Structure and evolution of transcriptional regulatory networks

Shen-Orr, 2002, Network motifs in the transcriptional regulation network of Escherichia coli, Nat Genet, 31, 64, 10.1038/ng881

Lee, 2002, Transcriptional regulatory networks in Saccharomyces cerevisiae, Science, 298, 799, 10.1126/science.1075090

Salgado, 2004, RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12, Nucleic Acids Res, 32, D303, 10.1093/nar/gkh140

Matys, 2003, TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res, 31, 374, 10.1093/nar/gkg108

Horak, 2002, Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae, Genes Dev, 16, 3017, 10.1101/gad.1039602

Mangan, 2003, The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks, J Mol Biol, 334, 197, 10.1016/j.jmb.2003.09.049

Yu, 2003, Genomic analysis of gene expression relationships in transcriptional regulatory networks, Trends Genet, 19, 422, 10.1016/S0168-9525(03)00175-6

Guelzim, 2002, Topological and causal structure of the yeast transcriptional regulatory network, Nat Genet, 31, 60, 10.1038/ng873

Dobrin, 2004, Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network, BMC Bioinformatics, 5, 10, 10.1186/1471-2105-5-10

Tavazoie, 1999, Systematic determination of genetic network architecture, Nat Genet, 22, 281, 10.1038/10343

Teichmann, 2002, Conservation of gene co-regulation in prokaryotes and eukaryotes, Trends Biotechnol, 20, 407, 10.1016/S0167-7799(02)02032-2

Stuart, 2003, A gene-coexpression network for global discovery of conserved genetic modules, Science, 302, 249, 10.1126/science.1087447

Ihmels, 2002, Revealing modular organization in the yeast transcriptional network, Nat Genet, 31, 370, 10.1038/ng941

Segal, 2003, Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data, Nat Genet, 34, 166, 10.1038/ng1165

Bar-Joseph, 2003, Computational discovery of gene modules and regulatory networks, Nat Biotechnol, 21, 1337, 10.1038/nbt890

Madan Babu, 2003, Evolution of transcription factors and the gene regulatory network in Escherichia coli, Nucleic Acids Res, 31, 1234, 10.1093/nar/gkg210

Yu H, Greenbaum D, Lu H, Zhu X, Gerstein M: Genomic analysis of essentiality within protein networks. Trends Genet 2004, in press.

Martinez-Antonio, 2003, Identifying global regulators in transcriptional regulatory networks in bacteria, Curr Opin Microbiol, 6, 482, 10.1016/j.mib.2003.09.002

Gutierrez-Rios, 2003, Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles, Genome Res, 13, 2435, 10.1101/gr.1387003

Schaffer, 1999, IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices, Bioinformatics, 15, 1000, 10.1093/bioinformatics/15.12.1000

Eddy, 1996, Hidden Markov models, Curr Opin Struct Biol, 6, 361, 10.1016/S0959-440X(96)80056-X

Bateman, 2004, The Pfam protein families database, Nucleic Acids Res, 32, D138, 10.1093/nar/gkh121

Gough, 2001, Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure, J Mol Biol, 313, 903, 10.1006/jmbi.2001.5080

Van Nimwegen, 2003, Scaling laws in the functional content of genomes, Trends Genet, 19, 479, 10.1016/S0168-9525(03)00203-8

Perez-Rueda, 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12, Nucleic Acids Res, 28, 1838, 10.1093/nar/28.8.1838

Aravind, 1999, DNA-binding proteins and evolution of transcription regulation in the archaea, Nucleic Acids Res, 27, 4658, 10.1093/nar/27.23.4658

Riechmann, 2000, Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes, Science, 290, 2105, 10.1126/science.290.5499.2105

Ledent, 2001, The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis, Genome Res, 11, 754, 10.1101/gr.177001

Morgenstern, 1999, Evolution of bHLH transcription factors: modular evolution by domain shuffling?, Mol Biol Evol, 16, 1654, 10.1093/oxfordjournals.molbev.a026079

Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062

Lespinet, 2002, The role of lineage-specific gene family expansion in the evolution of eukaryotes, Genome Res, 12, 1048, 10.1101/gr.174302

Coulson, 2001, Transcription-associated protein families are primarily taxon-specific, Bioinformatics, 17, 95, 10.1093/bioinformatics/17.1.95

Madan Babu, 2003, Functional determinants of transcription factors in Escherichia coli: protein families and binding sites, Trends Genet, 19, 75, 10.1016/S0168-9525(02)00039-2

Bozdech, 2003, The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum, PLoS Biol, 1, E5, 10.1371/journal.pbio.0000005

Abrahamsen, 2004, Complete genome sequence of the apicomplexan, Cryptosporidium parvum, Science, 304, 441, 10.1126/science.1094786

Papp, 2003, Evolution of cis-regulatory elements in duplicated genes of yeast, Trends Genet, 19, 417, 10.1016/S0168-9525(03)00174-4

Maslov, 2004, Upstream plasticity and downstream robustness in evolution of molecular networks, BMC Evol Biol, 4, 9, 10.1186/1471-2148-4-9

Teichmann, 2004, Gene regulatory network growth by duplication, Nat Genet, 36, 492, 10.1038/ng1340

Conant, 2003, Wagner A: Convergent evolution of gene circuits, Nat Genet, 34, 264, 10.1038/ng1181

Cripps, 2002, Control of cardiac development by an evolutionarily conserved transcriptional network, Dev Biol, 246, 14, 10.1006/dbio.2002.0666

Yu H, Luscombe N, Lu H, Zhu X, Xia Y, Han J, Bertin N, Chung S, Goh C, Vidal M, Gerstein M: Annotation transfer for genomics: assessing the transferability of protein-protein and protein-DNA interactions between organisms. Genome Res 2004, in press.

Hubbard, 2002, The Ensembl genome database project, Nucleic Acids Res, 30, 38, 10.1093/nar/30.1.38