Evolutionary dynamics of prokaryotic transcriptional regulatory networks.

[1]  M. Laubichler Does EvoDevo equal regulatory evolution. Review of: Carroll, Sean B.: Endless forms most beautiful: the new science of Evo Devo and the making of the animal kingdom. New York [u.a.]: Norton 2005 , 2006 .

[2]  Julio Collado-Vides,et al.  Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes. , 2005, Journal of molecular biology.

[3]  S. Andersson,et al.  Genome reduction in the α-Proteobacteria , 2005 .

[4]  U. Alon,et al.  Optimality and evolutionary tuning of the expression level of a protein , 2005, Nature.

[5]  A. Wagner Robustness and Evolvability in Living Systems , 2005 .

[6]  L. Aravind,et al.  The many faces of the helix-turn-helix domain: transcription regulation and beyond. , 2005, FEMS microbiology reviews.

[7]  Z. N. Oltvai,et al.  Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[8]  R. Karp,et al.  From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .

[9]  S. Carroll Endless forms most beautiful : the new science of evo devo and the making of the animal kingdom , 2005 .

[10]  Siv G. E. Andersson,et al.  Genome reduction in the alpha-Proteobacteria. , 2005, Current opinion in microbiology.

[11]  M. Vergassola,et al.  An evolutionary and functional assessment of regulatory network motifs , 2005, Genome Biology.

[12]  Inna Dubchak,et al.  Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria , 2004, Genome Biology.

[13]  Pathogens in decay , 2004, Nature Reviews Microbiology.

[14]  Antonis Rokas,et al.  Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Inna Dubchak,et al.  Reconstruction Of Regulatory And Metabolic Pathways In Metal-Reducing delta-Proteobacteria , 2004 .

[16]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[17]  Nicola J. Rinaldi,et al.  Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.

[18]  W. Wasserman,et al.  Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. , 2004, Genome research.

[19]  Roded Sharan,et al.  PathBLAST: a tool for alignment of protein interaction networks , 2004, Nucleic Acids Res..

[20]  Uri Alon,et al.  Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network , 2004, Cell.

[21]  M. Gerstein,et al.  Structure and evolution of transcriptional regulatory networks. , 2004, Current opinion in structural biology.

[22]  M. Gerstein,et al.  Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. , 2004, Genome research.

[23]  M. Gerstein,et al.  Genomic analysis of essentiality within protein networks. , 2004, Trends in genetics : TIG.

[24]  S. Teichmann,et al.  Gene regulatory network growth by duplication , 2004, Nature Genetics.

[25]  S. Shen-Orr,et al.  Superfamilies of Evolved and Designed Networks , 2004, Science.

[26]  Balaji S. Srinivasan,et al.  The evolution of genetic regulatory systems in bacteria , 2004, Nature Reviews Genetics.

[27]  Berend Snel,et al.  Quantifying modularity in the evolution of biomolecular systems. , 2004, Genome research.

[28]  Daniel W. A. Buchan,et al.  Evolution of protein superfamilies and bacterial genome size. , 2004, Journal of molecular biology.

[29]  Dmitrij Frishman,et al.  Conservation of protein-protein interactions - lessons from ascomycota. , 2004, Trends in genetics : TIG.

[30]  Markus J. Herrgård,et al.  Reconstruction of microbial transcriptional regulatory networks. , 2004, Current opinion in biotechnology.

[31]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[32]  Kenta Nakai,et al.  BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics , 2004, Nucleic Acids Res..

[33]  Julio Collado-Vides,et al.  RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 , 2004, Nucleic Acids Res..

[34]  M. Wall,et al.  Design of gene circuits: lessons from bacteria , 2004, Nature Reviews Genetics.

[35]  Julio Collado-Vides,et al.  Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach , 2003, Biotechnology and bioengineering.

[36]  J. Parkhill,et al.  Fitting the niche by genomic adaptation , 2003, Nature Reviews Microbiology.

[37]  Sergei Maslov,et al.  Upstream plasticity and downstream robustness in evolution of molecular networks , 2003, BMC Evolutionary Biology.

[38]  S. Mangan,et al.  Structure and function of the feed-forward loop network motif , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[39]  B. Snel,et al.  Systematic discovery of analogous enzymes in thiamin biosynthesis , 2003, Nature Biotechnology.

[40]  Andreas Wagner,et al.  Convergent evolution of gene circuits , 2003, Nature Genetics.

[41]  E. Nimwegen Scaling Laws in the Functional Content of Genomes , 2003, physics/0307001.

[42]  R. Lenski,et al.  Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation , 2003, Nature Reviews Genetics.

[43]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[44]  S. Teichmann,et al.  Evolution of transcription factors and the gene regulatory network in Escherichia coli. , 2003, Nucleic acids research.

[45]  M. Gelfand,et al.  Comparative Genomics of Thiamin Biosynthesis in Procaryotes , 2002, The Journal of Biological Chemistry.

[46]  S. Blair Hedges,et al.  The origin and evolution of model organisms , 2002, Nature Reviews Genetics.

[47]  Albert-László Barabási,et al.  Life's Complexity Pyramid , 2002, Science.

[48]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[49]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[50]  A. Barabasi,et al.  Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.

[51]  Janet M Thornton,et al.  Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. , 2002, Journal of molecular biology.

[52]  P. Bourgine,et al.  Topological and causal structure of the yeast transcriptional regulatory network , 2002, Nature Genetics.

[53]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[54]  L. Mirny,et al.  Structural analysis of conserved base pairs in protein-DNA complexes. , 2002, Nucleic acids research.

[55]  Nikolaus Rajewsky,et al.  The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. , 2002, Genome research.

[56]  Albert-László Barabási,et al.  Systems biology. Life's complexity pyramid. , 2002, Science.

[57]  S. Shen-Orr,et al.  Networks Network Motifs : Simple Building Blocks of Complex , 2002 .

[58]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[59]  D J Lipman,et al.  Lineage-specific loss and divergence of functionally linked genes in eukaryotes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[60]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[61]  A. Barabasi,et al.  Error and attack tolerance of complex networks , 2000, Nature.

[62]  D. Eisenberg,et al.  Protein function in the post-genomic era , 2000, Nature.

[63]  G. Church,et al.  Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. , 2000, Genome research.

[64]  J. Andersson,et al.  Insights into the evolutionary process of genome degradation. , 1999, Current opinion in genetics & development.

[65]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.