A Bayesian approach to predicting protein-protein interactions

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

[2]  K C Chou,et al.  Prediction of protein structural classes and subcellular locations. , 2000, Current protein & peptide science.

[3]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[4]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[5]  B. Séraphin,et al.  A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.

[6]  Réka Albert,et al.  Conserved network motifs allow protein-protein interaction prediction , 2004, Bioinform..

[7]  Michael Lässig,et al.  Local graph alignment and motif search in biological networks. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Satoru Miyano,et al.  Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data , 2005, ECCB/JBI.

[9]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[10]  M. Samanta,et al.  Predicting protein functions from redundancies in large-scale protein interaction networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Nello Cristianini,et al.  Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast , 2003, Pacific Symposium on Biocomputing.

[12]  Ting Chen,et al.  An Integrated Probabilistic Model for Functional Prediction of Proteins , 2004, J. Comput. Biol..

[13]  Lan V. Zhang,et al.  Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.

[14]  Ioannis Xenarios,et al.  DIP: the Database of Interacting Proteins , 2000, Nucleic Acids Res..

[15]  H. Herzel,et al.  Is there a bias in proteome research? , 2001, Genome research.

[16]  A. D. Barbour,et al.  Discrete small world networks , 2003, cond-mat/0304020.

[17]  M. Gerstein,et al.  TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. , 2004, Nucleic acids research.

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

[19]  Minoru Kanehisa,et al.  Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs , 2003, Bioinform..

[20]  J. Rice Mathematical Statistics and Data Analysis , 1988 .

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

[22]  Julio M. Ottino,et al.  Complex networks , 2004, Encyclopedia of Big Data.

[23]  S. Strogatz Exploring complex networks , 2001, Nature.

[24]  A. Valencia,et al.  Similarity of phylogenetic trees as indicator of protein-protein interaction. , 2001, Protein engineering.

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

[26]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[27]  S. Wuchty Scale-free behavior in protein domain networks. , 2001, Molecular biology and evolution.

[28]  Bernhard Schölkopf,et al.  Fast protein classification with multiple networks , 2005, ECCB/JBI.

[29]  Hunter B. Fraser,et al.  Modularity and evolutionary constraint on proteins , 2005, Nature Genetics.

[30]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[31]  A Vázquez,et al.  The topological relationship between the large-scale attributes and local interaction patterns of complex networks , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[32]  P. Bork,et al.  Measuring genome evolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Robert B. Russell,et al.  InterPreTS: protein Interaction Prediction through Tertiary Structure , 2003, Bioinform..

[34]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[35]  S. Havlin,et al.  Self-similarity of complex networks , 2005, Nature.

[36]  E. Sprinzak,et al.  Correlated sequence-signatures as markers of protein-protein interaction. , 2001, Journal of molecular biology.

[37]  D. Bu,et al.  Topological structure analysis of the protein-protein interaction network in budding yeast. , 2003, Nucleic acids research.

[38]  Sharon L. Milgram,et al.  The Small World Problem , 1967 .

[39]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[40]  S. Wuchty Evolution and topology in the yeast protein interaction network. , 2004, Genome research.

[41]  S. L. Wong,et al.  Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network , 2005, Journal of biology.

[42]  Julien Gagneur,et al.  Modular decomposition of protein-protein interaction networks , 2004, Genome Biology.

[43]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[44]  A. Valencia,et al.  Computational methods for the prediction of protein interactions. , 2002, Current opinion in structural biology.

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

[46]  Carsten Wiuf,et al.  Subnets of scale-free networks are not scale-free: sampling properties of networks. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[47]  R. Milo,et al.  Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[48]  David Baker,et al.  Protein–protein docking predictions for the CAPRI experiment , 2003, Proteins.

[49]  Shichao Yang Exploring complex networks by walking on them. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[50]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[51]  Tsuyoshi Kato,et al.  Selective integration of multiple biological data for supervised network inference , 2005, Bioinform..

[52]  Tom M. W. Nye,et al.  Statistical analysis of domains in interacting protein pairs , 2005, Bioinform..

[53]  Warren C. Lathe,et al.  Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. , 2000, Genome research.

[54]  Igor Jurisica,et al.  Modeling interactome: scale-free or geometric? , 2004, Bioinform..

[55]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[56]  William Stafford Noble,et al.  Learning kernels from biological networks by maximizing entropy , 2004, ISMB/ECCB.

[57]  M. Sternberg,et al.  Prediction of protein-protein interactions by docking methods. , 2002, Current opinion in structural biology.

[58]  Michael Krauthammer,et al.  Probabilistic inference of molecular networks from noisy data sources , 2004, Bioinform..

[59]  Steven H. Strogatz,et al.  Small-world networks , 1999 .

[60]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[61]  Arun K. Ramani,et al.  Protein interaction networks from yeast to human. , 2004, Current opinion in structural biology.

[62]  Antonio del Sol,et al.  Topology of small-world networks of protein?Cprotein complex structures , 2005, Bioinform..

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

[64]  Markus J. Herrgård,et al.  Untangling the web of functional and physical interactions in yeast , 2005, Journal of biology.

[65]  S. Mangan,et al.  Structure and function of the feed-forward loop network motif , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[66]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[67]  Mark Gerstein,et al.  Information assessment on predicting protein-protein interactions , 2004, BMC Bioinformatics.

[68]  Minghua Deng,et al.  Inferring Domain–Domain Interactions From Protein–Protein Interactions , 2002 .

[69]  A. Barabasi,et al.  Functional and topological characterization of protein interaction networks , 2004, Proteomics.

[70]  D. Bray Molecular Networks: The Top-Down View , 2003, Science.

[71]  C. Deane,et al.  Protein Interactions , 2002, Molecular & Cellular Proteomics.

[72]  Gary D Bader,et al.  A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules , 2001, Science.

[73]  Frank Alber,et al.  A structural perspective on protein-protein interactions. , 2004, Current opinion in structural biology.

[74]  Cyrus Chothia,et al.  SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments , 2002, Nucleic Acids Res..

[75]  Gesine Reinert,et al.  Small worlds , 2001, Random Struct. Algorithms.