Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.

[1]  David Botstein,et al.  Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Casey M. Warmbrand,et al.  A Network Analysis of Committees in the U.S. House of Representatives , 2013, Proceedings of the National Academy of Sciences of the United States of America.

[3]  M. Gerstein,et al.  Global analysis of protein phosphorylation in yeast , 2005, Nature.

[4]  Sergei Maslov,et al.  Computational architecture of the yeast regulatory network , 2005, Physical biology.

[5]  E. Davidson.  Genomic Regulatory Systems: Development and Evolution , 2005 .

[6]  Henry Horng-Shing Lu,et al.  Statistical methods for identifying yeast cell cycle transcription factors. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[7]  A. Ciechanover.  Intracellular protein degradation: from a vague idea, through the lysosome and the ubiquitin-proteasome system, and onto human diseases and drug targeting (Nobel lecture). , 2005, Angewandte Chemie.

[8]  George M Church,et al.  A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. , 2005, Genome research.

[9]  Yasubumi Sakakibara,et al.  Identifying cooperative transcriptional regulations using protein–protein interactions , 2005, Nucleic acids research.

[10]  Mark Ptashne,et al.  Regulation of transcription: from lambda to eukaryotes. , 2005, Trends in biochemical sciences.

[11]  P. Sternberg,et al.  Transcriptional network underlying Caenorhabditis elegans vulval development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  R. Zitomer,et al.  Combinatorial Repression of the Hypoxic Genes of Saccharomyces cerevisiae by DNA Binding Proteins Rox1 and Mot3 , 2005, Eukaryotic Cell.

[13]  Emmitt R. Jolly,et al.  Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Yael Garten,et al.  Extraction of transcription regulatory signals from genome-wide DNA–protein interaction data , 2005, Nucleic acids research.

[15]  H. Herzel,et al.  Inferring combinatorial regulation of transcription in silico , 2005, Nucleic acids research.

[16]  Aaron Ciechanover,et al.  Proteolysis: from the lysosome to ubiquitin and the proteasome , 2005, Nature Reviews Molecular Cell Biology.

[17]  M. Hall,et al.  TOR Regulates Ribosomal Protein Gene Expression via PKA and the Forkhead Transcription Factor FHL1 , 2004, Cell.

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

[19]  E. Koonin,et al.  Novel Predicted Peptidases with a Potential Role in the Ubiquitin Signaling Pathway , 2004, Cell cycle.

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

[21]  Michael Q. Zhang,et al.  Identifying combinatorial regulation of transcription factors and binding motifs , 2004, Genome Biology.

[22]  P. C. Ramos,et al.  Regulatory mechanisms controlling biogenesis of ubiquitin and the proteasome , 2004, FEBS letters.

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

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

[25]  Mark Ptashne,et al.  A Genetic Switch, Phage Lambda Revisited , 2004 .

[26]  A. Ciechanover,et al.  Ubiquitin as a central cellular regulator , 2004, Cell.

[27]  R. Zitomer,et al.  Recruitment of Tup1-Ssn6 by Yeast Hypoxic Genes and Chromatin-Independent Exclusion of TATA Binding Protein , 2003, Eukaryotic Cell.

[28]  Eric H Davidson,et al.  Developmental gene network analysis. , 2003, The International journal of developmental biology.

[29]  Michael Q. Zhang,et al.  Identifying cooperativity among transcription factors controlling the cell cycle in yeast. , 2003, Nucleic acids research.

[30]  N. Abramova,et al.  Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae. , 2003, Nucleic acids research.

[31]  R. Tjian,et al.  Transcription regulation and animal diversity , 2003, Nature.

[32]  A. Keating,et al.  Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays , 2003, Science.

[33]  M. Gerstein,et al.  Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. , 2002, Genes & development.

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

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

[36]  T. Hunter,et al.  Evolution of protein kinase signaling from yeast to man. , 2002, Trends in biochemical sciences.

[37]  E. Koonin,et al.  The role of lineage-specific gene family expansion in the evolution of eukaryotes. , 2002, Genome research.

[38]  Mark Ptashne,et al.  Telomere Looping Permits Repression “at a Distance” in Yeast , 2002, Current Biology.

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

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

[41]  L. Hood,et al.  A Genomic Regulatory Network for Development , 2002, Science.

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

[43]  M. Ptashne,et al.  Genes and Signals , 2001 .

[44]  G. Church,et al.  Identifying regulatory networks by combinatorial analysis of promoter elements , 2001, Nature Genetics.

[45]  Gary D. Stormo,et al.  Identifying target sites for cooperatively binding factors , 2001, Bioinform..

[46]  A. Varshavsky,et al.  RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Alejandro A. Schäffer,et al.  IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices , 1999, Bioinform..

[48]  Andreas Wagner,et al.  Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes , 1999, Bioinform..

[49]  H. Feldmann,et al.  Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast , 1999, FEBS letters.

[50]  M. Levine,et al.  Transcriptional coregulators in development. , 1999, Science.

[51]  Temple F. Smith,et al.  Comparison of the complete protein sets of worm and yeast: orthology and divergence. , 1998, Science.

[52]  S. Harrison,et al.  Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA , 1998, Nature.

[53]  T. Maniatis,et al.  Virus infection induces the assembly of coordinately activated transcription factors on the IFN-beta enhancer in vivo. , 1998, Molecular cell.

[54]  Song Tan,et al.  Crystal structure of the yeast MATα2/MCM1/DNA ternary complex , 1998, Nature.

[55]  T. Richmond,et al.  Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. , 1998, Nature.

[56]  A. Varshavsky,et al.  The N‐end rule pathway controls the import of peptides through degradation of a transcriptional repressor , 1998, The EMBO journal.

[57]  T. Maniatis,et al.  Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome , 1995, Cell.

[58]  Terrance G. Cooper,et al.  Complilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae , 1995 .

[59]  T. Cooper,et al.  Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. , 1995, Yeast.

[60]  L. Moore,et al.  Interaction of the yeast Swi4 and Swi6 cell cycle regulatory proteins in vitro. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[61]  Kim Nasmyth,et al.  The role of SWI4 and SWI6 in the activity of G1 cyclins in yeast , 1991, Cell.

[62]  R. Britten,et al.  Gene regulation for higher cells: a theory. , 1969, Science.