From elements to modules: regulatory evolution in Ascomycota fungi.

[1]  N. Barkai,et al.  A genetic signature of interspecies variations in gene expression , 2006, Nature Genetics.

[2]  S. Bergmann,et al.  Similarities and Differences in Genome-Wide Expression Data of Six Organisms , 2003, PLoS biology.

[3]  Sven Bergmann,et al.  Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage , 2005, Science.

[4]  S. Casaregola,et al.  Transcriptomic Analysis of Extensive Changes in Metabolic Regulation in Kluyveromyces lactis Strains , 2006, Eukaryotic Cell.

[5]  Sean B. Carroll,et al.  Gene duplication and the adaptive evolution of a classic genetic switch , 2007, Nature.

[6]  Amos Tanay,et al.  Extensive low-affinity transcriptional interactions in the yeast genome. , 2006, Genome research.

[7]  Scott A. Rifkin,et al.  Duplicate genes increase gene expression diversity within and between species , 2004, Nature Genetics.

[8]  Matthieu Legendre,et al.  Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability , 2009, Science.

[9]  K. H. Wolfe,et al.  Molecular evidence for an ancient duplication of the entire yeast genome , 1997, Nature.

[10]  N. Barkai,et al.  Comparative analysis indicates regulatory neofunctionalization of yeast duplicates , 2007, Genome Biology.

[11]  Adam P. Rosebrock,et al.  The Cell Cycle–Regulated Genes of Schizosaccharomyces pombe , 2005, PLoS biology.

[12]  M. King,et al.  Evolution at two levels in humans and chimpanzees. , 1975, Science.

[13]  A. E. Tsong,et al.  Evolution of a Combinatorial Transcriptional Circuit A Case Study in Yeasts , 2003, Cell.

[14]  Roded Sharan,et al.  Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  L. Fulton,et al.  Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting , 2003, Science.

[16]  Y. Pilpel,et al.  Transcription control reprogramming in genetic backup circuits , 2005, Nature Genetics.

[17]  A. Hinnebusch,et al.  Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons , 2007, Eukaryotic Cell.

[18]  Jens Nielsen,et al.  A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species , 2008, Proceedings of the National Academy of Sciences.

[19]  Scott Doniger,et al.  Frequent Gain and Loss of Functional Transcription Factor Binding Sites , 2007, PLoS Comput. Biol..

[20]  Rachel B. Brem,et al.  Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors , 2003, Nature Genetics.

[21]  Michael Lachmann,et al.  Evolution of primate gene expression , 2006, Nature Reviews Genetics.

[22]  S. Bergmann,et al.  Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program , 2005, PLoS genetics.

[23]  K. H. Wolfe,et al.  Reproductive toxicology. Chemical mixture. , 1997, Environmental health perspectives.

[24]  Scott A. Rifkin,et al.  Genetic Properties Influencing the Evolvability of Gene Expression , 2007, Science.

[25]  Duccio Cavalieri,et al.  Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. , 2006, Gene.

[26]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[27]  Alan M. Moses,et al.  Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi , 2004, PLoS biology.

[28]  Daniel J. Kvitek,et al.  Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates , 2008, PLoS genetics.

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

[30]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[31]  M. Whiteway,et al.  Transcriptional Activation Domains of the Candida albicans Gcn4p and Gal4p Homologs , 2006, Eukaryotic Cell.

[32]  Yaniv Ziv,et al.  Revealing modular organization in the yeast transcriptional network , 2002, Nature Genetics.

[33]  A. Regev,et al.  Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  A. Rokas,et al.  Transcriptional Rewiring: The Proof Is in the Eating , 2007, Current Biology.

[35]  Wendell A. Lim,et al.  Correction: Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species , 2009, PLoS Biology.

[36]  Naama Barkai,et al.  On the relation between promoter divergence and gene expression evolution , 2008, Molecular systems biology.

[37]  Noam Kaplan,et al.  Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization , 2009, Nature Genetics.

[38]  L. Wong,et al.  Identification of cell cycle-regulated genes in fission yeast. , 2005, Molecular biology of the cell.

[39]  L. Kruglyak,et al.  Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.

[40]  André Nantel,et al.  Transcription factor substitution during the evolution of fungal ribosome regulation. , 2008, Molecular cell.

[41]  D. Pe’er,et al.  Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.

[42]  A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation , 2009, Science.

[43]  W. Toone,et al.  Distinct regulatory proteins control the graded transcriptional response to increasing H(2)O(2) levels in fission yeast Schizosaccharomyces pombe. , 2002, Molecular biology of the cell.

[44]  Hao Li,et al.  The Evolution of Combinatorial Gene Regulation in Fungi , 2008, PLoS biology.

[45]  Wen-Hsiung Li,et al.  Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. , 2007, Genome research.

[46]  K. Ying,et al.  Cap1p is involved in multiple pathways of oxidative stress response in Candida albicans. , 2006, Free radical biology & medicine.

[47]  N. Barkai,et al.  Two strategies for gene regulation by promoter nucleosomes. , 2008, Genome research.

[48]  W. Lim,et al.  Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species , 2009, PLoS biology.

[49]  N. Friedman,et al.  Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.

[50]  Hao Li,et al.  Evolution of Eukaryotic Transcription Circuits , 2008, Science.

[51]  L. Kruglyak,et al.  Gene–Environment Interaction in Yeast Gene Expression , 2008, PLoS biology.

[52]  Hervé Hogues,et al.  Transcriptional Rewiring of Fungal Galactose-Metabolism Circuitry , 2007, Current Biology.

[53]  Justin C. Fay,et al.  Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae , 2005, PLoS genetics.

[54]  Leonid Kruglyak,et al.  Local Regulatory Variation in Saccharomyces cerevisiae , 2005, PLoS genetics.

[55]  David Botstein,et al.  The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast , 2008, PLoS genetics.

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

[57]  Justin C. Fay,et al.  A Catalog of Neutral and Deleterious Polymorphism in Yeast , 2008, PLoS genetics.

[58]  P. Bork,et al.  Co-evolution of transcriptional and post-translational cell-cycle regulation , 2006, Nature.

[59]  S. Labbé,et al.  A Transcription Factor Cascade Involving Fep1 and the CCAAT-Binding Factor Php4 Regulates Gene Expression in Response to Iron Deficiency in the Fission Yeast Schizosaccharomyces pombe , 2006, Eukaryotic Cell.

[60]  A. E. Tsong,et al.  Evolution of alternative transcriptional circuits with identical logic , 2006, Nature.

[61]  Yuanfang Guan,et al.  Functional Analysis of Gene Duplications in Saccharomyces cerevisiae , 2007, Genetics.

[62]  B. Birren,et al.  Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.

[63]  E. Dubois,et al.  Swapping Functional Specificity of a MADS Box Protein: Residues Required for Arg80 Regulation of Arginine Metabolism , 2002, Molecular and Cellular Biology.

[64]  Mark Gerstein,et al.  Divergence of transcription factor binding sites across related yeast species. , 2007, Science.

[65]  J. Raser,et al.  Control of Stochasticity in Eukaryotic Gene Expression , 2004, Science.

[66]  A. Mitchell,et al.  Regulation of the Candida albicans cell wall damage response by transcription factor Sko1 and PAS kinase Psk1. , 2008, Molecular biology of the cell.

[67]  Catherine Etchebest,et al.  Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata , 2008, Genome Biology.

[68]  S. Carroll,et al.  Emerging principles of regulatory evolution , 2007, Proceedings of the National Academy of Sciences.