Published in Bioinformatics on September 09, 2013
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Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. Bioinformatics (2016) 0.75
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Differential peak calling of ChIP-seq signals with replicates with THOR. Nucleic Acids Res (2016) 0.75
Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries. Nat Genet (2017) 0.75
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Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
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Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
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Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36
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PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
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Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet (2007) 9.88
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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature (2010) 6.87
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53
Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res (2012) 4.94
Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet (2006) 4.86
The Hox genes and their roles in oncogenesis. Nat Rev Cancer (2010) 3.97
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol (2009) 2.88
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics (2011) 2.86
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics (2008) 2.85
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics (2010) 2.79
A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics (2010) 2.66
Homeobox D10 induces phenotypic reversion of breast tumor cells in a three-dimensional culture model. Cancer Res (2005) 2.45
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics (2010) 2.41
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol (2010) 2.38
Regional copy number-independent deregulation of transcription in cancer. Nat Genet (2006) 2.33
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res (2011) 2.23
Agglomerative epigenetic aberrations are a common event in human breast cancer. Cancer Res (2008) 2.22
EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res (2010) 1.23
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HOXB13 is downregulated in colorectal cancer to confer TCF4-mediated transactivation. Br J Cancer (2005) 1.15
DLEC1 is a functional 3p22.3 tumour suppressor silenced by promoter CpG methylation in colon and gastric cancers. Br J Cancer (2009) 1.07
A novel epigenetic phenotype associated with the most aggressive pathway of bladder tumor progression. J Natl Cancer Inst (2010) 1.02
Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways. Oncogene (2012) 1.00
Up-regulation of HOXC6, HOXD1, and HOXD8 homeobox gene expression in human neuroblastoma cells following chemical induction of differentiation. Tumour Biol (1996) 0.96
Nebula--a web-server for advanced ChIP-seq data analysis. Bioinformatics (2012) 0.94
Histone modification therapy of cancer. Adv Genet (2010) 0.94
Expression and functions of EGF, FGF and TGFbeta-growth-factor family members and their receptors in invasive human transitional-cell-carcinoma cells. Int J Cancer (1997) 0.87
Genome-wide bovine H3K27me3 modifications and the regulatory effects on genes expressions in peripheral blood lymphocytes. PLoS One (2012) 0.86
Functional dissection of HOXD cluster genes in regulation of neuroblastoma cell proliferation and differentiation. PLoS One (2012) 0.84
Transcriptional repression of DLEC1 associates with the depth of tumor invasion in oral squamous cell carcinoma. Oral Oncol (2010) 0.82
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics (2004) 8.29
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
A critical function for transforming growth factor-beta, interleukin 23 and proinflammatory cytokines in driving and modulating human T(H)-17 responses. Nat Immunol (2008) 6.09
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatology (2007) 4.73
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell (2010) 3.70
Retracted RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet (2013) 2.91
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol (2009) 2.88
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics (2011) 2.86
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics (2010) 2.79
Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. Genome Biol (2004) 2.77
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics (2010) 2.63
Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res (2005) 2.46
Classification of microarray data using gene networks. BMC Bioinformatics (2007) 2.44
Genomic anatomy of the hippocampus. Neuron (2008) 2.37
Regional copy number-independent deregulation of transcription in cancer. Nat Genet (2006) 2.33
miR-181a and miR-630 regulate cisplatin-induced cancer cell death. Cancer Res (2010) 2.24
Beta-catenin status in paediatric medulloblastomas: correlation of immunohistochemical expression with mutational status, genetic profiles, and clinical characteristics. J Pathol (2009) 2.15
Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation. PLoS Genet (2009) 1.96
Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells. Breast Cancer Res (2008) 1.94
VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics (2006) 1.87
Spatial normalization of array-CGH data. BMC Bioinformatics (2006) 1.79
Activating mutations of the tyrosine kinase receptor FGFR3 are associated with benign skin tumors in mice and humans. Hum Mol Genet (2005) 1.74
Transcriptional network dynamics in macrophage activation. Genomics (2006) 1.72
Bayesian hierarchical model for identifying changes in gene expression from microarray experiments. J Comput Biol (2002) 1.70
Germline BAP1 mutations predispose to renal cell carcinomas. Am J Hum Genet (2013) 1.69
Gene expression signatures predict outcome in non-muscle-invasive bladder carcinoma: a multicenter validation study. Clin Cancer Res (2007) 1.68
BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas. Int J Cancer (2008) 1.66
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics (2007) 1.65
FGFR3 and TP53 gene mutations define two distinct pathways in urothelial cell carcinoma of the bladder. Cancer Res (2003) 1.64
The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. PLoS One (2009) 1.63
A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol (2008) 1.61
Molecular grading of urothelial cell carcinoma with fibroblast growth factor receptor 3 and MIB-1 is superior to pathologic grade for the prediction of clinical outcome. J Clin Oncol (2003) 1.58
Computational methods for prediction of T-cell epitopes--a framework for modelling, testing, and applications. Methods (2004) 1.55
Oncogenic properties of the mutated forms of fibroblast growth factor receptor 3b. Carcinogenesis (2005) 1.54
Molecular grade (FGFR3/MIB-1) and EORTC risk scores are predictive in primary non-muscle-invasive bladder cancer. Eur Urol (2010) 1.54
On the classification of long non-coding RNAs. RNA Biol (2013) 1.53
Integrated genomic and transcriptomic analysis of ductal carcinoma in situ of the breast. Clin Cancer Res (2008) 1.50
Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics (2011) 1.50
Identification of a proliferation gene cluster associated with HPV E6/E7 expression level and viral DNA load in invasive cervical carcinoma. Oncogene (2005) 1.50
Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol (2010) 1.49
Pseudo-messenger RNA: phantoms of the transcriptome. PLoS Genet (2006) 1.46
Prognostic impact of vitamin B6 metabolism in lung cancer. Cell Rep (2012) 1.45
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res (2012) 1.45
Establishment and characterization of a panel of human uveal melanoma xenografts derived from primary and/or metastatic tumors. Clin Cancer Res (2010) 1.42
Gene expression analysis by real-time reverse transcription polymerase chain reaction: influence of tissue handling. Anal Biochem (2004) 1.39
Characterization of the recurrent 8p11-12 amplicon identifies PPAPDC1B, a phosphatase protein, as a new therapeutic target in breast cancer. Cancer Res (2008) 1.39
Genome-wide redistribution of meiotic double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol (2006) 1.38
Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell (2011) 1.36
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PLoS One (2013) 1.36
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. Nucleic Acids Res (2006) 1.35
Classifying the estrogen receptor status of breast cancers by expression profiles reveals a poor prognosis subpopulation exhibiting high expression of the ERBB2 receptor. Hum Mol Genet (2003) 1.34
Prediction of promiscuous peptides that bind HLA class I molecules. Immunol Cell Biol (2002) 1.33
Frequent genomic structural alterations at HPV insertion sites in cervical carcinoma. J Pathol (2010) 1.30
De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res (2010) 1.30
HiTC: exploration of high-throughput 'C' experiments. Bioinformatics (2012) 1.29
CAPweb: a bioinformatics CGH array Analysis Platform. Nucleic Acids Res (2006) 1.28
Asf1b, the necessary Asf1 isoform for proliferation, is predictive of outcome in breast cancer. EMBO J (2010) 1.25
Information for the Coordinates of Exons (ICE): a human splice sites database. Genomics (2004) 1.24
DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Res (2011) 1.24
ERGDB: Estrogen Responsive Genes Database. Nucleic Acids Res (2004) 1.23
Genomic profiling and identification of high-risk uveal melanoma by array CGH analysis of primary tumors and liver metastases. Invest Ophthalmol Vis Sci (2009) 1.22
Database for exploration of functional context of genes implicated in ovarian cancer. Nucleic Acids Res (2008) 1.21
Identification in daily practice of patients with Lynch syndrome (hereditary nonpolyposis colorectal cancer): revised Bethesda guidelines-based approach versus molecular screening. Am J Gastroenterol (2008) 1.20
Sex differences in the recognition of and innate antiviral responses to Seoul virus in Norway rats. Brain Behav Immun (2007) 1.20
Polo-like kinase 1: a potential therapeutic option in combination with conventional chemotherapy for the management of patients with triple-negative breast cancer. Cancer Res (2012) 1.20
Multiparametric analysis of cytokine-driven human Th17 differentiation reveals a differential regulation of IL-17 and IL-22 production. Blood (2009) 1.18
An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics (2007) 1.18
Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach. PLoS One (2011) 1.17
Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biol (2010) 1.17
Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol (2003) 1.17
8p22 MTUS1 gene product ATIP3 is a novel anti-mitotic protein underexpressed in invasive breast carcinoma of poor prognosis. PLoS One (2009) 1.14
Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics (2009) 1.14
Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis. Genome Biol (2010) 1.13
TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer. PLoS One (2013) 1.13
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays. Bioinformatics (2008) 1.12
LICORN: learning cooperative regulation networks from gene expression data. Bioinformatics (2007) 1.12
Patient-derived xenografts recapitulate molecular features of human uveal melanomas. Mol Oncol (2013) 1.11
Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLoS Comput Biol (2013) 1.09
Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. Nucleic Acids Res (2004) 1.09
Combined microsatellite and FGFR3 mutation analysis enables a highly sensitive detection of urothelial cell carcinoma in voided urine. Clin Cancer Res (2003) 1.08
DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Res (2010) 1.07
myProMS, a web server for management and validation of mass spectrometry-based proteomic data. Proteomics (2007) 1.07
Independent transcriptional reprogramming and apoptosis induction by cisplatin. Cell Cycle (2012) 1.07
Mutations in TP53, but not FGFR3, in urothelial cell carcinoma of the bladder are influenced by smoking: contribution of exogenous versus endogenous carcinogens. Carcinogenesis (2004) 1.07
NormaCurve: a SuperCurve-based method that simultaneously quantifies and normalizes reverse phase protein array data. PLoS One (2012) 1.05