A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology

[1]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[2]  F. Govers,et al.  Effects of latrunculin B on the actin cytoskeleton and hyphal growth in Phytophthora infestans. , 2012, Fungal genetics and biology : FG & B.

[3]  H. Judelson Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution , 2012, Eukaryotic Cell.

[4]  Haiyuan Yu,et al.  Detecting overlapping protein complexes in protein-protein interaction networks , 2012, Nature Methods.

[5]  Michael F. Seidl,et al.  Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families , 2012, Genome biology and evolution.

[6]  R. Green,et al.  Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast , 2011, Proceedings of the National Academy of Sciences.

[7]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[8]  G. Van den Ackerveken,et al.  How do oomycete effectors interfere with plant life? , 2011, Current opinion in plant biology.

[9]  M. S. Mukhtar,et al.  Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network , 2011, Science.

[10]  Audrey M. V. Ah-Fong,et al.  New Role for Cdc14 Phosphatase: Localization to Basal Bodies in the Oomycete Phytophthora and Its Evolutionary Coinheritance with Eukaryotic Flagella , 2011, PloS one.

[11]  N. Chua,et al.  A comprehensive understanding of plant growth and development. , 2011, Current opinion in plant biology.

[12]  Audrey M. V. Ah-Fong,et al.  The kinome of Phytophthora infestans reveals oomycete-specific innovations and links to other taxonomic groups , 2010, BMC Genomics.

[13]  Michael F. Seidl,et al.  A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization1[W][OA] , 2010, Plant Physiology.

[14]  Gaston H. Gonnet,et al.  OMA 2011: orthology inference among 1000 complete genomes , 2010, Nucleic Acids Res..

[15]  Tobias Müller,et al.  Bioinformatics Applications Note Systems Biology Bionet: an R-package for the Functional Analysis of Biological Networks , 2022 .

[16]  E. Marcotte,et al.  Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana , 2010, Nature Biotechnology.

[17]  Jonathan D. G. Jones,et al.  Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans , 2009, Nature.

[18]  Acj Roth,et al.  Erratum: Algorithm of OMA for large-scale orthology inference (BMC Bioinformatics (2008) vol. 9 (518)) , 2009 .

[19]  Audrey M. V. Ah-Fong,et al.  Gene expression changes during asexual sporulation by the late blight agent Phytophthora infestans occur in discrete temporal stages , 2009, Molecular Genetics and Genomics.

[20]  Gaston H. Gonnet,et al.  Algorithm of OMA for large-scale orthology inference , 2008, BMC Bioinformatics.

[21]  F. Govers,et al.  RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members , 2008, Proceedings of the National Academy of Sciences.

[22]  Audrey M. V. Ah-Fong,et al.  Gene expression profiling during asexual development of the late blight pathogen Phytophthora infestans reveals a highly dynamic transcriptome. , 2008, Molecular plant-microbe interactions : MPMI.

[23]  Berend Snel,et al.  Coevolution of gene families in prokaryotes. , 2008, Genome research.

[24]  Paul Horton,et al.  Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .

[25]  H. Judelson,et al.  Transgene-Induced Silencing of the Zoosporogenesis-Specific NIFC Gene Cluster of Phytophthora infestans Involves Chromatin Alterations , 2007, Eukaryotic Cell.

[26]  Alan G Hinnebusch,et al.  eIF3: a versatile scaffold for translation initiation complexes. , 2006, Trends in biochemical sciences.

[27]  Matthew D. Welch,et al.  The ARP2/3 complex: an actin nucleator comes of age , 2006, Nature Reviews Molecular Cell Biology.

[28]  Laura Baxter,et al.  Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis , 2006, Science.

[29]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[30]  A. Hinnebusch,et al.  The Essential Vertebrate ABCE1 Protein Interacts with Eukaryotic Initiation Factors* , 2006, Journal of Biological Chemistry.

[31]  K. N. Chandrika,et al.  Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets , 2006, Nature Genetics.

[32]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[33]  H. Judelson,et al.  A bZIP transcription factor from Phytophthora interacts with a protein kinase and is required for zoospore motility and plant infection , 2005, Molecular microbiology.

[34]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[35]  Rex A. Dwyer,et al.  Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. , 2005, Molecular plant-microbe interactions : MPMI.

[36]  Thomas J. Begley,et al.  Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Peer Bork,et al.  Shared components of protein complexes--versatile building blocks or biochemical artefacts? , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[38]  A. Hinnebusch,et al.  The Essential ATP-binding Cassette Protein RLI1 Functions in Translation by Promoting Preinitiation Complex Assembly*♦ , 2004, Journal of Biological Chemistry.

[39]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[40]  W. Ligterink,et al.  A Gα subunit controls zoospore motility and virulence in the potato late blight pathogen Phytophthora infestans , 2004, Molecular microbiology.

[41]  M. Gerstein,et al.  A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.

[42]  H. Judelson,et al.  Cell cycle regulator Cdc14 is expressed during sporulation but not hyphal growth in the fungus‐like oomycete Phytophthora infestans , 2003, Molecular microbiology.

[43]  F. Govers,et al.  A Phytophthora infestans G-Protein β Subunit Is Involved in Sporangium Formation , 2003, Eukaryotic Cell.

[44]  F. Govers,et al.  Oomycetes and fungi: similar weaponry to attack plants. , 2003, Trends in microbiology.

[45]  B. Snel,et al.  Predicting gene function by conserved co-expression. , 2003, Trends in genetics : TIG.

[46]  T. Speed,et al.  Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.

[47]  F. Govers,et al.  Differential expression of G protein α and β subunit genes during development of Phytophthora infestans , 2002 .

[48]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[49]  B. Schwikowski,et al.  A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.

[50]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[51]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[52]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[53]  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.

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

[55]  Ron Edgar,et al.  Gene Expression Omnibus ( GEO ) : Microarray data storage , submission , retrieval , and analysis , 2008 .

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

[57]  David Botstein,et al.  The Stanford Microarray Database: data access and quality assessment tools , 2003, Nucleic Acids Res..

[58]  F. Govers,et al.  Differential expression of G protein alpha and beta subunit genes during development of Phytophthora infestans. , 2002, Fungal genetics and biology : FG & B.

[59]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..