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
, 2009. Needle track seeding: a real hazard after percutaneous radiofrequency ablation for colorectal liver metastasis. World J Gastroenterol 15(13):1653-5
, 2009. The role of microRNA-221 and microRNA-222 in androgen-independent prostate cancer cell lines. Cancer Res 69(8):3356-63
, 2009. Trps1, a regulator of chondrocyte proliferation and differentiation, interacts with the activator form of Gli3. Dev Biol 328(1):40-53
, 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. 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. Prominin1 (CD133) as an intestinal stem cell marker: promise and nuance. Gastroenterology 136(7):2051-4
, 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. FOXA1 is a potential oncogene in anaplastic thyroid carcinoma. Clin Cancer Res 15(11):3680-9
, 2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res 19(3):372-80
, 2009. Co-evolution of tumor cells and their microenvironment. Trends Genet 25(1):30-8
, 2009. Detection of psoriasin/S100A7 in the sera of patients with psoriasis. Br J Dermatol 160(2):325-32
, 2009. Cancer stem cells: a model in the making. Curr Opin Genet Dev 19(1):44-50
, 2009. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41(3):376-81
, 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. Role of the homeodomain transcription factor Bapx1 in mouse distal stomach development. Gastroenterology 136(5):1701-10
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Publication list retrieved from NCBI using ImpactPubs
., 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
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, 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
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, 2014. Research resource: Aorta- and liver-specific ERα-binding patterns and gene regulation by estrogen. Mol Endocrinol 28(8):1337-51
, 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
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, 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
Publication list retrieved from NCBI using ImpactPubs
., 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
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, 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
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, 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
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, 2008. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 22(21):2941-52
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, 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
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, 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
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, 2004. The anxiogenic drug yohimbine reinstates methamphetamine seeking in a rat model of drug relapse. Biol Psychiatry 55(11):1082-9
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, 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
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, 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
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, 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
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, 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
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, 2007. Dynamic visualization of thrombopoiesis within bone marrow. Science 317(5845):1767-70
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, 2006. MicroRNAs: regulators of gene expression and cell differentiation. Blood 108(12):3646-53
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, 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
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, 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
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, 2004. Lonely in Paris: when one gene copy isn't enough. J Clin Invest 114(1):17-9
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, 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
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, 1999. Consequences of GATA-1 deficiency in megakaryocytes and platelets. Blood 93(9):2867-75
, 1999. Pathophysiology of thrombocytopenia and anemia in mice lacking transcription factor NF-E2. Blood 94(9):3037-47
, 1999. Blood platelets are assembled principally at the ends of proplatelet processes produced by differentiated megakaryocytes. J Cell Biol 147(6):1299-312
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, 2015. Age- and Pregnancy-Associated DNA Methylation Changes in Mammary Epithelial Cells. Stem Cell Reports.
, 2014. Sorting out the FACS: a devil in the details. Cell Rep 6(5):779-81
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, 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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, 2014. JARID1B is a luminal lineage-driving oncogene in breast cancer. Cancer Cell 25(6):762-77
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, 2013. Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis. J Pathol 231(1):53-62
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, 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. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers. Genes Chromosomes Cancer 51(5):480-9
, 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
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