Redundancy and the Evolution of Cis-Regulatory Element Multiplicity
暂无分享,去创建一个
[1] P. Bourgine,et al. Topological and causal structure of the yeast transcriptional regulatory network , 2002, Nature Genetics.
[2] E. O’Shea,et al. Global analysis of protein expression in yeast , 2003, Nature.
[3] M. Huynen,et al. Neutral evolution of mutational robustness. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[4] C. Ofria,et al. Sexual reproduction reshapes the genetic architecture of digital organisms , 2006, Proceedings of the Royal Society B: Biological Sciences.
[5] Kevin P. White,et al. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression , 2005, Nature.
[6] J. Drake,et al. Rates of spontaneous mutation. , 1998, Genetics.
[7] Ronald W. Davis,et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.
[8] S. Freytag,et al. Synergistic activation of a human promoter in vivo by transcription factor Sp1 , 1991, Molecular and cellular biology.
[9] B. Birren,et al. Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.
[10] T. Hwa,et al. Physical constraints and functional characteristics of transcription factor–DNA interaction , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[11] Andy Gardner,et al. Recombination and the evolution of mutational robustness. , 2006, Journal of theoretical biology.
[12] D. Moerman,et al. Cis-regulatory Mutations in the Caenorhabditis elegans Homeobox Gene Locus cog-1 Affect Neuronal Development , 2009, Genetics.
[13] Terence Hwa,et al. On the Selection and Evolution of Regulatory DNA Motifs , 2001, Journal of Molecular Evolution.
[14] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[15] L. Steinmetz,et al. High-resolution mapping of meiotic crossovers and non-crossovers in yeast , 2008, Nature.
[16] Steven A Frank,et al. Author ' s personal copy Evolutionary dynamics of redundant regulatory control , 2008 .
[17] A. Clark,et al. Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. , 2002, Molecular biology and evolution.
[18] Martin A. Nowak,et al. Evolution of genetic redundancy , 1997, Nature.
[19] Andreas Wagner,et al. Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology , 2007, PLoS Comput. Biol..
[20] M. Lichten,et al. Mapping Meiotic Single-Strand DNA Reveals a New Landscape of DNA Double-Strand Breaks in Saccharomyces cerevisiae , 2007, PLoS biology.
[21] T. Storck,et al. Brachyury proteins regulate target genes through modular binding sites in a cooperative fashion. , 2002, Genes & development.
[22] L. Meyers,et al. How Mutational Networks Shape Evolution: Lessons from RNA Models , 2007 .
[23] Kristen K. Dang,et al. Sexual reproduction selects for robustness and negative epistasis in artificial gene networks , 2006, Nature.
[24] A. Wagner. Circuit topology and the evolution of robustness in two-gene circadian oscillators. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[25] M. Levine,et al. Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. , 1991, Science.
[26] Wolfgang Driever,et al. Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen , 1989, Nature.
[27] A. Clark,et al. Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. , 2003, Molecular biology and evolution.
[28] B. Birren,et al. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.
[29] D. S. Fields,et al. Specificity, free energy and information content in protein-DNA interactions. , 1998, Trends in biochemical sciences.
[30] Ronald W. Davis,et al. A high-resolution atlas of nucleosome occupancy in yeast , 2007, Nature Genetics.
[31] Allan R. Jones,et al. Networking the networks , 1995, SIGUCCS '95.
[32] Scott Doniger,et al. Frequent Gain and Loss of Functional Transcription Factor Binding Sites , 2007, PLoS Comput. Biol..
[33] J. Thomas,et al. Thinking about genetic redundancy. , 1993, Trends in genetics : TIG.
[34] Patrick C Phillips,et al. The Opportunity for Canalization and the Evolution of Genetic Networks , 2004, The American Naturalist.
[35] M. Lynch,et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans , 2005, Nature Genetics.
[36] Melanie A. Huntley,et al. Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.
[37] Mark Gerstein,et al. Divergence of transcription factor binding sites across related yeast species. , 2007, Science.
[38] Kerry J. Kim,et al. Effects of Ploidy and Recombination on Evolution of Robustness in a Model of the Segment Polarity Network , 2009, PLoS Comput. Biol..
[39] A. Wagner. Distributed robustness versus redundancy as causes of mutational robustness. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.
[40] Ting Wang,et al. An improved map of conserved regulatory sites for Saccharomyces cerevisiae , 2006, BMC Bioinformatics.
[41] Daniel E. Newburger,et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. , 2009, Genome research.
[42] Christopher L. Warren,et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. , 2008, Molecular cell.
[43] Johannes Berg,et al. Adaptive evolution of transcription factor binding sites , 2003, BMC Evolutionary Biology.
[44] Cheryl Middleton,et al. Networking, Networking, Networking , 2006 .
[45] Naama Barkai,et al. The design of transcription-factor binding sites is affected by combinatorial regulation , 2005, Genome Biology.
[46] A. Burt,et al. Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle , 2008, Proceedings of the National Academy of Sciences.
[47] Peter F Stadler,et al. A stochastic model for the evolution of transcription factor binding site abundance. , 2007, Journal of theoretical biology.
[48] Ronald W. Davis,et al. Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.
[49] M. Levine,et al. Regulation of even‐skipped stripe 2 in the Drosophila embryo. , 1992, The EMBO journal.
[50] Ronald W. Davis,et al. Role of duplicate genes in genetic robustness against null mutations , 2003, Nature.
[51] M. Levine,et al. The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. , 1996, Development.
[52] Andreas Wagner,et al. Energy constraints on the evolution of gene expression. , 2005, Molecular biology and evolution.
[53] G. Edelman,et al. Degeneracy and complexity in biological systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[54] J. Stone,et al. Rapid evolution of cis-regulatory sequences via local point mutations. , 2001, Molecular biology and evolution.
[55] Michael R. Green,et al. Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.
[56] D. Promislow,et al. Direct Selection on Genetic Robustness Revealed in the Yeast Transcriptome , 2007, PloS one.
[57] L. Hedges,et al. Statistical Methods for Meta-Analysis , 1987 .
[58] M Ptashne,et al. Cooperative DNA binding of the yeast transcriptional activator GAL4. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[59] H. Y. Steensma,et al. Enhanced meiotic recombination on the smallest chromosome of Saccharomyces cerevisiae. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[60] P. V. von Hippel,et al. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. , 1987, Journal of molecular biology.
[61] Andreas Wagner,et al. Redundant Gene Functions and Natural Selection , 1997 .
[62] B. Pugh,et al. Identification and Distinct Regulation of Yeast TATA Box-Containing Genes , 2004, Cell.
[63] Adi Livnat,et al. A mixability theory for the role of sex in evolution , 2008, Proceedings of the National Academy of Sciences.
[64] N. Patel,et al. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. , 1998, Development.
[65] E. Marcotte,et al. An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae , 2007, PloS one.
[66] M. Lynch. The evolution of genetic networks by non-adaptive processes , 2007, Nature Reviews Genetics.
[67] G. Stormo,et al. Additivity in protein-DNA interactions: how good an approximation is it? , 2002, Nucleic acids research.
[68] J. Derisi,et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise , 2006, Nature.
[69] Matthew W. Hahn,et al. The evolution of transcriptional regulation in eukaryotes. , 2003, Molecular biology and evolution.