Structure and evolution of transcriptional regulatory networks.

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol (2009) 7.11

Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63

Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science (2010) 4.78

Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer (2009) 4.40

An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell (2010) 3.60

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res (2004) 3.44

Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43

Principles of microRNA regulation of a human cellular signaling network. Mol Syst Biol (2006) 3.27

VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res (2005) 3.24

Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66

A map of human cancer signaling. Mol Syst Biol (2007) 2.50

DBD: a transcription factor prediction database. Nucleic Acids Res (2006) 2.46

STING and the innate immune response to nucleic acids in the cytosol. Nat Immunol (2013) 2.23

Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics (2004) 2.14

TFCat: the curated catalog of mouse and human transcription factors. Genome Biol (2009) 2.06

Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res (2006) 2.04

Function of alternative splicing. Gene (2012) 2.00

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res (2008) 1.99

Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res (2007) 1.79

A complex task? Direct modulation of transcription factors with small molecules. Curr Opin Chem Biol (2010) 1.75

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol (2009) 1.73

GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol (2008) 1.72

The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays (2009) 1.72

The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci (2006) 1.71

Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc Natl Acad Sci U S A (2007) 1.64

The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res (2006) 1.62

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res (2011) 1.62

Shifting players and paradigms in cell-specific transcription. Mol Cell (2009) 1.60

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics (2007) 1.56

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol (2014) 1.55

ChIPping away at gene regulation. EMBO Rep (2008) 1.54

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol (2008) 1.45

Stable evolutionary signal in a yeast protein interaction network. BMC Evol Biol (2006) 1.45

Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol (2010) 1.40

A systematic, large-scale comparison of transcription factor binding site models. BMC Genomics (2016) 1.39

Coding limits on the number of transcription factors. BMC Genomics (2006) 1.38

Regulation of transcription in plants: mechanisms controlling developmental switches. Nat Rev Genet (2010) 1.38

The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response. BMC Syst Biol (2008) 1.36

Legume transcription factor genes: what makes legumes so special? Plant Physiol (2009) 1.30

Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci U S A (2010) 1.24

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proc Natl Acad Sci U S A (2010) 1.19

Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli. J Mol Biol (2007) 1.18

Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis. PLoS One (2010) 1.13

Comprehensive functional annotation of seventy-one breast cancer risk Loci. PLoS One (2013) 1.10

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol (2006) 1.08

Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism. ISRN Biochem (2013) 1.07

Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity. PLoS One (2007) 1.07

Reconstruction of the core and extended regulons of global transcription factors. PLoS Genet (2010) 1.06

Enhancer activation requires trans-recruitment of a mega transcription factor complex. Cell (2014) 1.06

TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res (2010) 1.05

From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. Nucleic Acids Res (2009) 1.04

A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation. Nucleic Acids Res (2011) 1.03

Topology of molecular interaction networks. BMC Syst Biol (2013) 1.03

Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic (2009) 1.02

Lineage-specific transcription factors and the evolution of gene regulatory networks. Brief Funct Genomics (2010) 1.01

Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin. Mol Biol Evol (2010) 1.01

An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. Mol Cell (2015) 0.98

Prokaryotic genome regulation: a revolutionary paradigm. Proc Jpn Acad Ser B Phys Biol Sci (2012) 0.97

Transcription factor functionality and transcription regulatory networks. Mol Biosyst (2008) 0.96

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics (2006) 0.96

The developmental expression dynamics of Drosophila melanogaster transcription factors. Genome Biol (2010) 0.96

Insights from the architecture of the bacterial transcription apparatus. J Struct Biol (2011) 0.95

Evolutionary constraints permeate large metabolic networks. BMC Evol Biol (2009) 0.95

Network Inference and Biological Dynamics. Ann Appl Stat (2012) 0.94

Mapping functional transcription factor networks from gene expression data. Genome Res (2013) 0.94

Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data. Curr Genomics (2015) 0.93

Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Dev Cell (2016) 0.92

Topological comparison of methods for predicting transcriptional cooperativity in yeast. BMC Genomics (2008) 0.92

Refining transcriptional regulatory networks using network evolutionary models and gene histories. Algorithms Mol Biol (2010) 0.92

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol (2010) 0.92

Dynamics and processing in finite self-similar networks. J R Soc Interface (2012) 0.92

REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. BMC Genomics (2013) 0.91

Structure-dependent inhibition of the ETS-family transcription factor PU.1 by novel heterocyclic diamidines. Nucleic Acids Res (2013) 0.91

De novo evolution of complex, global and hierarchical gene regulatory mechanisms. J Mol Evol (2010) 0.90

Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Mol Syst Biol (2007) 0.90

The architecture of the gene regulatory networks of different tissues. Bioinformatics (2012) 0.90

Transcription factor beacons for the quantitative detection of DNA binding activity. J Am Chem Soc (2011) 0.90

Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal? Trends Genet (2008) 0.90

Transcription factor networks in Drosophila melanogaster. Cell Rep (2014) 0.89

Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nat Protoc (2009) 0.89

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods. Biol Direct (2012) 0.88

Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics. PLoS Comput Biol (2013) 0.88

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella. BMC Genomics (2011) 0.88

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria. BMC Genomics (2008) 0.88

Dynamic changes in subgraph preference profiles of crucial transcription factors. PLoS Comput Biol (2006) 0.87

High throughput interaction data reveals degree conservation of hub proteins. Pac Symp Biocomput (2009) 0.86

Evolution of gene regulatory networks by fluctuating selection and intrinsic constraints. PLoS Comput Biol (2010) 0.86

Modeling the relationship of epigenetic modifications to transcription factor binding. Nucleic Acids Res (2015) 0.86

Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy. Trends Endocrinol Metab (2014) 0.85

An interaction-motif-based scoring function for protein-ligand docking. BMC Bioinformatics (2010) 0.85

The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth. J Theor Biol (2013) 0.85

On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks. Nucleic Acids Res (2010) 0.85

Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure. BioData Min (2015) 0.85

Trapping of transcription factors with symmetrical DNA using thiol-disulfide exchange chemistry. J Chromatogr A (2008) 0.85

Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. BMC Syst Biol (2012) 0.84

On the contributions of topological features to transcriptional regulatory network robustness. BMC Bioinformatics (2012) 0.84

Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res (2010) 0.84

Tumor suppressor maspin as a rheostat in HDAC regulation to achieve the fine-tuning of epithelial homeostasis. Crit Rev Eukaryot Gene Expr (2012) 0.84

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99

Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (2009) 32.97

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33

Landscape of transcription in human cells. Nature (2012) 20.18

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85

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

Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science (1998) 13.64

De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature (2004) 12.41

Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32

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

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res (1999) 11.30

Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science (2000) 10.82

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

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature (2010) 8.87

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41

The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24

Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol (2001) 8.14

Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science (1999) 8.01

Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93

Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49

Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46

Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10

Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics (1999) 6.91

Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol (2002) 6.85

The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol (2000) 6.50

Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (1998) 6.28

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

Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol (2010) 5.98

Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78

Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science (2004) 5.64

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26

DNA-binding specificities of human transcription factors. Cell (2013) 5.14

Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95

A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75

AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71

Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62

Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res (2006) 4.49

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39

Common origin of four diverse families of large eukaryotic DNA viruses. J Virol (2001) 4.28

The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28

Evolution of the protein repertoire. Science (2003) 4.24

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14

Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet (1998) 4.10

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00

Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol (2000) 3.99

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92

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Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science (1998) 3.83

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res (1999) 3.62

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61

Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods (2013) 3.61

Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52

Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51

Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48

Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science (2008) 3.48

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res (2010) 3.46

Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res (1999) 3.44

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41

Structured digital abstract makes text mining easy. Nature (2007) 3.38

Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36

Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28

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Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27

Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol (2003) 3.26

The impact of comparative genomics on our understanding of evolution. Cell (2000) 3.25

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22

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TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol (2013) 3.18

DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res (2007) 3.18

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell (2008) 3.18