An integrated ChIP-seq analysis platform with customizable workflows.

EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell (2013) 3.13

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet (2012) 2.94

The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol (2012) 1.96

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun (2014) 1.84

Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature (2012) 1.80

Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature (2014) 1.73

N6-methyladenosine marks primary microRNAs for processing. Nature (2015) 1.58

Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling. Immunity (2013) 1.55

Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region. Immunity (2016) 1.43

HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events. Cell (2015) 1.34

Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. Cancer Discov (2012) 1.33

NFIB is a governor of epithelial-melanocyte stem cell behaviour in a shared niche. Nature (2013) 1.29

A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep (2013) 1.28

RUNX1 is a key target in t(4;11) leukemias that contributes to gene activation through an AF4-MLL complex interaction. Cell Rep (2013) 1.22

BCL6 orchestrates Tfh cell differentiation via multiple distinct mechanisms. J Exp Med (2015) 1.14

Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation. PLoS Genet (2014) 1.09

The transcriptional modulator BCL6 as a molecular target for breast cancer therapy. Oncogene (2014) 1.05

Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis. Nat Med (2015) 1.04

Profiling genome-wide chromatin methylation with engineered posttranslation apparatus within living cells. J Am Chem Soc (2013) 1.04

Identification of biologically relevant enhancers in human erythroid cells. J Biol Chem (2013) 1.03

A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature (2013) 0.99

Epigenomic evolution in diffuse large B-cell lymphomas. Nat Commun (2015) 0.98

Epigenomic alterations in localized and advanced prostate cancer. Neoplasia (2013) 0.96

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data. Genes Cells (2013) 0.95

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. Brief Bioinform (2013) 0.90

Zfx facilitates tumorigenesis caused by activation of the Hedgehog pathway. Cancer Res (2014) 0.88

High-resolution chromatin immunoprecipitation (ChIP) sequencing reveals novel binding targets and prognostic role for SOX11 in mantle cell lymphoma. Oncogene (2014) 0.88

Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res (2013) 0.87

C26 cancer-induced muscle wasting is IKKβ-dependent and NF-kappaB-independent. PLoS One (2014) 0.86

Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PLoS One (2013) 0.86

Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment. Transl Psychiatry (2013) 0.85

Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. Database (Oxford) (2013) 0.81

CREBBP Inactivation Promotes the Development of HDAC3 Dependent Lymphomas. Cancer Discov (2016) 0.81

The ChIP-seq-defined networks of Bcl-3 gene binding support its required role in skeletal muscle atrophy. PLoS One (2012) 0.80

The Crebbp Acetyltransferase is a Haploinsufficient Tumor Suppressor in B Cell Lymphoma. Cancer Discov (2017) 0.80

RNA-Seq and ChIP-Seq reveal SQSTM1/p62 as a key mediator of JunB suppression of NF-κB-dependent inflammation. J Invest Dermatol (2014) 0.79

jChIP: a graphical environment for exploratory ChIP-Seq data analysis. BMC Res Notes (2014) 0.79

The transcriptional repressor Hes1 attenuates inflammation by regulating transcription elongation. Nat Immunol (2016) 0.78

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics (2016) 0.78

Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells. Nat Commun (2016) 0.78

The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers. PLoS Genet (2015) 0.78

Detection and classification of peaks in 5' cap RNA sequencing data. BMC Genomics (2013) 0.77

Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts. Genes Dev (2016) 0.77

fluff: exploratory analysis and visualization of high-throughput sequencing data. PeerJ (2016) 0.75

Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo. PLoS Genet (2016) 0.75

Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection. PLoS One (2015) 0.75

EpiMINE, a computational program for mining epigenomic data. Epigenetics Chromatin (2016) 0.75

IFN-γ Induces Histone 3 Lysine 27 Trimethylation in a Small Subset of Promoters to Stably Silence Gene Expression in Human Macrophages. Cell Rep (2016) 0.75

Common nonmutational NOTCH1 activation in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A (2017) 0.75

Epigenetic Identity in AML Depends on Disruption of Non-promoter Regulatory Elements and is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. Cancer Discov (2017) 0.75

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18

Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92

BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23

Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63

The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 38.24

Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell (2010) 23.97

Capturing chromosome conformation. Science (2002) 23.93

Open source clustering software. Bioinformatics (2004) 23.17

JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res (2004) 19.32

ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol (1987) 17.53

Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol (2010) 17.00

GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72

Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol (2000) 14.30

An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96

ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89

Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics (2007) 8.80

Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev (2005) 7.21

The KEGG database. Novartis Found Symp (2002) 6.86

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res (2008) 6.83

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53

Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity (2010) 6.48

ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res (2009) 5.98

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res (2007) 5.97

The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods (2006) 5.72

ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods (2009) 4.69

A universal framework for regulatory element discovery across all genomes and data types. Mol Cell (2007) 4.50

CEAS: cis-regulatory element annotation system. Bioinformatics (2009) 4.26

Gene regulation mediated by calcium signals in T lymphocytes. Nat Immunol (2001) 4.09

seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res (2010) 3.74

Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev (2007) 3.56

CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15

Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A (2007) 3.00

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics (2009) 2.70

Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res (2006) 2.67

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics (2010) 2.65

Revealing global regulatory perturbations across human cancers. Mol Cell (2009) 2.62

DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet (2009) 2.56

Expression profiles frame the promoter specificity dilemma of the ETS family of transcription factors. Nucleic Acids Res (2004) 2.55

BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics (2009) 2.47

Defective activation and survival of T cells lacking the Ets-1 transcription factor. Nature (1995) 2.46

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics (2010) 2.41

Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev (2010) 2.31

EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood (2010) 2.11

Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics (2009) 2.02

Reactome knowledgebase of human biological pathways and processes. Methods Mol Biol (2011) 1.91

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res (2010) 1.90

Changes in the expression of many Ets family transcription factors and of potential target genes in normal mammary tissue and tumors. J Biol Chem (2003) 1.72

Chromatin loops in gene regulation. Biochim Biophys Acta (2008) 1.57

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics (2010) 1.57

The c-ets-1 proto-oncogene has oncogenic activity and is positively autoregulated. Oncogene (1990) 1.46

Shape-based peak identification for ChIP-Seq. BMC Bioinformatics (2011) 1.38

Gene expression profiles during human CD4+ T cell differentiation. Int Immunol (2004) 1.27

EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res (2010) 1.23

First exons and introns--a survey of GC content and gene structure in the human genome. In Silico Biol (2006) 1.19

GPAT: retrieval of genomic annotation from large genomic position datasets. BMC Bioinformatics (2008) 1.19

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol (2011) 1.07

ChIPseqR: analysis of ChIP-seq experiments. BMC Bioinformatics (2011) 0.91

Punctuated evolution of prostate cancer genomes. Cell (2013) 7.23

Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell (2012) 6.99

Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol (2007) 3.53

EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell (2013) 3.13

Revealing global regulatory perturbations across human cancers. Mol Cell (2009) 2.62

EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood (2010) 2.11

Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol (2005) 2.04

The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL. Blood (2009) 2.04

Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog (2010) 2.00

Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration. Dev Cell (2013) 1.89

Human ESC-derived hemogenic endothelial cells undergo distinct waves of endothelial to hematopoietic transition. Blood (2012) 1.87

DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood (2010) 1.77

Efficient direct reprogramming of mature amniotic cells into endothelial cells by ETS factors and TGFβ suppression. Cell (2012) 1.74

Mutations in FLVCR1 cause posterior column ataxia and retinitis pigmentosa. Am J Hum Genet (2010) 1.72

let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts. J Biol Chem (2009) 1.65

The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry. Nat Neurosci (2013) 1.57

Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling. Immunity (2013) 1.55

Using transcriptome sequencing to identify mechanisms of drug action and resistance. Nat Chem Biol (2012) 1.53

Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet (2013) 1.50

Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol (2006) 1.49

DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood (2011) 1.40

Oncogene-mediated alterations in chromatin conformation. Proc Natl Acad Sci U S A (2012) 1.40

Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer Res (2012) 1.40

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition. Development (2009) 1.34

Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. Cancer Discov (2012) 1.33

NFIB is a governor of epithelial-melanocyte stem cell behaviour in a shared niche. Nature (2013) 1.29

Faster sequencers, larger datasets, new challenges. Genome Biol (2012) 1.29

A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep (2013) 1.28

A panel of four miRNAs accurately differentiates malignant from benign indeterminate thyroid lesions on fine needle aspiration. Clin Cancer Res (2012) 1.28

AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes. Nature (2013) 1.18

EZH2 mutations are frequent and represent an early event in follicular lymphoma. Blood (2013) 1.17

Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2013) 1.13

Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One (2010) 1.11

A novel approach for characterizing microsatellite instability in cancer cells. PLoS One (2013) 1.10

Vascular niche promotes hematopoietic multipotent progenitor formation from pluripotent stem cells. J Clin Invest (2015) 1.08

A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature (2013) 0.99

Metabolic alterations in lung cancer-associated fibroblasts correlated with increased glycolytic metabolism of the tumor. Mol Cancer Res (2013) 0.97

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas. Genome Biol (2014) 0.96

Epigenomic alterations in localized and advanced prostate cancer. Neoplasia (2013) 0.96

Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma. PLoS One (2012) 0.96

Downregulation of FOXP1 is required during germinal center B-cell function. Blood (2013) 0.94

Antagonistic function of the RNA-binding protein HuR and miR-200b in post-transcriptional regulation of vascular endothelial growth factor-A expression and angiogenesis. J Biol Chem (2012) 0.94

Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk. Proc Natl Acad Sci U S A (2012) 0.91

Akt suppression of TGFβ signaling contributes to the maintenance of vascular identity in embryonic stem cell-derived endothelial cells. Stem Cells (2014) 0.88

Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res (2013) 0.87

Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest (2016) 0.86

Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease. PLoS One (2012) 0.85

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. BMC Bioinformatics (2009) 0.82

A primer on precision medicine informatics. Brief Bioinform (2015) 0.78

Silencing of UCHL1 by CpG promoter hyper-methylation is associated with metastatic gastroenteropancreatic well-differentiated neuroendocrine (carcinoid) tumors. Ann Surg Oncol (2014) 0.77

Calcimimetics versus parathyroidectomy for treatment of primary hyperparathyroidism: retrospective chart analysis of a prospective database. Ann Surg (2012) 0.76

Integrative Clinical Genomics of Advanced Prostate Cancer. Cell (2015) 0.75