Access the most recent version at doi: 10.1101/gr.5235706 Supplementary

IOA Freely available online through the Genome Research Open Access option. service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article-sign up in the box at the Notes object identifier (DOIs) and date of initial publication. by PubMed from initial publication. Citations to Advance online articles must include the digital publication). Advance online articles are citable and establish publication priority; they are indexed appeared in the paper journal (edited, typeset versions may be posted when available prior to final Advance online articles have been peer reviewed and accepted for publication but have not yet

[1]  Serafim Batzoglou,et al.  Integrated Protein Interaction Networks for 11 Microbes , 2006, RECOMB.

[2]  Ron Y. Pinter,et al.  Alignment of metabolic pathways , 2005, Bioinform..

[3]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[4]  S. Batzoglou,et al.  Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.

[5]  M. Gerstein,et al.  Assessing the limits of genomic data integration for predicting protein networks. , 2005, Genome research.

[6]  C. Wilke,et al.  Why highly expressed proteins evolve slowly. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Wojciech Szpankowski,et al.  Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution , 2005, RECOMB.

[8]  Serafim Batzoglou,et al.  The many faces of sequence alignment , 2005, Briefings Bioinform..

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

[10]  John B. Anderson,et al.  CDD: a Conserved Domain Database for protein classification , 2004, Nucleic Acids Res..

[11]  David Botstein,et al.  GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes , 2004, Bioinform..

[12]  Colin N. Dewey,et al.  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution , 2004, Nature.

[13]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[14]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[15]  Mario Vento,et al.  Thirty Years Of Graph Matching In Pattern Recognition , 2004, Int. J. Pattern Recognit. Artif. Intell..

[16]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[17]  S. Batzoglou,et al.  Characterization of evolutionary rates and constraints in three Mammalian genomes. , 2004, Genome research.

[18]  Jeremy Buhler,et al.  Designing multiple simultaneous seeds for DNA similarity search , 2004, J. Comput. Biol..

[19]  Roded Sharan,et al.  Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data , 2004, J. Comput. Biol..

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

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

[22]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.

[23]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[24]  Lior Pachter,et al.  MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.

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

[26]  C. Adami,et al.  Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein–protein interactions data sets , 2003, BMC Evolutionary Biology.

[27]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[28]  T. Speed,et al.  Biological Sequence Analysis , 1998 .

[29]  L. Pachter,et al.  SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. , 2003, Genome research.

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

[31]  Francesca Chiaromonte,et al.  Scoring Pairwise Genomic Sequence Alignments , 2001, Pacific Symposium on Biocomputing.

[32]  M. Vidal,et al.  Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". , 2001, Genome research.

[33]  W. Wackernagel,et al.  Identification and characterization of novel competence genes comA and exbB involved in natural genetic transformation of Pseudomonas stutzeri. , 2001, Research in microbiology.

[34]  K. Schulten,et al.  Phylogenetic Analysis of Metabolic Pathways , 2001, Journal of Molecular Evolution.

[35]  Ian Korf,et al.  Integrating genomic homology into gene structure prediction , 2001, ISMB.

[36]  M. Kanehisa,et al.  A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. , 2000, Nucleic acids research.

[37]  Daniel H. Huson,et al.  The Conserved Exon Method for Gene Finding , 2000, ISMB.

[38]  Jill P. Mesirov,et al.  Human and mouse gene structure: comparative analysis and application to exon prediction , 2000, RECOMB '00.

[39]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[40]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[41]  D. Dubnau,et al.  DNA uptake in bacteria. , 1999, Annual review of microbiology.

[42]  B. Snel,et al.  Pathway alignment: application to the comparative analysis of glycolytic enzymes. , 1999, The Biochemical journal.

[43]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[44]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[45]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[46]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[47]  H. Hara,et al.  A promoter for the first nine genes of the Escherichia coli mra cluster of cell division and cell envelope biosynthesis genes, including ftsI and ftsW , 1997, Journal of bacteriology.

[48]  P. Legrain,et al.  Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens , 1997, Nature Genetics.

[49]  T. Kogoma Is RecF a DNA replication protein? , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[50]  S Henikoff,et al.  Performance evaluation of amino acid substitution matrices , 1993, Proteins.

[51]  P. March,et al.  A GTP-binding protein (Era) has an essential role in growth rate and cell cycle control in Escherichia coli , 1991, Journal of bacteriology.

[52]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[53]  S F Altschul,et al.  Weights for data related by a tree. , 1989, Journal of molecular biology.

[54]  R. Doolittle,et al.  Progressive sequence alignment as a prerequisitetto correct phylogenetic trees , 2007, Journal of Molecular Evolution.

[55]  G. Sumara,et al.  A Probabilistic Functional Network of Yeast Genes , 2004 .

[56]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

[57]  Kara Dolinski,et al.  Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms , 2004, Nucleic Acids Res..

[58]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[59]  The FlyBase database of the Drosophila genome projects and community literature. , 2003, Nucleic acids research.

[60]  Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[61]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[62]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[63]  N. Miyajima,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome. , 1995, DNA research : an international journal for rapid publication of reports on genes and genomes.