Bayesian network analysis of targeting interactions in chromatin.

Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88

The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PLoS One (2010) 1.09

Identical functional organization of nonpolytene and polytene chromosomes in Drosophila melanogaster. PLoS One (2011) 1.03

Late replication domains in polytene and non-polytene cells of Drosophila melanogaster. PLoS One (2012) 1.02

BNFinder2: Faster Bayesian network learning and Bayesian classification. Bioinformatics (2013) 0.98

Emerging patterns of epigenomic variation. Trends Genet (2011) 0.95

Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes. Sci Rep (2012) 0.94

Global quantitative modeling of chromatin factor interactions. PLoS Comput Biol (2014) 0.89

Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. BMC Syst Biol (2011) 0.87

Functional conservation of the Drosophila hybrid incompatibility gene Lhr. BMC Evol Biol (2011) 0.86

A novel Bayesian network inference algorithm for integrative analysis of heterogeneous deep sequencing data. Cell Res (2013) 0.85

Chromatin evolution and molecular drive in speciation. Int J Evol Biol (2011) 0.82

Predictive models of gene regulation from high-throughput epigenomics data. Comp Funct Genomics (2012) 0.81

EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes. Nucleic Acids Res (2012) 0.81

Modeling exon expression using histone modifications. PLoS One (2013) 0.80

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. Genome Biol (2016) 0.78

A nucleosomal approach to inferring causal relationships of histone modifications. BMC Genomics (2014) 0.77

Detection of type 2 diabetes related modules and genes based on epigenetic networks. BMC Syst Biol (2014) 0.77

Algorithms for modeling global and context-specific functional relationship networks. Brief Bioinform (2015) 0.76

Regulatory functions and chromatin loading dynamics of linker histone H1 during endoreplication in Drosophila. Genes Dev (2017) 0.75

Modeling to optimize terminal stem cell differentiation. Scientifica (Cairo) (2013) 0.75

A protein interaction map of Drosophila melanogaster. Science (2003) 20.06

The complex language of chromatin regulation during transcription. Nature (2007) 16.97

Using Bayesian networks to analyze expression data. J Comput Biol (2000) 15.98

A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07

The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83

Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer (2006) 11.48

The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41

Inferring cellular networks using probabilistic graphical models. Science (2004) 9.91

The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev (2004) 7.57

Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet (2005) 7.22

Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet (2006) 6.47

Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2007) 6.27

Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J (2002) 5.70

Groucho is required for Drosophila neurogenesis, segmentation, and sex determination and interacts directly with hairy-related bHLH proteins. Cell (1994) 4.95

Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet (2002) 4.68

Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev (2003) 4.68

Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol (2008) 4.50

Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics (2004) 4.14

Inferring subnetworks from perturbed expression profiles. Bioinformatics (2001) 3.93

A functional interaction between the histone deacetylase Rpd3 and the corepressor groucho in Drosophila development. Genes Dev (1999) 3.91

Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat Genet (2006) 3.83

Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science (2006) 3.77

Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet (2006) 3.44

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.06

Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc Natl Acad Sci U S A (1992) 2.80

Chromatin remodeling: insights and intrigue from single-molecule studies. Nat Struct Mol Biol (2007) 2.79

Drosophila CtBP: a Hairy-interacting protein required for embryonic segmentation and hairy-mediated transcriptional repression. EMBO J (1998) 2.74

Prospero acts as a binary switch between self-renewal and differentiation in Drosophila neural stem cells. Dev Cell (2006) 2.69

Network inference using informative priors. Proc Natl Acad Sci U S A (2008) 1.96

Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev (2003) 1.96

Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding. Proc Natl Acad Sci U S A (2003) 1.89

Rules and regulation in the primary structure of chromatin. Curr Opin Cell Biol (2007) 1.86

Bayesian network analysis of signaling networks: a primer. Sci STKE (2005) 1.85

Inferring causal relationships among different histone modifications and gene expression. Genome Res (2008) 1.84

Mapping of genetic and epigenetic regulatory networks using microarrays. Nat Genet (2005) 1.80

The Drosophila BRM complex facilitates global transcription by RNA polymerase II. EMBO J (2002) 1.78

Genome-wide mapping of protein-DNA interactions by chromatin immunoprecipitation and DNA microarray hybridization. Methods Mol Biol (2003) 1.67

Hairy transcriptional repression targets and cofactor recruitment in Drosophila. PLoS Biol (2004) 1.63

High-resolution mapping reveals links of HP1 with active and inactive chromatin components. PLoS Genet (2007) 1.59

The Rpd3 histone deacetylase is required for segmentation of the Drosophila embryo. Proc Natl Acad Sci U S A (1999) 1.55

A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet (2007) 1.53

DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol (2006) 1.52

Evaluating functional network inference using simulations of complex biological systems. Bioinformatics (2002) 1.49

Global chromatin domain organization of the Drosophila genome. PLoS Genet (2008) 1.45

Global patterns of histone modifications. Curr Opin Genet Dev (2007) 1.45

Seeded Bayesian Networks: constructing genetic networks from microarray data. BMC Syst Biol (2008) 1.40

The genomic silencing of position-effect variegation in Drosophila melanogaster: interaction between the heterochromatin-associated proteins Su(var)3-7 and HP1. J Cell Sci (2000) 1.37

Novel Jun- and Fos-related proteins in Drosophila are functionally homologous to enhancer factor AP-1. EMBO J (1988) 1.29

HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. EMBO J (2007) 1.27

Chromosomal localization links the SIN3-RPD3 complex to the regulation of chromatin condensation, histone acetylation and gene expression. EMBO J (2000) 1.20

SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila. J Cell Sci (2007) 1.14

Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies. Chromosoma (2008) 1.12

The transcriptional repressor dMnt is a regulator of growth in Drosophila melanogaster. Mol Cell Biol (2005) 1.11

Transcription factor access to promoter elements. J Cell Biochem (2007) 1.09

Context-specific Bayesian clustering for gene expression data. J Comput Biol (2002) 1.09

High-resolution mapping of heterochromatin redistribution in a Drosophila position-effect variegation model. Epigenetics Chromatin (2009) 1.03

Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo. Chromosoma (1996) 1.00

The Drosophila MBD2/3 protein mediates interactions between the MI-2 chromatin complex and CpT/A-methylated DNA. Development (2004) 0.91

Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment. Bioinformatics (2005) 0.91

Functional dissection of the Drosophila modifier of variegation Su(var)3-7. Development (2002) 0.90

Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76

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

Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18

Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell (2010) 9.50

Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol (2003) 9.13

Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell (2008) 8.41

Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A (2005) 7.48

The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J (2005) 7.10

Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07

A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53

An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24

Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res (2002) 5.42

Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol (2005) 5.38

Human host factors required for influenza virus replication. Nature (2010) 5.28

Modeling cellular machinery through biological network comparison. Nat Biotechnol (2006) 5.01

Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A (2003) 4.68

Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science (2008) 4.36

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol (2010) 4.32

Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog (2009) 4.24

Rewiring of genetic networks in response to DNA damage. Science (2010) 4.03

enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89

Functional genomic screen for modulators of ciliogenesis and cilium length. Nature (2010) 3.63

A systems approach to mapping DNA damage response pathways. Science (2006) 3.55

Inferring pathway activity toward precise disease classification. PLoS Comput Biol (2008) 3.48

PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res (2004) 3.20

Network-based stratification of tumor mutations. Nat Methods (2013) 3.12

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell (2008) 2.96

A gene ontology inferred from molecular networks. Nat Biotechnol (2013) 2.95

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol (2006) 2.80

Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet (2007) 2.77

A human MAP kinase interactome. Nat Methods (2010) 2.62

Systematic identification of functional orthologs based on protein network comparison. Genome Res (2006) 2.47

Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol (2008) 2.46

eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol (2008) 2.45

Physical network models. J Comput Biol (2004) 2.44

Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J Biol Chem (2003) 2.36

Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol (2002) 2.30

A decade of systems biology. Annu Rev Cell Dev Biol (2010) 2.30

Integrative approaches for finding modular structure in biological networks. Nat Rev Genet (2013) 2.19

A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol (2007) 2.13

Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol (2006) 2.04

Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol (2005) 2.03

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol (2005) 2.02

Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet (2012) 2.02

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res (2005) 1.97

Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol (2004) 1.90

Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell (2012) 1.88

A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Curr Biol (2010) 1.86

Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol Cell (2004) 1.81

Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol (2006) 1.81

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A (2009) 1.79

Dissection of DNA damage responses using multiconditional genetic interaction maps. Mol Cell (2012) 1.78

The Plasmodium protein network diverges from those of other eukaryotes. Nature (2005) 1.76

Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog (2009) 1.67

Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity (2011) 1.66

Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nat Protoc (2011) 1.66

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife (2013) 1.64

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (2007) 1.60

A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics (2006) 1.56

Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol (2013) 1.49

Global chromatin domain organization of the Drosophila genome. PLoS Genet (2008) 1.45

Global architecture of genetic interactions on the protein network. Nat Biotechnol (2003) 1.40

NetworkBLAST: comparative analysis of protein networks. Bioinformatics (2008) 1.37

Cost-effective strategies for completing the interactome. Nat Methods (2008) 1.25

Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet (2009) 1.23

Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res (2008) 1.22

Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol (2013) 1.20

Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells. Nat Genet (2010) 1.20

Point: Are we prepared for the future doctor visit? Nat Biotechnol (2011) 1.20

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics (2010) 1.19

Protein networks as logic functions in development and cancer. PLoS Comput Biol (2011) 1.19

DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO J (2012) 1.17

Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood (2012) 1.16

Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res (2010) 1.16

A network model of the molecular organization of chromatin in Drosophila. Mol Cell (2013) 1.13

PKCε promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell (2012) 1.11

The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PLoS One (2010) 1.09

CellCircuits: a database of protein network models. Nucleic Acids Res (2006) 1.08

Mitochondria, energetics, epigenetics, and cellular responses to stress. Environ Health Perspect (2014) 1.03

Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput (2006) 1.03

The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe. Nucleus (2012) 1.03

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics (2010) 1.02

Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. J Proteome Res (2012) 1.01

High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-β family member growth differentiation factor 6. J Biol Chem (2011) 1.01

PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics (2011) 1.00

Genotype to phenotype via network analysis. Curr Opin Genet Dev (2013) 0.99

Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin. Nucleic Acids Res (2011) 0.99

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol (2010) 0.97

Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Sci Signal (2013) 0.94

An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. J Neurosci (2009) 0.93

Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol (2012) 0.93

Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. Plant Cell (2010) 0.92

Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. J Proteome Res (2013) 0.91

The conserved cysteine-rich domain of a tesmin/TSO1-like protein binds zinc in vitro and TSO1 is required for both male and female fertility in Arabidopsis thaliana. J Exp Bot (2007) 0.91

Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genet (2009) 0.90

Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics (2007) 0.88

NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res (2013) 0.88