Published in BMC Genomics on September 16, 2008
Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One (2010) 3.99
Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44
Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics (2009) 2.02
Epigenetic alterations in the breast: Implications for breast cancer detection, prognosis and treatment. Semin Cancer Biol (2009) 1.41
RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS One (2010) 1.07
ChIPing the cistrome of PXR in mouse liver. Nucleic Acids Res (2010) 1.01
A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Syst Biol (2011) 0.99
LANA binds to multiple active viral and cellular promoters and associates with the H3K4methyltransferase hSET1 complex. PLoS Pathog (2014) 0.94
The mouse RANKL gene locus is defined by a broad pattern of histone H4 acetylation and regulated through distinct distal enhancers. J Cell Biochem (2011) 0.92
POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization. Nucleic Acids Res (2011) 0.88
Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2009) 0.88
An empirical Bayes model for gene expression and methylation profiles in antiestrogen resistant breast cancer. BMC Med Genomics (2010) 0.88
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research. BMC Genomics (2008) 0.83
Transcriptional regulation prediction of antiestrogen resistance in breast cancer based on RNA polymerase II binding data. BMC Bioinformatics (2014) 0.76
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Analysis of variance for gene expression microarray data. J Comput Biol (2000) 16.28
On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J Comput Biol (2001) 10.48
Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol (2001) 10.38
Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc (2006) 7.29
Diverse gene expression and DNA methylation profiles correlate with differential adaptation of breast cancer cells to the antiestrogens tamoxifen and fulvestrant. Cancer Res (2006) 2.63
Gamma-Normal-Gamma mixture model for detecting differentially methylated loci in three breast cancer cell lines. Cancer Inform (2007) 1.12
Epigenetic hypothesis tests for methylation and acetylation in a triple microarray system. J Comput Biol (2005) 1.01
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinformatics (2006) 0.94
Identification and characterization of ovarian cancer-initiating cells from primary human tumors. Cancer Res (2008) 6.38
miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res (2008) 6.30
CYP2D6 genotype, antidepressant use, and tamoxifen metabolism during adjuvant breast cancer treatment. J Natl Cancer Inst (2005) 5.92
Rethinking ovarian cancer: recommendations for improving outcomes. Nat Rev Cancer (2011) 5.28
Protective variant for hippocampal atrophy identified by whole exome sequencing. Ann Neurol (2015) 5.10
Quantitative effect of CYP2D6 genotype and inhibitors on tamoxifen metabolism: implication for optimization of breast cancer treatment. Clin Pharmacol Ther (2006) 4.81
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res (2008) 3.33
Diverse gene expression and DNA methylation profiles correlate with differential adaptation of breast cancer cells to the antiestrogens tamoxifen and fulvestrant. Cancer Res (2006) 2.63
Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Mol Cell (2006) 2.48
EGFR and MET receptor tyrosine kinase-altered microRNA expression induces tumorigenesis and gefitinib resistance in lung cancers. Nat Med (2011) 2.46
Changes in gene expression during pegylated interferon and ribavirin therapy of chronic hepatitis C virus distinguish responders from nonresponders to antiviral therapy. J Virol (2007) 2.45
Estradiol-regulated microRNAs control estradiol response in breast cancer cells. Nucleic Acids Res (2009) 2.27
Predicting intrinsic disorder in proteins: an overview. Cell Res (2009) 2.24
Heterogeneity of Gleason grade in multifocal adenocarcinoma of the prostate. Cancer (2004) 2.22
Inhibition of MCL-1 enhances lapatinib toxicity and overcomes lapatinib resistance via BAK-dependent autophagy. Cancer Biol Ther (2009) 2.21
Composite functional genetic and comedication CYP2D6 activity score in predicting tamoxifen drug exposure among breast cancer patients. J Clin Pharmacol (2010) 2.15
Sorafenib enhances pemetrexed cytotoxicity through an autophagy-dependent mechanism in cancer cells. Cancer Res (2011) 2.13
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res (2009) 2.03
Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics (2009) 2.02
Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res (2008) 1.99
Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Res (2004) 1.97
Oxysterols direct B-cell migration through EBI2. Nature (2011) 1.94
MicroRNA cluster 221-222 and estrogen receptor alpha interactions in breast cancer. J Natl Cancer Inst (2010) 1.94
Prospective characterization of musculoskeletal symptoms in early stage breast cancer patients treated with aromatase inhibitors. Breast Cancer Res Treat (2007) 1.92
Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. Clin Cancer Res (2002) 1.91
Predictors of aromatase inhibitor discontinuation as a result of treatment-emergent symptoms in early-stage breast cancer. J Clin Oncol (2012) 1.91
Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer. BMC Med Genomics (2009) 1.91
Estrogen receptor genotypes influence hot flash prevalence and composite score before and after tamoxifen therapy. J Clin Oncol (2008) 1.91
Epigenetic resensitization to platinum in ovarian cancer. Cancer Res (2012) 1.88
Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation. Alcohol Clin Exp Res (2011) 1.88
Impact of CYP2B6 polymorphism on hepatic efavirenz metabolism in vitro. Pharmacogenomics (2007) 1.84
Endoxifen, a secondary metabolite of tamoxifen, and 4-OH-tamoxifen induce similar changes in global gene expression patterns in MCF-7 breast cancer cells. J Pharmacol Exp Ther (2006) 1.84
Lactate inhibits lipolysis in fat cells through activation of an orphan G-protein-coupled receptor, GPR81. J Biol Chem (2008) 1.75
Trends in mortality from cancers of the breast, colon, prostate, esophagus, and stomach in East Asia: role of nutrition transition. Eur J Cancer Prev (2012) 1.73
Optimal graph search segmentation using arc-weighted graph for simultaneous surface detection of bladder and prostate. Med Image Comput Comput Assist Interv (2009) 1.69
CHIP (carboxyl terminus of Hsc70-interacting protein) promotes basal and geldanamycin-induced degradation of estrogen receptor-alpha. Mol Endocrinol (2005) 1.66
Differential gene induction by type I and type II interferons and their combination. J Interferon Cytokine Res (2006) 1.61
Literature based drug interaction prediction with clinical assessment using electronic medical records: novel myopathy associated drug interactions. PLoS Comput Biol (2012) 1.58
Prognostic DNA methylation biomarkers in ovarian cancer. Clin Cancer Res (2006) 1.53
Nuclear factor-kappaB is constitutively activated in prostate cancer in vitro and is overexpressed in prostatic intraepithelial neoplasia and adenocarcinoma of the prostate. Clin Cancer Res (2004) 1.53
Alcohol exposure alters DNA methylation profiles in mouse embryos at early neurulation. Epigenetics (2009) 1.53
EGFR signaling in breast cancer: bad to the bone. Semin Cell Dev Biol (2010) 1.52
Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucleic Acids Res (2004) 1.50
Minireview: epigenetic changes in ovarian cancer. Endocrinology (2009) 1.49
Independent influence of dietary protein on markers of kidney function and disease in obesity. Kidney Int (2010) 1.48
Cytokine receptor CXCR4 mediates estrogen-independent tumorigenesis, metastasis, and resistance to endocrine therapy in human breast cancer. Cancer Res (2010) 1.45
Aberrant expression of CARM1, a transcriptional coactivator of androgen receptor, in the development of prostate carcinoma and androgen-independent status. Cancer (2004) 1.45
Identification of novel DNA methylation markers in cervical cancer. Int J Cancer (2008) 1.42
The epigenetics of ovarian cancer drug resistance and resensitization. Am J Obstet Gynecol (2004) 1.41
Association of polymorphisms of angiogenesis genes with breast cancer. Breast Cancer Res Treat (2007) 1.41
Antimitogenic and chemosensitizing effects of the methylation inhibitor zebularine in ovarian cancer. Mol Cancer Ther (2005) 1.40
Knee loading dynamically alters intramedullary pressure in mouse femora. Bone (2006) 1.40
Triple analysis of the cancer epigenome: an integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation. Cancer Res (2003) 1.38
Prioritization of disease microRNAs through a human phenome-microRNAome network. BMC Syst Biol (2010) 1.37
Knee-loading modality drives molecular transport in mouse femur. Ann Biomed Eng (2006) 1.36
Fulvestrant (ICI 182,780)-dependent interacting proteins mediate immobilization and degradation of estrogen receptor-alpha. J Biol Chem (2006) 1.35
High-level expression of EphA2 receptor tyrosine kinase in prostatic intraepithelial neoplasia. Am J Pathol (2003) 1.35
Proteomic analysis of tumor necrosis factor-alpha resistant human breast cancer cells reveals a MEK5/Erk5-mediated epithelial-mesenchymal transition phenotype. Breast Cancer Res (2008) 1.35
A phase 1 and pharmacodynamic study of decitabine in combination with carboplatin in patients with recurrent, platinum-resistant, epithelial ovarian cancer. Cancer (2010) 1.34
Gene expression patterns in bone following mechanical loading. J Bone Miner Res (2011) 1.32
Hepatic FoxOs regulate lipid metabolism via modulation of expression of the nicotinamide phosphoribosyltransferase gene. J Biol Chem (2011) 1.31
The NEDD8 pathway is required for proteasome-mediated degradation of human estrogen receptor (ER)-alpha and essential for the antiproliferative activity of ICI 182,780 in ERalpha-positive breast cancer cells. Mol Endocrinol (2002) 1.30
Inhibition of MCL-1 in breast cancer cells promotes cell death in vitro and in vivo. Cancer Biol Ther (2010) 1.28
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. Bioinformatics (2013) 1.28
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. Bioinformatics (2008) 1.27
Epigenetic therapies for chemoresensitization of epithelial ovarian cancer. Gynecol Oncol (2009) 1.26
Estrogen mediated-activation of miR-191/425 cluster modulates tumorigenicity of breast cancer cells depending on estrogen receptor status. PLoS Genet (2013) 1.24
Effects of HIV protease inhibitor ritonavir on Akt-regulated cell proliferation in breast cancer. Clin Cancer Res (2006) 1.23
Estrogen receptor genotype is associated with risk of venous thromboembolism during tamoxifen therapy. Breast Cancer Res Treat (2008) 1.21
Dominant-negative histone H3 lysine 27 mutant derepresses silenced tumor suppressor genes and reverses the drug-resistant phenotype in cancer cells. Cancer Res (2006) 1.21
AKT alters genome-wide estrogen receptor alpha binding and impacts estrogen signaling in breast cancer. Mol Cell Biol (2008) 1.21
Hypermethylation of 18S and 28S ribosomal DNAs predicts progression-free survival in patients with ovarian cancer. Clin Cancer Res (2005) 1.20
Association between CYP2D6 genotype and tamoxifen-induced hot flashes in a prospective cohort. Breast Cancer Res Treat (2009) 1.20
Potential roles of microRNAs in regulating long intergenic noncoding RNAs. BMC Med Genomics (2013) 1.19
Loss of 14-3-3sigma in prostate cancer and its precursors. Clin Cancer Res (2004) 1.19
Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. Genome Res (2010) 1.18
Increased risk of vincristine neurotoxicity associated with low CYP3A5 expression genotype in children with acute lymphoblastic leukemia. Pediatr Blood Cancer (2010) 1.18
Promoter hypermethylation of FBXO32, a novel TGF-beta/SMAD4 target gene and tumor suppressor, is associated with poor prognosis in human ovarian cancer. Lab Invest (2010) 1.17
An integrated pharmacokinetics ontology and corpus for text mining. BMC Bioinformatics (2013) 1.17
Spatiotemporal distribution of malaria and the association between its epidemic and climate factors in Hainan, China. Malar J (2010) 1.15
Targeted methylation of two tumor suppressor genes is sufficient to transform mesenchymal stem cells into cancer stem/initiating cells. Cancer Res (2011) 1.15
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. BMC Genomics (2008) 1.15
Variability of heart rate correction methods for the QT interval. Br J Clin Pharmacol (2003) 1.15
Estrogen receptor-alpha hinge-region lysines 302 and 303 regulate receptor degradation by the proteasome. Mol Endocrinol (2008) 1.14
Gamma-Normal-Gamma mixture model for detecting differentially methylated loci in three breast cancer cell lines. Cancer Inform (2007) 1.12
INSL5 is a high affinity specific agonist for GPCR142 (GPR100). J Biol Chem (2004) 1.12
Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells. BMC Genomics (2008) 1.12
Diabetes mellitus increases the in vivo activity of cytochrome P450 2E1 in humans. Br J Clin Pharmacol (2003) 1.11
A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. Bioinformatics (2007) 1.11
Physiologically based pharmacokinetic model of mechanism-based inhibition of CYP3A by clarithromycin. Drug Metab Dispos (2009) 1.11
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res (2010) 1.10