A Bayesian approach to predicting protein-protein interactions
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[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.