directed control of pluripotency and differentiation in embryo stem cells.  Stem Cells 31(12):2667-79
,2013. CistromeFinder for ChIP-seq and DNase-seq data reuse.  Bioinformatics 29(10):1352-4
,2013. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.  Mol Cell Biol 33(2):281-92
,2013. Amplitude modulation of androgen signaling by c-MYC.  Genes Dev 27(7):734-48
,2013. Cellular heterogeneity and molecular evolution in cancer.  Annu Rev Pathol 8:277-302
,2013. Peroral endoscopic myotomy for treatment of achalasia: from bench to bedside (with video).  Gastrointest Endosc 77(1):29-38
,2013. Single nucleotide polymorphisms and risk of recurrence of renal-cell carcinoma: a cohort study.  Lancet Oncol 14(1):81-7
,2013. Chromatin marks identify critical cell types for fine mapping complex trait variants.  Nat Genet 45(2):124-30
,2013. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.  Cell 152(3):633-41
,2013. Cancer. Cancer cell phenotypes, in fifty shades of grey.  Science 339(6119):528-9
,2013. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.  Mol Plant 6(5):1463-72
,2013. Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX.  J Biol Chem 288(13):9017-27
,2013. Deconvoluting complex tissues for expression quantitative trait locus-based analyses.  Philos Trans R Soc Lond B Biol Sci 368(1620):20120363
,2013. Somatic mutation of CDKN1B in small intestine neuroendocrine tumors.  Nat Genet 45(12):1483-6
,2013. Glutamine sensitivity analysis identifies the xCT antiporter as a common triple-negative breast tumor therapeutic target.  Cancer Cell 24(4):450-65
,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
,2013. D538G mutation in estrogen receptor-α: A novel mechanism for acquired endocrine resistance in breast cancer.  Cancer Res 73(23):6856-64
,2013. Target analysis by integration of transcriptome and ChIP-seq data with BETA.  Nat Protoc 8(12):2502-15
,2013. Aspirin use, 8q24 single nucleotide polymorphism rs6983267, and colorectal cancer according to CTNNB1 alterations.  J Natl Cancer Inst 105(24):1852-61
,2013. RNA sequencing of cancer reveals novel splicing alterations.  Sci Rep 3:1689
,2013. Biochar and microbial signaling: production conditions determine effects on microbial communication.  Environ Sci Technol 47(20):11496-503
,2013. Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation.  Cell 155(6):1380-95
,2013. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor.  Cancer Cell 24(3):365-78
,2013. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.  Nat Struct Mol Biol 20(7):908-13
,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
,2013. Digital quantification of gene expression in sequential breast cancer biopsies reveals activation of an immune response.  PLoS One 8(5):e64225
,2013. Tracking tumor resistance using 'liquid biopsies'.  Nat Med 19(6):676-7
,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
,2013. PDEF promotes luminal differentiation and acts as a survival factor for ER-positive breast cancer cells.  Cancer Cell 23(6):753-67
,2013. Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis.  J Pathol 231(1):53-62
,2012. Should we get married? The effect of parents' marriage on out-of-wedlock children.  Econ Inq 50(1):17-38
,2012. On chromatin remodeling in mammary gland differentiation and breast tumorigenesis.  Cold Spring Harb Perspect Biol 4.
,2012. Progress in breast cancer research.  Proc Natl Acad Sci U S A 109(8):2715-7
,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
,2012. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.  Bioinformatics 28(10):1411-2
,2012. Intra-tumour heterogeneity: a looking glass for cancer?  Nat Rev Cancer 12(5):323-34
,2012. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.  Genome Res 22(6):1015-25
,2012. A transposase strategy for creating libraries of circularly permuted proteins.  Nucleic Acids Res 40(9):e71
,2012. Computational inference of mRNA stability from histone modification and transcriptome profiles.  Nucleic Acids Res 40(14):6414-23
,2012. GEFs on the RhoAd to a colossal nucleus.  Dev Cell 22(3):471-2
,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
,2012. PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling.  Oncogene 31(29):3397-408
,2012. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.  Genome Res 22(2):292-8
,2012. Laparoscopic-assisted versus open resection of right-sided colonic cancer--a prospective randomized controlled trial.  Int J Colorectal Dis 27(1):95-102
,2012. Altered antisense-to-sense transcript ratios in breast cancer.  Proc Natl Acad Sci U S A 109(8):2820-4
,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
,2012. Systematic evaluation of factors influencing ChIP-seq fidelity.  Nat Methods 9(6):609-14
,2012. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers.  Genes Chromosomes Cancer 51(5):480-9
,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
,2012. The DNLZ/HEP zinc-binding subdomain is critical for regulation of the mitochondrial chaperone HSPA9.  Protein Sci 21(2):258-67
,2012. Differential WNT activity in colorectal cancer confers limited tumorigenic potential and is regulated by MAPK signaling.  Cancer Res 72(6):1547-56
,2012. Evolutionary pathways in BRCA1-associated breast tumors.  Cancer Discov 2(6):503-11
,2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.  Genome Res 22(9):1813-31
,2012. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.  Mol Endocrinol 26(10):1651-9
,2012. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.  Science 338(6113):1465-9
,2012. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.  Bioinformatics 28(21):2782-8
,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
,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
,2012. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.  Cell 151(6):1200-13
,2012. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.  Cancer Res 72(24):6319-24
,2012. Estrogen receptor prevents p53-dependent apoptosis in breast cancer.  Proc Natl Acad Sci U S A 109(44):18060-5
,2012. Targeted disruption of the BCL9/β-catenin complex inhibits oncogenic Wnt signaling.  Sci Transl Med 4(148):148ra117
,2012. SnapShot: breast cancer.  Cancer Cell 22(4):562-562.e1
,2012. Endoscopic submucosal dissection (ESD) compared with gastrectomy for treatment of early gastric neoplasia: a retrospective cohort study.  Surg Endosc 26(12):3584-91
,2012. The expression of Psoriasin (S100A7) and CD24 is linked and related to the differentiation of mammary epithelial cells.  PLoS One 7(12):e53119
,2012. DiNuP: a systematic approach to identify regions of differential nucleosome positioning.  Bioinformatics 28(15):1965-71
,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
,2012. Sequence analysis of mutations and translocations across breast cancer subtypes.  Nature 486(7403):405-9
,2012. Stem cell niches: famished Paneth cells, gluttonous stem cells.  Curr Biol 22(14):R579-80
,2012. On using functional genetics to understand breast cancer biology.  Cold Spring Harb Perspect Biol 4(7):a013516
,2012. The challenges posed by cancer heterogeneity.  Nat Biotechnol 30(7):604-10
,2012. Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis.  Cancer Res 72(17):4383-93
,2011. Notch signaling in stomach epithelial stem cell homeostasis.  J Exp Med 208(4):677-88
,2011. Essential and redundant functions of caudal family proteins in activating adult intestinal genes.  Mol Cell Biol 31(10):2026-39
,2011. Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.  Cancer Res 71(10):3471-81
,2011. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism.  Science 331(6022):1315-9
,2011. BINOCh: binding inference from nucleosome occupancy changes.  Bioinformatics 27(13):1867-8
,2011. Targeting the missing links for cancer therapy.  Nat Med 17(3):283-4
,2011. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.  PLoS Genet 7(4):e1001369
,2011. β-Catenin is a useful adjunct immunohistochemical marker for the diagnosis of pulmonary lymphangioleiomyomatosis.  Am J Clin Pathol 135(5):776-82
,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
,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
,2011. Gastric epithelial stem cells.  Gastroenterology 140(2):412-24
,2011. Inherited variants in the chemokine CCL2 gene and prostate cancer aggressiveness in a Caucasian cohort.  Clin Cancer Res 17(6):1546-52
,2011. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.  Nature 473(7347):394-7
,2011. Broad chromosomal domains of histone modification patterns in C. elegans.  Genome Res 21(2):227-36
,2011. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.  Nucleic Acids Res 39(Database issue):D968-74
,2011. Regulation of mouse stomach development and Barx1 expression by specific microRNAs.  Development 138(6):1081-6
,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
,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
,2011. Association of prostate cancer risk Loci with disease aggressiveness and prostate cancer-specific mortality.  Cancer Prev Res (Phila) 4(5):719-28
,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
,2011. Altering residues N125 and D149 impacts sugar effector binding and allosteric parameters in Escherichia coli lactose repressor.  Biochemistry 50(42):9002-13
,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
,2011. Activation of ERBB2 signaling causes resistance to the EGFR-directed therapeutic antibody cetuximab.  Sci Transl Med 3(99):99ra86
,2011. Unraveling the complexity of basal-like breast cancer.  Oncotarget 2(8):588-9
,2011. Heterogeneity in breast cancer.  J Clin Invest 121(10):3786-8
,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
,2011. Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.  Front Genet 2:25
,2011. Genomics in 2011: challenges and opportunities.  Genome Biol 12(12):137
,2011. The microenvironment in breast cancer progression: biology and implications for treatment.  Breast Cancer Res 13(6):227
,2011. Cistrome: an integrative platform for transcriptional regulation studies.  Genome Biol 12(8):R83
,2011. The genetics of cancer risk.  Cancer J 17(6):416-22
,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
,2011. Boundaries, junctions and transitions in the gastrointestinal tract.  Exp Cell Res 317(19):2711-8
,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
,2011. Targeting PI3K signaling as a therapeutic approach for colorectal cancer.  Gastroenterology 141(1):50-61
,2011. Targeting androgen receptor in estrogen receptor-negative breast cancer.  Cancer Cell 20(1):119-31
,2011. Endodermal Hedgehog signals modulate Notch pathway activity in the developing digestive tract mesenchyme.  Development 138(15):3225-33
,2011. Principles for the post-GWAS functional characterization of cancer risk loci.  Nat Genet 43(6):513-8
,2011. Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation.  PLoS One 6(7):e22493
,2010. Estrogen-dependent and estrogen-independent mechanisms contribute to AIB1-mediated tumor formation.  Cancer Res 70(10):4102-11
,2010. Hedgehog signaling controls mesenchymal growth in the developing mammalian digestive tract.  Development 137(10):1721-9
,2010. Giant Meckel's diverticulitis: a rare condition complicating pregnancy.  Am J Surg 200(1):184-5
,2010. Stem cells in the human breast.  Cold Spring Harb Perspect Biol 2(5):a003160
,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
,2010. The role of the microenvironment in mammary gland development and cancer.  Cold Spring Harb Perspect Biol 2(11):a003244
,2010. PIK3CA mutations in in situ and invasive breast carcinomas.  Cancer Res 70(14):5674-8
,2010. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.  Cancer Cell 17(4):348-61
,2010. The learning curve for endorectal ultrasonography in rectal cancer staging.  Surg Endosc 24(12):3054-9
,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
,2010. MYC regulation of a "poor-prognosis" metastatic cancer cell state.  Proc Natl Acad Sci U S A 107(8):3698-703
,2010. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.  Nature 463(7279):374-8
,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
,2010. Platelets contribute to postnatal occlusion of the ductus arteriosus.  Nat Med 16(1):75-82
,2010. Tumor heterogeneity: causes and consequences.  Biochim Biophys Acta 1805(1):105-17
,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
,2010. Knock in of the AKT1 E17K mutation in human breast epithelial cells does not recapitulate oncogenic PIK3CA mutations.  Oncogene 29(16):2337-45
,2010. Chromatin signature of embryonic pluripotency is established during genome activation.  Nature 464(7290):922-6
,2010. Nucleosome dynamics define transcriptional enhancers.  Nat Genet 42(4):343-7
,2010. Heterogeneity for stem cell-related markers according to tumor subtype and histologic stage in breast cancer.  Clin Cancer Res 16(3):876-87
,2010. Analyzing 'omics data using hierarchical models.  Nat Biotechnol 28(4):337-40
,2010. Radiofrequency ablation for benign aldosterone-producing adenoma: a scarless technique to an old disease.  Ann Surg 252(6):1058-64
,2010. Characterization of a necrotizing enterocolitis model in newborn mice.  Int J Clin Exp Med 3(4):293-302
,2010. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2.  Nature 468(7325):839-43
,2010. Gene expression profiling of human breast tissue samples using SAGE-Seq.  Genome Res 20(12):1730-9
,2010. Stem cells: The intestinal-crypt casino.  Nature 467(7319):1055-6
,2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26
,2010. Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis.  PLoS Genet 6(11):e1001204
,2010. Chromosome 8q24-Associated Cancers and MYC.  Genes Cancer 1(6):555-9
,2010. PTK6 regulates IGF-1-induced anchorage-independent survival.  PLoS One 5(7):e11729
,2010. Genetics of prostate cancer risk.  Mt Sinai J Med 77(6):643-54
,2010. The origins and implications of intratumor heterogeneity.  Cancer Prev Res (Phila) 3(11):1361-4
,2010. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.  Science 330(6012):1775-87
,2010. Fatty acid synthase polymorphisms, tumor expression, body mass index, prostate cancer risk, and survival.  J Clin Oncol 28(25):3958-64
,2010. Live cell monitoring of hiPSC generation and differentiation using differential expression of endogenous microRNAs.  PLoS One 5(7):e11834
,2010. Molecular markers for the diagnosis and management of ductal carcinoma in situ.  J Natl Cancer Inst Monogr 2010(41):210-3
,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
,2010. Going small is the new big.  Nat Methods 7(8):597, 599-600
,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
,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
,2010. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.  Genes Dev 24(19):2219-27
,2010. Single-nucleotide polymorphisms in p53 pathway and aggressiveness of prostate cancer in a Caucasian population.  Clin Cancer Res 16(21):5244-51
,2009. Coactivator function defines the active estrogen receptor alpha cistrome.  Mol Cell Biol 29(12):3413-23
,2009. Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits.  Nat Rev Cancer 9(4):265-73
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,1998. Erythroid maturation and globin gene expression in mice with combined deficiency of NF-E2 and nrf-2.  Blood 91(9):3459-66
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,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
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.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
,2015. Measuring Residual Estrogen Receptor Availability during Fulvestrant Therapy in Patients with Metastatic Breast Cancer.  Cancer Discov 5(1):72-81
,2014. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway.  Nature 508(7494):103-7
,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
,2014. Coregulator control of androgen receptor action by a novel nuclear receptor-binding motif.  J Biol Chem 289(13):8839-51
,2014. Emergence of constitutively active estrogen receptor-α mutations in pretreated advanced estrogen receptor-positive breast cancer.  Clin Cancer Res 20(7):1757-67
,2014. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity.  Cell Rep 9(5):1618-27
,2014. Importance of Breast Cancer Subtype in the Development of Androgen Receptor Directed Therapy.  Curr Breast Cancer Rep 6(2):71-78
,2014. NF-κB activation-induced anti-apoptosis renders HER2-positive cells drug resistant and accelerates tumor growth.  Mol Cancer Res 12(3):408-20
,2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.  Nat Methods 11(1):73-8
,2014. Control of steroid receptor dynamics and function by genomic actions of the cochaperones p23 and Bag-1L.  Nucl Recept Signal 12:e005
,2014. Androgen receptor CAG repeat polymorphism and risk of TMPRSS2:ERG-positive prostate cancer.  Cancer Epidemiol Biomarkers Prev 23(10):2027-31
,2014. PARP1-driven poly-ADP-ribosylation regulates BRCA1 function in homologous recombination-mediated DNA repair.  Cancer Discov 4(12):1430-47
,2014. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.  Genome Biol 15(12):554
,2014. Breast-cancer predisposition in multiple endocrine neoplasia type 1.  N Engl J Med 371(6):583-4
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,2013. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.  Nat Struct Mol Biol 20(7):908-13
,2013. Amplitude modulation of androgen signaling by c-MYC.  Genes Dev 27(7):734-48
,2013. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.  J Clin Invest 123(3):1109-22
,2013. Digital quantification of gene expression in sequential breast cancer biopsies reveals activation of an immune response.  PLoS One 8(5):e64225
,2013. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.  Cell 152(3):633-41
,2013. CistromeFinder for ChIP-seq and DNase-seq data reuse.  Bioinformatics 29(10):1352-4
,2013. Protein kinase C α is a central signaling node and therapeutic target for breast cancer stem cells.  Cancer Cell 24(3):347-64
,2013. D538G mutation in estrogen receptor-α: A novel mechanism for acquired endocrine resistance in breast cancer.  Cancer Res 73(23):6856-64
,2013. Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts.  Genome Biol 14(11):R125
,2013. Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing.  BMC Med Genomics 6:21
,2013. PET imaging of oestrogen receptors in patients with breast cancer.  Lancet Oncol 14(11):e465-75
,2013. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor.  Cancer Cell 24(3):365-78
,2013. PDEF promotes luminal differentiation and acts as a survival factor for ER-positive breast cancer cells.  Cancer Cell 23(6):753-67
,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
,2012. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.  Genome Res 22(6):1015-25
,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
,2012. Estrogen receptor prevents p53-dependent apoptosis in breast cancer.  Proc Natl Acad Sci U S A 109(44):18060-5
,2012. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.  Science 338(6113):1465-9
,2011. BINOCh: binding inference from nucleosome occupancy changes.  Bioinformatics 27(13):1867-8
,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
,2011. PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B.  Nat Cell Biol 13(6):668-75
,2011. Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.  Genome Res 21(4):555-65
,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
,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
,2011. β-Catenin is a useful adjunct immunohistochemical marker for the diagnosis of pulmonary lymphangioleiomyomatosis.  Am J Clin Pathol 135(5):776-82
,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
,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
,2011. Targeting androgen receptor in estrogen receptor-negative breast cancer.  Cancer Cell 20(1):119-31
,2011. A comprehensive view of nuclear receptor cancer cistromes.  Cancer Res 71(22):6940-7
,2011. GlcNAcylation of histone H2B facilitates its monoubiquitination.  Nature 480(7378):557-60
,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
,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
,2011. Cistrome: an integrative platform for transcriptional regulation studies.  Genome Biol 12(8):R83
,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
,2010. Nucleosome dynamics define transcriptional enhancers.  Nat Genet 42(4):343-7
,2010. MYC regulation of a "poor-prognosis" metastatic cancer cell state.  Proc Natl Acad Sci U S A 107(8):3698-703
,2010. Multimodal regulation of E2F1 gene expression by progestins.  Mol Cell Biol 30(8):1866-77
,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
,2010. Estrogen-dependent and estrogen-independent mechanisms contribute to AIB1-mediated tumor formation.  Cancer Res 70(10):4102-11
,2010. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.  Genes Dev 24(19):2219-27
,2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26
,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
,2009. The role of microRNA-221 and microRNA-222 in androgen-independent prostate cancer cell lines.  Cancer Res 69(8):3356-63
,2009. Coactivator function defines the active estrogen receptor alpha cistrome.  Mol Cell Biol 29(12):3413-23
,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
,2009. Cistromics of hormone-dependent cancer.  Endocr Relat Cancer 16(2):381-9
,2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.  Genome Res 19(3):372-80
,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
,2009. Control of cyclin D1 and breast tumorigenesis by the EglN2 prolyl hydroxylase.  Cancer Cell 16(5):413-24
,2009. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer.  Cell 138(2):245-56
,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
,2009. Estradiol-regulated microRNAs control estradiol response in breast cancer cells.  Nucleic Acids Res 37(14):4850-61
,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
,2009. Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies.  Methods Mol Biol 556:155-64
,2009. FOXA1 is a potential oncogene in anaplastic thyroid carcinoma.  Clin Cancer Res 15(11):3680-9
,2008. Targeting NF-kappaB in Waldenstrom macroglobulinemia.  Blood 111(10):5068-77
,2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.  Cell 132(6):958-70
,2008. Androgen receptor mediates the expression of UDP-glucuronosyltransferase 2 B15 and B17 genes.  Prostate 68(8):839-48
,2008. Estrogen protects bone by inducing Fas ligand in osteoblasts to regulate osteoclast survival.  EMBO J 27(3):535-45
,2008. xMAN: extreme MApping of OligoNucleotides.  BMC Genomics 9 Suppl 1:S20
,2008. CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1.  Cancer Res 68(1):301-6
,2008. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.  Genome Res 18(3):393-403
,2008. Unraveling estrogen action in osteoporosis.  Cell Cycle 7(10):1348-52
,2008. Model-based analysis of ChIP-Seq (MACS).  Genome Biol 9(9):R137
,2008. Unique ERalpha cistromes control cell type-specific gene regulation.  Mol Endocrinol 22(11):2393-406
,2008. Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen.  Nature 456(7222):663-6
,2008. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity.  Cancer Res 68(18):7380-5
,2008. AKT alters genome-wide estrogen receptor alpha binding and impacts estrogen signaling in breast cancer.  Mol Cell Biol 28(24):7487-503
,2008. Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase.  Mol Endocrinol 22(11):2420-32
,2008. CD151 accelerates breast cancer by regulating alpha 6 integrin function, signaling, and molecular organization.  Cancer Res 68(9):3204-13
,2008. Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer.  J Natl Cancer Inst 100(11):815-25
,2007. Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer.  Cancer Res 67(13):6477-83
,2007. The OXR domain defines a conserved family of eukaryotic oxidation resistance proteins.  BMC Cell Biol 8:13
,2007. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.  Mol Cell 27(3):380-92
,2006. X chromosomal abnormalities in basal-like human breast cancer.  Cancer Cell 9(2):121-32
,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
,2006. p63 regulates an adhesion programme and cell survival in epithelial cells.  Nat Cell Biol 8(6):551-61
,2006. The joint effect of smoking and AIB1 on breast cancer risk in BRCA1 mutation carriers.  Carcinogenesis 27(3):599-605
,2006. Estrogen receptor target gene: an evolving concept.  Mol Endocrinol 20(8):1707-14
,2006. Genome-wide analysis of estrogen receptor binding sites.  Nat Genet 38(11):1289-97
,2006. Primate-specific evolution of an LDLR enhancer.  Genome Biol 7(8):R68
,2006. Targeting the AIB1 oncogene through mammalian target of rapamycin inhibition in the mammary gland.  Cancer Res 66(23):11381-8
,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
,2006. Model-based analysis of tiling-arrays for ChIP-chip.  Proc Natl Acad Sci U S A 103(33):12457-62
,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
,2005. Androgen mediated regulation and functional implications of fkbp51 expression in prostate cancer.  J Urol 173(5):1772-7
,2005. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.  Cell 122(1):33-43
,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
,2005. Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking.  Mol Cell 19(5):631-42
,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
,2004. Advances in estrogen receptor biology: prospects for improvements in targeted breast cancer therapy.  Breast Cancer Res 6(1):39-52
,2004. Coactivator AIB1 links estrogen receptor transcriptional activity and stability.  Proc Natl Acad Sci U S A 101(32):11599-604
,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
,2003. Coregulator expression and breast cancer: improving the predictive power of estrogen receptor alpha.  Clin Cancer Res 9(4):1229-30
,2003. Agonist and chemopreventative ligands induce differential transcriptional cofactor recruitment by aryl hydrocarbon receptor.  Mol Cell Biol 23(21):7920-5
,2002. The androgen receptor CAG repeat polymorphism and risk of breast cancer in the Nurses' Health Study.  Cancer Res 62(4):1045-9
,2002. Growth factor requirements and basal phenotype of an immortalized mammary epithelial cell line.  Cancer Res 62(1):89-98
,2002. No association between a single nucleotide polymorphism in CYP19 and breast cancer risk.  Cancer Epidemiol Biomarkers Prev 11(2):215-6
,2002. ERAP140, a conserved tissue-specific nuclear receptor coactivator.  Mol Cell Biol 22(10):3358-72
,2002. Overview consensus statement. Newer approaches to androgen deprivation therapy in prostate cancer.  Urology 60(3 Suppl 1):1-6
,2002. Formation of the androgen receptor transcription complex.  Mol Cell 9(3):601-10
,2002. Molecular determinants for the tissue specificity of SERMs.  Science 295(5564):2465-8
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.2015. Big data mining yields novel insights on cancer.  Nat Genet 47(2):103-4
,2015. Inhibition of Foxp3 in cancer cells induces apoptosis of thyroid cancer cells.  Mol Cell Endocrinol 399:228-34
,2015. The role of notch receptors in transcriptional regulation.  J Cell Physiol 230(5):982-8
,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
,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.
,2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.  Nat Methods 11(1):73-8
,2014. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers.  Proc Natl Acad Sci U S A 111(2):705-10
,2014. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.  J Clin Invest 124(4):1636-45
,2014. Canonical nucleosome organization at promoters forms during genome activation.  Genome Res 24(2):260-6
,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
,2014. Training of child and adolescent psychiatry fellows in autism and intellectual disability.  Autism 18(4):471-5
,2014. The cross-talk between estrogen receptor and peroxisome proliferator-activated receptor gamma in thyroid cancer.  Cancer 120(1):142-53
,2014. REST and stress resistance in ageing and Alzheimer's disease.  Nature 507(7493):448-54
,2014. Morphologic change in computed tomography of aldosterone-producing adenoma after radiofrequency ablation.  Can Assoc Radiol J 65(1):86-90
,2014. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway.  Nature 508(7494):103-7
,2014. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity.  Cell Rep 9(5):1618-27
,2014. Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability.  Cell 159(7):1538-48
,2014. Novel oesophago-gastro-duodenal stenting for gastric leaks after laparoscopic sleeve gastrectomy.  Obes Res Clin Pract.
,2014. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells.  Genes Dev 28(16):1827-39
,2014. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.  Nat Rev Genet 15(11):709-21
,2014. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma.  Cancer Discov 4(10):1154-67
,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
,2014. JARID1B is a luminal lineage-driving oncogene in breast cancer.  Cancer Cell 25(6):762-77
,2014. PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression.  Sci Rep 4:5008
,2013. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.  J Clin Invest 123(3):1109-22
,2013. Bifidobacteria stabilize claudins at tight junctions and prevent intestinal barrier dysfunction in mouse necrotizing enterocolitis.  Am J Pathol 182(5):1595-606
,2013. A genetically encoded and gate for cell-targeted metabolic labeling of proteins.  J Am Chem Soc 135(8):2979-82
,2013. Chromatin marks identify critical cell types for fine mapping complex trait variants.  Nat Genet 45(2):124-30
,2013. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.  Mol Cell Biol 33(2):281-92
,2013. Gene regulatory networks mediating canonical Wnt signal-directed control of pluripotency and differentiation in embryo stem cells.  Stem Cells 31(12):2667-79
,2013. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.  Mol Plant 6(5):1463-72
,2013. Peroral endoscopic myotomy for treatment of achalasia: from bench to bedside (with video).  Gastrointest Endosc 77(1):29-38
,2013. Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation.  Cell 155(6):1380-95
,2013. Target analysis by integration of transcriptome and ChIP-seq data with BETA.  Nat Protoc 8(12):2502-15
,2013. CistromeFinder for ChIP-seq and DNase-seq data reuse.  Bioinformatics 29(10):1352-4
,2013. Biochar and microbial signaling: production conditions determine effects on microbial communication.  Environ Sci Technol 47(20):11496-503
,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
,2013. Amplitude modulation of androgen signaling by c-MYC.  Genes Dev 27(7):734-48
,2013. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.  Nat Struct Mol Biol 20(7):908-13
,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
,2012. Computational inference of mRNA stability from histone modification and transcriptome profiles.  Nucleic Acids Res 40(14):6414-23
,2012. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.  Bioinformatics 28(10):1411-2
,2012. Should we get married? The effect of parents' marriage on out-of-wedlock children.  Econ Inq 50(1):17-38
,2012. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.  Genome Res 22(6):1015-25
,2012. Altered antisense-to-sense transcript ratios in breast cancer.  Proc Natl Acad Sci U S A 109(8):2820-4
,2012. Systematic evaluation of factors influencing ChIP-seq fidelity.  Nat Methods 9(6):609-14
,2012. Laparoscopic-assisted versus open resection of right-sided colonic cancer--a prospective randomized controlled trial.  Int J Colorectal Dis 27(1):95-102
,2012. A transposase strategy for creating libraries of circularly permuted proteins.  Nucleic Acids Res 40(9):e71
,2012. The DNLZ/HEP zinc-binding subdomain is critical for regulation of the mitochondrial chaperone HSPA9.  Protein Sci 21(2):258-67
,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
,2012. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.  Cell 151(6):1200-13
,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
,2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.  Genome Res 22(9):1813-31
,2012. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent.  Science 338(6113):1465-9
,2012. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.  Mol Endocrinol 26(10):1651-9
,2012. Endoscopic submucosal dissection (ESD) compared with gastrectomy for treatment of early gastric neoplasia: a retrospective cohort study.  Surg Endosc 26(12):3584-91
,2012. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.  Bioinformatics 28(21):2782-8
,2012. DiNuP: a systematic approach to identify regions of differential nucleosome positioning.  Bioinformatics 28(15):1965-71
,2011. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism.  Science 331(6022):1315-9
,2011. Essential and redundant functions of caudal family proteins in activating adult intestinal genes.  Mol Cell Biol 31(10):2026-39
,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
,2011. Broad chromosomal domains of histone modification patterns in C. elegans.  Genome Res 21(2):227-36
,2011. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.  Nucleic Acids Res 39(Database issue):D968-74
,2011. BINOCh: binding inference from nucleosome occupancy changes.  Bioinformatics 27(13):1867-8
,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
,2011. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.  PLoS Genet 7(4):e1001369
,2011. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.  Nature 473(7347):394-7
,2011. Genomics in 2011: challenges and opportunities.  Genome Biol 12(12):137
,2011. Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.  Front Genet 2:25
,2011. Altering residues N125 and D149 impacts sugar effector binding and allosteric parameters in Escherichia coli lactose repressor.  Biochemistry 50(42):9002-13
,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
,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
,2011. Cistrome: an integrative platform for transcriptional regulation studies.  Genome Biol 12(8):R83
,2011. Targeting androgen receptor in estrogen receptor-negative breast cancer.  Cancer Cell 20(1):119-31
,2010. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.  Cancer Cell 17(4):348-61
,2010. Giant Meckel's diverticulitis: a rare condition complicating pregnancy.  Am J Surg 200(1):184-5
,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
,2010. The learning curve for endorectal ultrasonography in rectal cancer staging.  Surg Endosc 24(12):3054-9
,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
,2010. Analyzing 'omics data using hierarchical models.  Nat Biotechnol 28(4):337-40
,2010. Nucleosome dynamics define transcriptional enhancers.  Nat Genet 42(4):343-7
,2010. Chromatin signature of embryonic pluripotency is established during genome activation.  Nature 464(7290):922-6
,2010. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.  Nature 463(7279):374-8
,2010. MYC regulation of a "poor-prognosis" metastatic cancer cell state.  Proc Natl Acad Sci U S A 107(8):3698-703
,2010. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2.  Nature 468(7325):839-43
,2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26
,2010. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.  Science 330(6012):1775-87
,2010. Live cell monitoring of hiPSC generation and differentiation using differential expression of endogenous microRNAs.  PLoS One 5(7):e11834
,2010. Characterization of a necrotizing enterocolitis model in newborn mice.  Int J Clin Exp Med 3(4):293-302
,2010. Radiofrequency ablation for benign aldosterone-producing adenoma: a scarless technique to an old disease.  Ann Surg 252(6):1058-64
,2010. Gene expression profiling of human breast tissue samples using SAGE-Seq.  Genome Res 20(12):1730-9
,2010. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.  Genes Dev 24(19):2219-27
,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
,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
,2009. Coactivator function defines the active estrogen receptor alpha cistrome.  Mol Cell Biol 29(12):3413-23
,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
,2009. Needle track seeding: a real hazard after percutaneous radiofrequency ablation for colorectal liver metastasis.  World J Gastroenterol 15(13):1653-5
,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
,2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.  Genome Res 19(3):372-80
,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
,2009. Differential chromatin marking of introns and expressed exons by H3K36me3.  Nat Genet 41(3):376-81
,2009. ChIP-Chip: algorithms for calling binding sites.  Methods Mol Biol 556:165-75
,2009. More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells.  Cell Res 19(10):1127-38
,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
,2009. CEAS: cis-regulatory element annotation system.  Bioinformatics 25(19):2605-6
,2009. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer.  Cell 138(2):245-56
,2009. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.  Nat Struct Mol Biol 16(8):847-52
,2008. A high-resolution map of nucleosome positioning on a fission yeast centromere.  Genome Res 18(7):1064-72
,2008. xMAN: extreme MApping of OligoNucleotides.  BMC Genomics 9 Suppl 1:S20
,2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.  Cell 132(6):958-70
,2008. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.  Genome Res 18(3):393-403
,2008. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments.  Biometrics 64(2):468-78
,2008. Thermostability promotes the cooperative function of split adenylate kinases.  Protein Eng Des Sel 21(5):303-10
,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. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.  BMC Genomics 9:537
,2008. Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase.  Mol Endocrinol 22(11):2420-32
,2008. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale.  Genes Dev 22(21):2941-52
,2008. Chromatin structure analyses identify miRNA promoters.  Genes Dev 22(22):3172-83
,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
,2008. Model-based analysis of ChIP-Seq (MACS).  Genome Biol 9(9):R137
,2007. Microarray blob-defect removal improves array analysis.  Bioinformatics 23(8):966-71
,2007. Rectal stump lavage: simple procedure resulting in life-threatening complication.  Asian J Surg 30(1):72-4
,2007. High-throughput mapping of the chromatin structure of human promoters.  Nat Biotechnol 25(2):244-8
,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
,2007. Undifferentiated sex cord-stromal tumor in a young adult.  Int Urol Nephrol 39(2):561-4
,2007. Critical appraisal on the role and outcome of emergency colectomy for uncomplicated right-sided colonic diverticulitis.  World J Surg 31(2):383-7
,2007. Alu elements mediate MYB gene tandem duplication in human T-ALL.  J Exp Med 204(13):3059-66
,2007. Striated muscle and nerve fascicle distribution in the female rat urethral sphincter.  Anat Rec (Hoboken) 290(2):145-54
,2007. Getting started in tiling microarray analysis.  PLoS Comput Biol 3(10):1842-4
,2007. Model-based analysis of two-color arrays (MA2C).  Genome Biol 8(8):R178
,2007. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.  Genome Res 17(10):1471-7
,2007. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence.  Mol Cell 26(4):539-51
,2007. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth.  Mol Cell 27(3):380-92
,2006. Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia.  Blood 108(3):986-92
,2006. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.  Genome Res 16(7):912-21
,2006. Identification of human STAT5-dependent gene regulatory elements based on interspecies homology.  J Biol Chem 281(36):26216-24
,2006. Radiology for the surgeon. Soft-tissue case 58: incarcerated Grynfeltt hernia.  Can J Surg 49(2):129-30
,2006. Genome-wide analysis of estrogen receptor binding sites.  Nat Genet 38(11):1289-97
,2006. CEAS: cis-regulatory element annotation system.  Nucleic Acids Res 34(Web Server issue):W551-4
,2006. Multi-limb necrotizing fasciitis in a patient with rectal cancer.  World J Gastroenterol 12(32):5256-8
,2006. Model-based analysis of tiling-arrays for ChIP-chip.  Proc Natl Acad Sci U S A 103(33):12457-62
,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
,2005. A boosting approach for motif modeling using ChIP-chip data.  Bioinformatics 21(11):2636-43
,2005. Central amygdala ERK signaling pathway is critical to incubation of cocaine craving.  Nat Neurosci 8(2):212-9
,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
,2005. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.  Cell 122(1):33-43
,2004. The anxiogenic drug yohimbine reinstates methamphetamine seeking in a rat model of drug relapse.  Biol Psychiatry 55(11):1082-9
,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
,2004. Eukaryotic regulatory element conservation analysis and identification using comparative genomics.  Genome Res 14(3):451-8
,2004. A suite of web-based programs to search for transcriptional regulatory motifs.  Nucleic Acids Res 32(Web Server issue):W204-7
,2004. A role of ventral tegmental area glutamate in contextual cue-induced relapse to heroin seeking.  J Neurosci 24(47):10726-30
,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
,2003. Empirical analysis of transcriptional activity in the Arabidopsis genome.  Science 302(5646):842-6
,2003. Integrating regulatory motif discovery and genome-wide expression analysis.  Proc Natl Acad Sci U S A 100(6):3339-44
,2002. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.  Nat Biotechnol 20(8):835-9
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.2015. The use of murine-derived fundic organoids in studies of gastric physiology.  J Physiol.
,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
,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
,2014. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity.  Nature 506(7489):511-5
,2014. An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer.  Oncogene 33(49):5637-48
,2014. Radiation redux: reserve intestinal stem cells miss the call to duty.  Cell Stem Cell 14(2):135-6
,2014. Indian Hedgehog mediates gastrin-induced proliferation in stomach of adult mice.  Gastroenterology 147(3):655-666.e9
,2014. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells.  Genes Dev 28(16):1827-39
,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
,2014. Dissecting engineered cell types and enhancing cell fate conversion via CellNet.  Cell 158(4):889-902
,2013. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.  Mol Cell Biol 33(2):281-92
,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
,2013. Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX.  J Biol Chem 288(13):9017-27
,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
,2013. Somatic mutation of CDKN1B in small intestine neuroendocrine tumors.  Nat Genet 45(12):1483-6
,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
,2012. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.  Genome Res 22(2):292-8
,2012. Differential WNT activity in colorectal cancer confers limited tumorigenic potential and is regulated by MAPK signaling.  Cancer Res 72(6):1547-56
,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
,2012. Targeted disruption of the BCL9/β-catenin complex inhibits oncogenic Wnt signaling.  Sci Transl Med 4(148):148ra117
,2012. Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis.  Cancer Res 72(17):4383-93
,2012. Stem cell niches: famished Paneth cells, gluttonous stem cells.  Curr Biol 22(14):R579-80
,2012. GEFs on the RhoAd to a colossal nucleus.  Dev Cell 22(3):471-2
,2011. Notch signaling in stomach epithelial stem cell homeostasis.  J Exp Med 208(4):677-88
,2011. Regulation of mouse stomach development and Barx1 expression by specific microRNAs.  Development 138(6):1081-6
,2011. Gastric epithelial stem cells.  Gastroenterology 140(2):412-24
,2011. Essential and redundant functions of caudal family proteins in activating adult intestinal genes.  Mol Cell Biol 31(10):2026-39
,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
,2011. Targeting PI3K signaling as a therapeutic approach for colorectal cancer.  Gastroenterology 141(1):50-61
,2011. Boundaries, junctions and transitions in the gastrointestinal tract.  Exp Cell Res 317(19):2711-8
,2011. Activation of ERBB2 signaling causes resistance to the EGFR-directed therapeutic antibody cetuximab.  Sci Transl Med 3(99):99ra86
,2011. Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation.  PLoS One 6(7):e22493
,2011. Endodermal Hedgehog signals modulate Notch pathway activity in the developing digestive tract mesenchyme.  Development 138(15):3225-33
,2010. Hedgehog signaling controls mesenchymal growth in the developing mammalian digestive tract.  Development 137(10):1721-9
,2010. Platelets contribute to postnatal occlusion of the ductus arteriosus.  Nat Med 16(1):75-82
,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
,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
,2010. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.  Dev Cell 19(5):713-26
,2010. Stem cells: The intestinal-crypt casino.  Nature 467(7319):1055-6
,2009. Prominin1 (CD133) as an intestinal stem cell marker: promise and nuance.  Gastroenterology 136(7):2051-4
,2009. Trps1, a regulator of chondrocyte proliferation and differentiation, interacts with the activator form of Gli3.  Dev Biol 328(1):40-53
,2009. Role of the homeodomain transcription factor Bapx1 in mouse distal stomach development.  Gastroenterology 136(5):1701-10
,2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.  Genome Res 19(3):372-80
,2009. Relationship of CDX2 loss with molecular features and prognosis in colorectal cancer.  Clin Cancer Res 15(14):4665-73
,2009. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer.  Nat Genet 41(8):882-4
,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
,2009. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.  Nat Genet 41(11):1238-42
,2009. Profiling critical cancer gene mutations in clinical tumor samples.  PLoS One 4(11):e7887
,2009. Regulation of platelet biogenesis: insights from the May-Hegglin anomaly and other MYH9-related disorders.  J Thromb Haemost 7 Suppl 1:272-6
,2009. The microtubule modulator RanBP10 plays a critical role in regulation of platelet discoid shape and degranulation.  Blood 114(27):5532-40
,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
,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
,2008. Visualization of microtubule growth in living platelets reveals a dynamic marginal band with multiple microtubules.  Blood 111(9):4605-16
,2008. Uncoupling of chondrocyte differentiation and perichondrial mineralization underlies the skeletal dysplasia in tricho-rhino-phalangeal syndrome.  Hum Mol Genet 17(14):2244-54
,2008. PU.1 is a major downstream target of AML1 (RUNX1) in adult mouse hematopoiesis.  Nat Genet 40(1):51-60
,2008. RanBP10 is a cytoplasmic guanine nucleotide exchange factor that modulates noncentrosomal microtubules.  J Biol Chem 283(20):14109-19
,2008. Transcription factor foxq1 controls mucin gene expression and granule content in mouse stomach surface mucous cells.  Gastroenterology 135(2):591-600
,2008. Wnt signaling in gut organogenesis.  Organogenesis 4(2):87-91
,2008. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity.  Nature 455(7212):547-51
,2008. Tricho-rhino-phalangeal syndrome with supernumerary teeth.  J Dent Res 87(11):1027-31
,2008. Expression and function of Nkx6.3 in vertebrate hindbrain.  Brain Res 1222:42-50
,2007. Phases of canonical Wnt signaling during the development of mouse intestinal epithelium.  Gastroenterology 133(2):529-38
,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
,2007. Independent functions and mechanisms for homeobox gene Barx1 in patterning mouse stomach and spleen.  Development 134(20):3603-13
,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
,2007. Dynamic visualization of thrombopoiesis within bone marrow.  Science 317(5845):1767-70
,2007. Loss of the PlagL2 transcription factor affects lacteal uptake of chylomicrons.  Cell Metab 6(5):406-13
,2006. Characterization of the megakaryocyte demarcation membrane system and its role in thrombopoiesis.  Blood 107(10):3868-75
,2006. MicroRNAs: regulators of gene expression and cell differentiation.  Blood 108(12):3646-53
,2006. A dynamic expression survey identifies transcription factors relevant in mouse digestive tract development.  Development 133(20):4119-29
,2005. The stomach mesenchymal transcription factor Barx1 specifies gastric epithelial identity through inhibition of transient Wnt signaling.  Dev Cell 8(4):611-22
,2005. Hic-5 regulates an epithelial program mediated by PPARgamma.  Genes Dev 19(3):362-75
,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
,2005. Mechanisms of thrombopoiesis.  J Thromb Haemost 3(8):1717-24
,2005. Differential roles of microtubule assembly and sliding in proplatelet formation by megakaryocytes.  Blood 106(13):4076-85
,2005. Culture, expansion, and differentiation of murine megakaryocytes.  Curr Protoc Immunol Chapter 22:Unit 22F.6
,2005. Mechanisms of organelle transport and capture along proplatelets during platelet production.  Blood 106(13):4066-75
,2005. Overlapping gene expression in fetal mouse intestine development and human colorectal cancer.  Cancer Res 65(19):8715-22
,2004. Megakaryocyte-osteoblast interaction revealed in mice deficient in transcription factors GATA-1 and NF-E2.  J Bone Miner Res 19(4):652-60
,2004. Small-molecule antagonists of the oncogenic Tcf/beta-catenin protein complex.  Cancer Cell 5(1):91-102
,2004. Regulation of mammalian epithelial differentiation and intestine development by class I histone deacetylases.  Mol Cell Biol 24(8):3132-9
,2004. Lonely in Paris: when one gene copy isn't enough.  J Clin Invest 114(1):17-9
,2004. Complexity of CNC transcription factors as revealed by gene targeting of the Nrf3 locus.  Mol Cell Biol 24(8):3286-94
,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
,2004. Molecular mechanisms of megakaryocyte differentiation.  Semin Thromb Hemost 30(4):389-98
,2003. Mechanisms and implications of platelet discoid shape.  Blood 101(12):4789-96
,2003. Megakaryocytes and beyond: the birth of platelets.  J Thromb Haemost 1(6):1174-82
,2003. A role for Rab27b in NF-E2-dependent pathways of platelet formation.  Blood 102(12):3970-9
,2002. An animal model for myelofibrosis.  Blood 100(4):1109
,2002. A Phase II study of gemcitabine and docetaxel in patients with metastatic pancreatic carcinoma.  Cancer 94(1):97-103
,2002. Molecular regulation of vertebrate early endoderm development.  Dev Biol 249(2):191-203
,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
,2002. Characterization of a novel mammalian Groucho isoform and its role in transcriptional regulation.  J Biol Chem 277(49):47732-40
,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
,2001. Toward mechanism-based cancer care.  JAMA 285(5):588-93
,2001. Transcriptional repression and developmental functions of the atypical vertebrate GATA protein TRPS1.  EMBO J 20(7):1715-25
,2001. Downregulation of Hedgehog signaling is required for organogenesis of the small intestine in Xenopus.  Dev Biol 229(1):188-202
,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
,2001. Structure of a human Tcf4-beta-catenin complex.  Nat Struct Biol 8(12):1053-7
,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
,2001. Molecular and transcriptional regulation of megakaryocyte differentiation.  Stem Cells 19(5):397-407
,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
,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
,2000. Structure and expression of a novel frizzled gene isolated from the developing mouse gut.  Biochem J 349 Pt 3:829-34
,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
,1999. Consequences of GATA-1 deficiency in megakaryocytes and platelets.  Blood 93(9):2867-75
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,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
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,1997. Characterization of adult alpha- and beta-globin genes in the zebrafish.  Blood 89(2):688-700
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,2014. Sorting out the FACS: a devil in the details.  Cell Rep 6(5):779-81
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,2014. Oncogene-like induction of cellular invasion from centrosome amplification.  Nature 510(7503):167-71
,2014. Genetic and phenotypic diversity in breast tumor metastases.  Cancer Res 74(5):1338-48
,2014. Tumor heterogeneity confounds and illuminates: a case for Darwinian tumor evolution.  Nat Med 20(4):344-6
,2014. BRCA1 haploinsufficiency for replication stress suppression in primary cells.  Nat Commun 5:5496
,2014. MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis.  Cell Stem Cell 15(6):762-74
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,2013. Glutamine sensitivity analysis identifies the xCT antiporter as a common triple-negative breast tumor therapeutic target.  Cancer Cell 24(4):450-65
,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
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,2012. PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling.  Oncogene 31(29):3397-408
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,2012. Altered antisense-to-sense transcript ratios in breast cancer.  Proc Natl Acad Sci U S A 109(8):2820-4
,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
,2012. Evolutionary pathways in BRCA1-associated breast tumors.  Cancer Discov 2(6):503-11
,2012. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.  Cancer Res 72(24):6319-24
,2012. The expression of Psoriasin (S100A7) and CD24 is linked and related to the differentiation of mammary epithelial cells.  PLoS One 7(12):e53119
,2012. The challenges posed by cancer heterogeneity.  Nat Biotechnol 30(7):604-10
,2012. SnapShot: breast cancer.  Cancer Cell 22(4):562-562.e1
,2012. On using functional genetics to understand breast cancer biology.  Cold Spring Harb Perspect Biol 4(7):a013516
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,2011. Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.  Cancer Res 71(10):3471-81
,2011. Targeting the missing links for cancer therapy.  Nat Med 17(3):283-4
,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
,2011. Heterogeneity in breast cancer.  J Clin Invest 121(10):3786-8
,2011. The microenvironment in breast cancer progression: biology and implications for treatment.  Breast Cancer Res 13(6):227
,2011. Unraveling the complexity of basal-like breast cancer.  Oncotarget 2(8):588-9
,2011. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.  PLoS Genet 7(4):e1001369
,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
,2010. Heterogeneity for stem cell-related markers according to tumor subtype and histologic stage in breast cancer.  Clin Cancer Res 16(3):876-87
,2010. Knock in of the AKT1 E17K mutation in human breast epithelial cells does not recapitulate oncogenic PIK3CA mutations.  Oncogene 29(16):2337-45
,2010. Tumor heterogeneity: causes and consequences.  Biochim Biophys Acta 1805(1):105-17
,2010. Stem cells in the human breast.  Cold Spring Harb Perspect Biol 2(5):a003160
,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
,2010. PIK3CA mutations in in situ and invasive breast carcinomas.  Cancer Res 70(14):5674-8
,2010. Molecular markers for the diagnosis and management of ductal carcinoma in situ.  J Natl Cancer Inst Monogr 2010(41):210-3
,2010. Gene expression profiling of human breast tissue samples using SAGE-Seq.  Genome Res 20(12):1730-9
,2010. Going small is the new big.  Nat Methods 7(8):597, 599-600
,2010. The origins and implications of intratumor heterogeneity.  Cancer Prev Res (Phila) 3(11):1361-4
,2010. PTK6 regulates IGF-1-induced anchorage-independent survival.  PLoS One 5(7):e11729
,2010. The role of the microenvironment in mammary gland development and cancer.  Cold Spring Harb Perspect Biol 2(11):a003244
,2009. Origin of carcinoma associated fibroblasts.  Cell Cycle 8(4):589-95
,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
,2009. Cancer stem cells: a model in the making.  Curr Opin Genet Dev 19(1):44-50
,2009. Co-evolution of tumor cells and their microenvironment.  Trends Genet 25(1):30-8
,2009. Epigenetic patterns of embryonic and adult stem cells.  Cell Cycle 8(6):809-17
,2009. Detection of psoriasin/S100A7 in the sera of patients with psoriasis.  Br J Dermatol 160(2):325-32
,2009. Control of cyclin D1 and breast tumorigenesis by the EglN2 prolyl hydroxylase.  Cancer Cell 16(5):413-24
,2009. Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits.  Nat Rev Cancer 9(4):265-73
,2009. An intraductal human-in-mouse transplantation model mimics the subtypes of ductal carcinoma in situ.  Breast Cancer Res 11(5):R66
,2009. Profiling critical cancer gene mutations in clinical tumor samples.  PLoS One 4(11):e7887
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,2009. Identification of CD44v6(+)/CD24- breast carcinoma cells in primary human tumors by quantum dot-conjugated antibodies.  Lab Invest 89(8):857-66
,2008. No evidence of clonal somatic genetic alterations in cancer-associated fibroblasts from human breast and ovarian carcinomas.  Nat Genet 40(5):650-5
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,2008. The cancer stem cell hypothesis: in search of definitions, markers, and relevance.  Lab Invest 88(5):459-63
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,2008. Cyclooxygenase-2 expression during immortalization and breast cancer progression.  Cancer Res 68(2):467-75
,2008. Is breast tumor progression really linear?  Clin Cancer Res 14(2):339-41
,2008. S100A7-downregulation inhibits epidermal growth factor-induced signaling in breast cancer cells and blocks osteoclast formation.  PLoS One 3(3):e1741
,2008. Microenvironmental regulation of cancer development.  Curr Opin Genet Dev 18(1):27-34
,2008. Genome-wide functional synergy between amplified and mutated genes in human breast cancer.  Cancer Res 68(22):9532-40
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,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
,2008. The epithelial-mesenchymal transition generates cells with properties of stem cells.  Cell 133(4):704-15
,2008. Epithelial and stromal cathepsin K and CXCL14 expression in breast tumor progression.  Clin Cancer Res 14(17):5357-67
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,2006. Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression.  Cancer Res 66(8):4065-78
,2006. Pregnancy and breast cancer: the other side of the coin.  Cancer Cell 9(3):151-3
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,2005. Contribution of bone marrow-derived endothelial cells to human tumor vasculature.  Nat Med 11(3):261-2
,2005. Distinct epigenetic changes in the stromal cells of breast cancers.  Nat Genet 37(8):899-905
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,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
,2005. A putative role for psoriasin in breast tumor progression.  Cancer Res 65(24):11326-34
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,2004. Very high frequency of hypermethylated genes in breast cancer metastasis to the bone, brain, and lung.  Clin Cancer Res 10(9):3104-9
,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
,2004. Ductal carcinoma in situ of the breast.  N Engl J Med 350(14):1430-41
,2004. Molecular characterization of the tumor microenvironment in breast cancer.  Cancer Cell 6(1):17-32
,2004. EMSY links breast cancer gene 2 to the 'Royal Family'.  Breast Cancer Res 6(5):201-3
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,2003. Lack of HIN-1 methylation in BRCA1-linked and "BRCA1-like" breast tumors.  Cancer Res 63(9):2024-7
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,2003. The hairy powers of oncogenes: from biological function to cancer therapy.  Cancer Biol Ther 2(5):592-4
,2002. Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression).  Oncogene 21(5):836-43
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,2002. Psoriasin expression in mammary epithelial cells in vitro and in vivo.  Cancer Res 62(1):43-7
,2002. An anatomy of normal and malignant gene expression.  Proc Natl Acad Sci U S A 99(17):11287-92
,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
,2002. Breast cancer gene discovery.  Expert Rev Mol Med 4(18):1-18
,2002. Is p53 a breast cancer gene?  Cancer Biol Ther 1(1):37-8
,2002. Cellular and molecular targets of estrogen in normal human breast tissue.  Cancer Res 62(16):4540-4
,2001. Gene discovery using the serial analysis of gene expression technique: implications for cancer research.  J Clin Oncol 19(11):2948-58
,2001. Monitoring of the natural environment by chemical speciation of elements in aerosol and sediment samples.  J Environ Monit 3(1):74-80
,2001. A SAGE (serial analysis of gene expression) view of breast tumor progression.  Cancer Res 61(15):5697-702
,2001. Chemical fractionation of a fly ash sample by a sequential leaching method.  Fresenius J Anal Chem 371(6):838-42
,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
,2001. On the birth of breast cancer.  Biochim Biophys Acta 1552(1):1-13
,2000. p53-dependent expression of PIG3 during proliferation, genotoxic stress, and reversible growth arrest.  Cancer Lett 156(1):63-72
,2000. Phenol sulfotransferases: hormonal regulation, polymorphism, and age of onset of breast cancer.  Cancer Res 60(24):6859-63
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,1999. CDX2 is mutated in a colorectal cancer with normal APC/beta-catenin signaling.  Oncogene 18(35):5010-4
,1999. Analysis of human transcriptomes.  Nat Genet 23(4):387-8
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,1998. Somatic mutations of the mitochondrial genome in human colorectal tumours.  Nat Genet 20(3):291-3
,1997. Less death in the dying.  Cell Death Differ 4(3):242-6
,1997. 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression.  Mol Cell 1(1):3-11
,1997. A model for p53-induced apoptosis.  Nature 389(6648):300-5
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,1996. Negative regulation of cell growth by TGF beta.  Biochim Biophys Acta 1242(3):185-99
,1996. A syndrome of multiorgan hyperplasia with features of gigantism, tumorigenesis, and female sterility in p27(Kip1)-deficient mice.  Cell 85(5):733-44
,1996. Genetic determinants of p53-induced apoptosis and growth arrest.  Genes Dev 10(15):1945-52
,1996. Early alteration of cell-cycle-regulated gene expression in colorectal neoplasia.  Am J Pathol 149(2):381-7
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,1994. Cyclins, Cdks, and cyclin kinase inhibitors.  Cold Spring Harb Symp Quant Biol 59:31-8
,1994. p27Kip1, a cyclin-Cdk inhibitor, links transforming growth factor-beta and contact inhibition to cell cycle arrest.  Genes Dev 8(1):9-22
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,2014. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.  Hum Mol Genet 23(19):5294-302
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,2013. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.  Cell 152(3):633-41
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,2013. Aspirin use, 8q24 single nucleotide polymorphism rs6983267, and colorectal cancer according to CTNNB1 alterations.  J Natl Cancer Inst 105(24):1852-61
,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
,2011. Association of prostate cancer risk Loci with disease aggressiveness and prostate cancer-specific mortality.  Cancer Prev Res (Phila) 4(5):719-28
,2011. Inherited variants in the chemokine CCL2 gene and prostate cancer aggressiveness in a Caucasian cohort.  Clin Cancer Res 17(6):1546-52
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