Published in Genome Res on March 10, 2010
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol (2011) 2.68
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet (2011) 2.65
Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res (2012) 2.24
Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol (2010) 2.04
Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics (2011) 1.47
TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinformatics (2011) 1.39
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics (2010) 1.22
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst Biol (2012) 1.11
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. Nat Commun (2015) 1.10
A flexible integrative approach based on random forest improves prediction of transcription factor binding sites. Nucleic Acids Res (2012) 0.99
Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One (2011) 0.96
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics (2012) 0.96
Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res (2013) 0.94
Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation. PLoS Genet (2015) 0.91
Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis. BMC Med Genomics (2013) 0.91
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis. BMC Bioinformatics (2013) 0.91
Identifying proteins controlling key disease signaling pathways. Bioinformatics (2013) 0.90
A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites. PLoS One (2011) 0.90
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. Nucleic Acids Res (2015) 0.90
Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One (2011) 0.87
The E2F transcription factors regulate tumor development and metastasis in a mouse model of metastatic breast cancer. Mol Cell Biol (2014) 0.86
Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. Nucleic Acids Res (2011) 0.85
Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast. PLoS Comput Biol (2015) 0.84
Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. Genome Biol (2011) 0.83
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Res (2012) 0.83
A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. Front Bioeng Biotechnol (2014) 0.83
Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS Comput Biol (2013) 0.82
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. BMC Genomics (2011) 0.82
CTF: a CRF-based transcription factor binding sites finding system. BMC Genomics (2012) 0.80
Predicting tissue specific transcription factor binding sites. BMC Genomics (2013) 0.80
The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines. PLoS One (2013) 0.80
PriorsEditor: a tool for the creation and use of positional priors in motif discovery. Bioinformatics (2010) 0.80
Models incorporating chromatin modification data identify functionally important p53 binding sites. Nucleic Acids Res (2013) 0.79
The impact of trans-regulation on the evolutionary rates of metazoan proteins. Nucleic Acids Res (2013) 0.78
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites. Bioinformatics (2015) 0.78
Imputation for transcription factor binding predictions based on deep learning. PLoS Comput Biol (2017) 0.77
Multitask learning of signaling and regulatory networks with application to studying human response to flu. PLoS Comput Biol (2014) 0.77
The differential disease regulome. BMC Genomics (2011) 0.77
Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. BMC Syst Biol (2013) 0.77
SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. Bioinformatics (2014) 0.77
LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data. Nucleic Acids Res (2011) 0.77
A wavelet approach to detect enriched regions and explore epigenomic landscapes. J Comput Biol (2014) 0.76
Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data. BMC Bioinformatics (2015) 0.76
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. BMC Genomics (2012) 0.76
Transcription factor binding sites prediction based on modified nucleosomes. PLoS One (2014) 0.76
Nucleosome organization in the vicinity of transcription factor binding sites in the human genome. BMC Genomics (2014) 0.75
Differences in local genomic context of bound and unbound motifs. Gene (2012) 0.75
Identifying pathogenic processes by integrating microarray data with prior knowledge. BMC Bioinformatics (2014) 0.75
A stationary wavelet entropy-based clustering approach accurately predicts gene expression. J Comput Biol (2014) 0.75
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. Bioinformatics (2016) 0.75
Uncovering MicroRNA Regulatory Hubs that Modulate Plasma Cell Differentiation. Sci Rep (2015) 0.75
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. BMC Syst Biol (2017) 0.75
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. BMC Bioinformatics (2017) 0.75
Three TF Co-expression Modules Regulate Pressure-Overload Cardiac Hypertrophy in Male Mice. Sci Rep (2017) 0.75
The human genome browser at UCSC. Genome Res (2002) 168.23
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res (1999) 49.21
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
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
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-wide location and function of DNA binding proteins. Science (2000) 31.25
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
DNA binding sites: representation and discovery. Bioinformatics (2000) 16.01
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Dynamic regulation of nucleosome positioning in the human genome. Cell (2008) 15.60
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46
E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev (2002) 10.06
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42
Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A (2006) 5.27
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res (2006) 4.32
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet (2007) 3.75
Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol (2006) 3.16
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol (2008) 3.02
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 comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res (2007) 2.97
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res (2008) 2.62
Reconstructing dynamic regulatory maps. Mol Syst Biol (2007) 2.36
Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res (2007) 2.27
A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol (2007) 2.15
Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell (2007) 2.05
Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol (2006) 2.04
Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res (2008) 1.83
Probabilistic inference of transcription factor binding from multiple data sources. PLoS One (2008) 1.58
Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics (2006) 1.45
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res (2008) 1.36
Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function. PLoS Comput Biol (2007) 1.19
The human genomic melting map. PLoS Comput Biol (2007) 1.14
Finding motifs in promoter regions. J Comput Biol (2005) 1.09
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet (2006) 10.47
STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics (2006) 5.21
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet (2006) 4.97
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell (2003) 4.12
The sirtuin SIRT6 regulates lifespan in male mice. Nature (2012) 4.07
Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol (2009) 3.96
Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins (2006) 3.78
Clustering short time series gene expression data. Bioinformatics (2005) 3.48
Continuous representations of time-series gene expression data. J Comput Biol (2003) 3.32
Reconstructing dynamic regulatory maps. Mol Syst Biol (2007) 2.36
Random forest similarity for protein-protein interaction prediction from multiple sources. Pac Symp Biocomput (2005) 2.25
Global organization of replication time zones of the mouse genome. Genome Res (2008) 2.11
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A (2003) 2.10
The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol Cell (2002) 2.10
Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet (2012) 2.01
A probabilistic generative model for GO enrichment analysis. Nucleic Acids Res (2008) 2.01
Modulation of the vitamin D3 response by cancer-associated mutant p53. Cancer Cell (2010) 1.95
MILANO--custom annotation of microarray results using automatic literature searches. BMC Bioinformatics (2005) 1.77
Chemical probes identify a role for histone deacetylase 3 in Friedreich's ataxia gene silencing. Chem Biol (2009) 1.70
Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways. Am J Respir Crit Care Med (2014) 1.69
Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet (2010) 1.68
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife (2013) 1.64
A biological solution to a fundamental distributed computing problem. Science (2011) 1.62
Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol (2008) 1.61
Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly. EMBO J (2003) 1.59
Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report. Am J Respir Crit Care Med (2014) 1.54
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A (2008) 1.53
Deconvolving cell cycle expression data with complementary information. Bioinformatics (2004) 1.51
Cross species analysis of microarray expression data. Bioinformatics (2009) 1.47
A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol (2008) 1.40
Discovering pathways by orienting edges in protein interaction networks. Nucleic Acids Res (2010) 1.32
Protein complex identification by supervised graph local clustering. Bioinformatics (2008) 1.32
Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol (2009) 1.27
A mixture of feature experts approach for protein-protein interaction prediction. BMC Bioinformatics (2007) 1.24
Genome-wide analysis of the replication program in mammals. Chromosome Res (2010) 1.23
Alignment and classification of time series gene expression in clinical studies. Bioinformatics (2008) 1.22
Biological interaction networks are conserved at the module level. BMC Syst Biol (2011) 1.16
Chromatin immunoprecipitation-on-chip reveals stress-dependent p53 occupancy in primary normal cells but not in established cell lines. Cancer Res (2008) 1.16
Extracting dynamics from static cancer expression data. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.14
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res (2012) 1.14
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst Biol (2012) 1.11
Combined analysis reveals a core set of cycling genes. Genome Biol (2007) 1.10
The DcpS inhibitor RG3039 improves survival, function and motor unit pathologies in two SMA mouse models. Hum Mol Genet (2013) 1.09
Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol (2005) 1.09
Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Mol Biol Cell (2009) 1.09
Retracted Comparative expression profile of miRNA and mRNA in primary peripheral blood mononuclear cells infected with human immunodeficiency virus (HIV-1). PLoS One (2011) 1.09
Probabilistic error correction for RNA sequencing. Nucleic Acids Res (2013) 1.08
Reconstructing dynamic microRNA-regulated interaction networks. Proc Natl Acad Sci U S A (2013) 1.01
MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. BMC Infect Dis (2013) 1.00
The DcpS inhibitor RG3039 improves motor function in SMA mice. Hum Mol Genet (2013) 0.99
DECOD: fast and accurate discriminative DNA motif finding. Bioinformatics (2011) 0.98
A patient-gene model for temporal expression profiles in clinical studies. J Comput Biol (2007) 0.98
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. Bioinformatics (2013) 0.97
Identifying cycling genes by combining sequence homology and expression data. Bioinformatics (2006) 0.97
Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol (2010) 0.97
Algorithms in nature: the convergence of systems biology and computational thinking. Mol Syst Biol (2011) 0.96
ExpressionBlast: mining large, unstructured expression databases. Nat Methods (2013) 0.96
An analysis of intra array repeats: the good, the bad and the non informative. BMC Genomics (2006) 0.95
Competition between small RNAs: a quantitative view. Biophys J (2012) 0.95
Rationale for the development of 2-aminobenzamide histone deacetylase inhibitors as therapeutics for Friedreich ataxia. J Child Neurol (2012) 0.95
Tamoxifen induces heparanase expression in estrogen receptor-positive breast cancer. Clin Cancer Res (2007) 0.92
Inferring pairwise regulatory relationships from multiple time series datasets. Bioinformatics (2007) 0.92
DNA methylation and gene expression. Wiley Interdiscip Rev Syst Biol Med (2010) 0.91
Identifying proteins controlling key disease signaling pathways. Bioinformatics (2013) 0.90
Systematic prediction of human membrane receptor interactions. Proteomics (2009) 0.90
A network-based approach for predicting missing pathway interactions. PLoS Comput Biol (2012) 0.90
A high-throughput framework to detect synapses in electron microscopy images. Bioinformatics (2013) 0.90
Molecular characteristics of liver metastases from uveal melanoma. Invest Ophthalmol Vis Sci (2007) 0.89
Cross-species queries of large gene expression databases. Bioinformatics (2010) 0.89
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells. BMC Syst Biol (2013) 0.87
Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes. BMC Genomics (2010) 0.86
A combined expression-interaction model for inferring the temporal activity of transcription factors. J Comput Biol (2009) 0.86
Discriminative motif finding for predicting protein subcellular localization. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.86
Evaluation of histone deacetylase inhibitors as therapeutics for neurodegenerative diseases. Methods Mol Biol (2011) 0.85
Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization. PLoS One (2012) 0.84
Continuous hidden process model for time series expression experiments. Bioinformatics (2007) 0.84
Computational methods for analyzing dynamic regulatory networks. Methods Mol Biol (2010) 0.82
Genome-wide analysis of androgen receptor targets reveals COUP-TF1 as a novel player in human prostate cancer. PLoS One (2012) 0.80
IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability. PLoS One (2009) 0.79
Integrative analysis of methylome and transcriptome reveals the importance of unmethylated CpGs in non-CpG island gene activation. Biomed Res Int (2013) 0.79
Matching experiments across species using expression values and textual information. Bioinformatics (2012) 0.79
cDREM: inferring dynamic combinatorial gene regulation. J Comput Biol (2015) 0.78
Learning cellular sorting pathways using protein interactions and sequence motifs. J Comput Biol (2011) 0.77
Cross species expression analysis of innate immune response. J Comput Biol (2010) 0.77
Topological properties of robust biological and computational networks. J R Soc Interface (2014) 0.75
Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men. AIDS (2017) 0.75
Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue. J Comput Biol (2011) 0.75
The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression. Methods Mol Biol (2016) 0.75