Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
暂无分享,去创建一个
Mona Singh | Bernard Chazelle | Elena Nabieva | Amit Agarwal | Kam Jim | Mona Singh | B. Chazelle | A. Agarwal | Kam-Chuen Jim | E. Nabieva
[1] Dmitrij Frishman,et al. MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..
[2] A. Owen,et al. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae) , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[3] Alexander Rives,et al. Modular organization of cellular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[4] 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.
[5] S. L. Wong,et al. A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.
[6] 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.
[7] Gary D Bader,et al. Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.
[8] D. Eisenberg,et al. A combined algorithm for genome-wide prediction of protein function , 1999, Nature.
[9] Christian von Mering,et al. STRING: a database of predicted functional associations between proteins , 2003, Nucleic Acids Res..
[10] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[11] D. Eisenberg,et al. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. , 2003, Nucleic acids research.
[12] Mihalis Yannakakis,et al. The complexity of multiway cuts (extended abstract) , 1992, STOC '92.
[13] Brian W. Kernighan,et al. AMPL: A Modeling Language for Mathematical Programming , 1993 .
[14] P. Legrain,et al. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens , 1997, Nature Genetics.
[15] T. Takagi,et al. Assessment of prediction accuracy of protein function from protein–protein interaction data , 2001, Yeast.
[16] T. Ideker. A systems approach to discovering signaling and regulatory pathways--or, how to digest large interaction networks into relevant pieces. , 2004, Advances in experimental medicine and biology.
[17] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[18] P. Bork,et al. Genome evolution reveals biochemical networks and functional modules , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[19] Michael Lappe,et al. From gene networks to gene function. , 2003, Genome research.
[20] 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.
[21] Alessandro Vespignani,et al. Global protein function prediction from protein-protein interaction networks , 2003, Nature Biotechnology.
[22] B. Snel,et al. Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.
[23] James R. Knight,et al. A Protein Interaction Map of Drosophila melanogaster , 2003, Science.
[24] 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.
[25] Shailesh V. Date,et al. A Probabilistic Functional Network of Yeast Genes , 2004, Science.
[26] J. Wojcik,et al. The protein–protein interaction map of Helicobacter pylori , 2001, Nature.
[27] Alex E. Lash,et al. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..
[28] M. Tyers,et al. The GRID: The General Repository for Interaction Datasets , 2003, Genome Biology.
[29] William Stafford Noble,et al. Learning kernels from biological networks by maximizing entropy , 2004, ISMB/ECCB.
[30] B. Snel,et al. Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.
[31] Nicola J. Rinaldi,et al. Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.
[32] M. Gerstein,et al. A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.
[33] Anton J. Enright,et al. Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.
[34] Ronald L. Rivest,et al. Introduction to Algorithms , 1990 .
[35] Gary D Bader,et al. Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.
[36] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[37] Ting Chen,et al. Assessment of the reliability of protein-protein interactions and protein function prediction , 2002, Pacific Symposium on Biocomputing.
[38] James R. Knight,et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.
[39] David Martin,et al. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network , 2003, Genome Biology.
[40] Shmuel Sattath,et al. How reliable are experimental protein-protein interaction data? , 2003, Journal of molecular biology.
[41] S. Kasif,et al. Whole-genome annotation by using evidence integration in functional-linkage networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[42] Dmitrij Frishman,et al. MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..
[43] T Gaasterland,et al. Constructing multigenome views of whole microbial genomes. , 1998, Microbial & comparative genomics.
[44] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[45] P. Bork,et al. Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.
[46] T. Ito,et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[47] B. Schwikowski,et al. A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.