Transcriptional networking.

A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19

The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J (2007) 8.09

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

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

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (2010) 5.56

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

Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48

Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89

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

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

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

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

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89

Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet (2012) 2.80

Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters. Science (2012) 2.75

Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell (2013) 2.67

Gene loops enhance transcriptional directionality. Science (2012) 2.50

Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. J Bacteriol (2008) 2.47

iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biol (2010) 2.39

Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol (2006) 2.36

CREB binds to multiple loci on human chromosome 22. Mol Cell Biol (2004) 2.28

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet (2011) 2.16

Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome. PLoS Genet (2010) 1.94

iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp (2011) 1.80

Arrangements in the modular evolution of proteins. Trends Biochem Sci (2008) 1.78

Metabolism of halophilic archaea. Extremophiles (2008) 1.75

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res (2010) 1.71

TreeWiz: interactive exploration of huge trees. Bioinformatics (2002) 1.70

The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell (2010) 1.68

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics (2011) 1.61

Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO Rep (2004) 1.59

Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature (2012) 1.56

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics (2003) 1.55

The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54

Domain deletions and substitutions in the modular protein evolution. FEBS J (2006) 1.51

Perspectives on protein evolution from simple exact models. Appl Bioinformatics (2002) 1.47

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res (2013) 1.45

Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans. Immunobiology (2008) 1.43

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Res (2002) 1.40

Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Curr Biol (2012) 1.40

Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach. PLoS One (2012) 1.37

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res (2010) 1.35

Transcriptional regulatory networks in bacteria: from input signals to output responses. Curr Opin Microbiol (2006) 1.30

Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc Natl Acad Sci U S A (2002) 1.28

The look-ahead effect of phenotypic mutations. Biol Direct (2008) 1.28

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life. BMC Evol Biol (2011) 1.25

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res (2011) 1.23

Evolution of circular permutations in multidomain proteins. Mol Biol Evol (2006) 1.22

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun (2012) 1.19

A structural model of latent evolutionary potentials underlying neutral networks in proteins. HFSP J (2007) 1.15

Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res (2008) 1.14

Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity. Nucleic Acids Res (2010) 1.14

Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biol Evol (2013) 1.13

Proteome of Hydra nematocyst. J Biol Chem (2012) 1.11

Non-random mutation: the evolution of targeted hypermutation and hypomutation. Bioessays (2012) 1.09

Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants. BMC Plant Biol (2010) 1.09

Just how versatile are domains? BMC Evol Biol (2008) 1.09

The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet (2012) 1.08

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res (2011) 1.05

The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex. Dev Cell (2012) 1.02

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Mol Ecol (2012) 0.99

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods Enzymol (2006) 0.99

Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness. Proc Natl Acad Sci U S A (2012) 0.99

Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol (2012) 0.99

Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species. Proc Natl Acad Sci U S A (2011) 0.98

Cellular resolution models for even skipped regulation in the entire Drosophila embryo. Elife (2013) 0.98

Comparative analysis of expressed sequence tag (EST) libraries in the seagrass Zostera marina subjected to temperature stress. Mar Biotechnol (NY) (2008) 0.98

Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network. BMC Genomics (2006) 0.97

Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins. Mol Biol Evol (2006) 0.96

The dynamics and evolutionary potential of domain loss and emergence. Mol Biol Evol (2011) 0.95

The sieve element occlusion gene family in dicotyledonous plants. Plant Signal Behav (2011) 0.94

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Syst Biol (2007) 0.94

Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Res (2011) 0.93

Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts. PLoS Comput Biol (2012) 0.92

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast. Nucleic Acids Res (2014) 0.92

Rapid motif-based prediction of circular permutations in multi-domain proteins. Bioinformatics (2005) 0.92

Distribution of gibberellin biosynthetic genes and gibberellin production in the Gibberella fujikuroi species complex. Phytochemistry (2005) 0.91

Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics (2013) 0.89

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. Mol Genet Genomics (2008) 0.88

Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree. Biochim Biophys Acta (2013) 0.88

DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins. Bioinformatics (2013) 0.87

Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm. Biophys J (2004) 0.87

Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis. BMC Genomics (2014) 0.85

The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Mol Cell Proteomics (2011) 0.85

SpeCond: a method to detect condition-specific gene expression. Genome Biol (2011) 0.85

Sensitized phenotypic screening identifies gene dosage sensitive region on chromosome 11 that predisposes to disease in mice. EMBO Mol Med (2011) 0.84

Response to Comments on "Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters". Science (2013) 0.83

Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN). Bioinformatics (2007) 0.83

A putative transcription factor inducing mobility in Mycoplasma pneumoniae. Microbiology (2002) 0.82

Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness. Integr Biol (Camb) (2012) 0.81

Genomic divergence between nine- and three-spined sticklebacks. BMC Genomics (2013) 0.81

The evolution of protein interaction networks in regulatory proteins. Comp Funct Genomics (2004) 0.81

m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. Genome Biol (2012) 0.81

Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs. Gene (2005) 0.81

Robustness versus evolvability: a paradigm revisited. HFSP J (2010) 0.81

Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements. Genome Res (2013) 0.80

Know your limits: assumptions, constraints and interpretation in systems biology. Biochim Biophys Acta (2009) 0.80

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome. Methods Mol Biol (2012) 0.79