Published in Cell on March 05, 2010
Architecture of the human regulatory network derived from ENCODE data. Nature (2012) 10.28
Macrophage biology in development, homeostasis and disease. Nature (2013) 8.28
The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet (2011) 5.95
Charting a dynamic DNA methylation landscape of the human genome. Nature (2013) 5.80
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
T follicular helper cell differentiation, function, and roles in disease. Immunity (2014) 3.29
ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res (2010) 2.79
A decade of systems biology. Annu Rev Cell Dev Biol (2010) 2.30
A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program. Neuron (2016) 2.26
Compensatory dendritic cell development mediated by BATF-IRF interactions. Nature (2012) 2.25
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet (2011) 2.22
Integrative approaches for finding modular structure in biological networks. Nat Rev Genet (2013) 2.19
AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res (2011) 2.15
Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biol (2011) 2.08
Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet (2012) 2.02
Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci U S A (2013) 1.94
CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Genome Res (2010) 1.77
Large scale comparison of global gene expression patterns in human and mouse. Genome Biol (2010) 1.77
Molecular regulation of effector and memory T cell differentiation. Nat Immunol (2014) 1.70
Transcriptional regulation of brain gene expression in response to a territorial intrusion. Proc Biol Sci (2012) 1.60
Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res (2011) 1.58
Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Res (2011) 1.53
DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature (2015) 1.50
Specificity through cooperation: BATF-IRF interactions control immune-regulatory networks. Nat Rev Immunol (2013) 1.50
Enhancer evolution across 20 mammalian species. Cell (2015) 1.48
The genomic landscapes of inflammation. Genes Dev (2011) 1.45
Alterations of immune response of Non-Small Cell Lung Cancer with Azacytidine. Oncotarget (2013) 1.44
Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors. Nat Cell Biol (2016) 1.42
Characterization of CD8+ T cell differentiation following SIVΔnef vaccination by transcription factor expression profiling. PLoS Pathog (2015) 1.42
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol (2011) 1.39
Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol (2011) 1.35
Evolution of transcription factor binding in metazoans - mechanisms and functional implications. Nat Rev Genet (2014) 1.33
Measuring the evolutionary rate of protein-protein interaction. Proc Natl Acad Sci U S A (2011) 1.32
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat Struct Mol Biol (2011) 1.31
Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. Nucleic Acids Res (2011) 1.31
The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev (2011) 1.30
Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas. Nat Genet (2013) 1.26
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. Nucleic Acids Res (2014) 1.25
MiR-34a expression has an effect for lower risk of metastasis and associates with expression patterns predicting clinical outcome in breast cancer. PLoS One (2011) 1.24
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res (2012) 1.22
Separated at birth? The functional and molecular divergence of OLIG1 and OLIG2. Nat Rev Neurosci (2012) 1.22
Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling. Mol Cell Proteomics (2010) 1.22
Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Mol Cell (2013) 1.21
Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol (2013) 1.20
Protein networks as logic functions in development and cancer. PLoS Comput Biol (2011) 1.19
Cooperative transcription factor associations discovered using regulatory variation. Proc Natl Acad Sci U S A (2011) 1.18
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res (2012) 1.17
What does biologically meaningful mean? A perspective on gene regulatory network validation. Genome Biol (2011) 1.16
NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res (2013) 1.15
Evolution of transcription networks--lessons from yeasts. Curr Biol (2010) 1.12
Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev (2012) 1.11
Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'. Trends Genet (2014) 1.10
Networks of bZIP protein-protein interactions diversified over a billion years of evolution. Science (2013) 1.08
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res (2010) 1.08
The distinct and overlapping phenotypic spectra of FOXP1 and FOXP2 in cognitive disorders. Hum Genet (2012) 1.08
Discovering modulators of gene expression. Nucleic Acids Res (2010) 1.07
Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates. Dev Dyn (2013) 1.07
Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues. Sci Rep (2014) 1.06
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res (2010) 1.05
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PLoS Genet (2012) 1.04
Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci (2013) 1.03
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Res (2013) 1.02
Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics (2010) 1.02
Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics (2010) 1.01
Experimental strategies for studying transcription factor-DNA binding specificities. Brief Funct Genomics (2010) 1.01
DEEP: a general computational framework for predicting enhancers. Nucleic Acids Res (2014) 1.01
Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods (2015) 1.00
Differential network analysis for the identification of condition-specific pathway activity and regulation. Bioinformatics (2013) 0.99
The RIKEN integrated database of mammals. Nucleic Acids Res (2010) 0.99
AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. Nucleic Acids Res (2014) 0.99
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol (2015) 0.98
Dynamic HoxB4-regulatory network during embryonic stem cell differentiation to hematopoietic cells. Blood (2012) 0.98
Identification of epistatic effects using a protein-protein interaction database. Hum Mol Genet (2010) 0.98
Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts. PLoS One (2012) 0.98
EKLF/KLF1, a tissue-restricted integrator of transcriptional control, chromatin remodeling, and lineage determination. Mol Cell Biol (2012) 0.98
In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation. Immunity (2014) 0.98
Comparative transcriptional profiling of renal cortex in rats with inherited stress-induced arterial hypertension and normotensive Wistar Albino Glaxo rats. BMC Genet (2016) 0.97
Genome-wide transcriptome analysis of hypothalamus in rats with inherited stress-induced arterial hypertension. BMC Genet (2016) 0.97
Genomic perspectives of transcriptional regulation in forebrain development. Neuron (2015) 0.97
Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Res (2013) 0.97
Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control. BMC Genomics (2015) 0.97
Human gene-centered transcription factor networks for enhancers and disease variants. Cell (2015) 0.97
Systematic clustering of transcription start site landscapes. PLoS One (2011) 0.95
Transcriptional networks in epithelial-mesenchymal transition. PLoS One (2011) 0.95
The grammar of transcriptional regulation. Hum Genet (2014) 0.95
What evidence is there for the homology of protein-protein interactions? PLoS Comput Biol (2012) 0.95
Repair of oxidative DNA damage and cancer: recent progress in DNA base excision repair. Antioxid Redox Signal (2013) 0.95
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res (2015) 0.95
Integrated module and gene-specific regulatory inference implicates upstream signaling networks. PLoS Comput Biol (2013) 0.94
Constitutive patterns of gene expression regulated by RNA-binding proteins. Genome Biol (2014) 0.94
Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol (2014) 0.94
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. BMC Biol (2011) 0.93
Plenary perspective: the complexity of constitutive and inducible gene expression in mononuclear phagocytes. J Leukoc Biol (2012) 0.93
The Cellular and Molecular Landscapes of the Developing Human Central Nervous System. Neuron (2016) 0.93
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines. BMC Genomics (2013) 0.93
Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Med (2015) 0.92
Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR. Nucleic Acids Res (2011) 0.92
Integration of biological networks and pathways with genetic association studies. Hum Genet (2012) 0.92
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
Genome-wide atlas of gene expression in the adult mouse brain. Nature (2006) 28.02
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res (2005) 9.90
A genomic regulatory network for development. Science (2002) 9.67
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci U S A (1998) 9.06
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature (2007) 5.81
The functional landscape of mouse gene expression. J Biol (2004) 5.65
Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol (2009) 5.41
Regulatory networks define phenotypic classes of human stem cell lines. Nature (2008) 4.98
Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev (2008) 4.77
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science (2008) 4.36
Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature (2009) 2.88
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res (2006) 2.50
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res (2006) 2.26
Evolution of eukaryotic transcription circuits. Science (2008) 2.24
Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide. Proc Natl Acad Sci U S A (2006) 1.96
Protein-protein interaction panel using mouse full-length cDNAs. Genome Res (2001) 1.84
A role for AP-1 in apoptosis: the case for and against. Biochimie (2003) 1.66
Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proc Natl Acad Sci U S A (2007) 1.63
Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Cancer Res (2008) 1.58
EWS-FLI1 suppresses NOTCH-activated p53 in Ewing's sarcoma. Cancer Res (2008) 1.38
NetworkBLAST: comparative analysis of protein networks. Bioinformatics (2008) 1.37
A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc Natl Acad Sci U S A (2008) 1.30
Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. Genome Biol (2008) 1.29
Hyaluronan facilitates transforming growth factor-beta1-mediated fibroblast proliferation. J Biol Chem (2008) 1.28
Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks. Nucleic Acids Res (2005) 1.27
Nuclear architecture and gene regulation. Biochim Biophys Acta (2008) 1.23
Role of homeobox genes in the patterning, specification, and differentiation of ectodermal appendages in mammals. J Cell Physiol (2008) 1.21
Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS One (2007) 1.11
Integrated approaches to uncovering transcription regulatory networks in mammalian cells. Genomics (2008) 1.09
Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Bioinformatics (2005) 1.04
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. BMC Syst Biol (2008) 1.03
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Genome Biol (2005) 0.97
Stem cells, pluripotency and nuclear reprogramming. J Thromb Haemost (2009) 0.97
In vitro pull-down assay without expression constructs. Biotechniques (2004) 0.92
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (2010) 26.76
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Landscape of transcription in human cells. Nature (2012) 20.18
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res (2004) 19.32
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
The accessible chromatin landscape of the human genome. Nature (2012) 16.86
Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet (2008) 15.94
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature (2004) 13.27
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol (2003) 12.34
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
Big data: The future of biocuration. Nature (2008) 10.81
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res (2009) 9.42
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res (2007) 8.79
DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature (2011) 8.75
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell (2008) 8.41
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J (2002) 7.70
Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A (2005) 7.48
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet (2003) 7.25
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res (2004) 6.72
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res (2002) 6.61
HIN-200 proteins regulate caspase activation in response to foreign cytoplasmic DNA. Science (2009) 6.59
A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53
A promoter-level mammalian expression atlas. Nature (2014) 6.25