Computational methods for protein function analysis.
暂无分享,去创建一个
[1] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[2] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[3] S. Fields,et al. A novel genetic system to detect proteinprotein interactions , 1989, Nature.
[4] S. Henikoff,et al. Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[5] S. P. Fodor,et al. Multiplexed biochemical assays with biological chips , 1993, Nature.
[6] S A Benner,et al. Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix. , 1994, Biochemical and biophysical research communications.
[7] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[8] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[9] Ronald W. Davis,et al. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.
[10] Charles Elkan,et al. The Value of Prior Knowledge in Discovering Motifs with MEME , 1995, ISMB.
[11] Takahashi,et al. E-CELL: Software Environment for Whole Cell Simulation. , 1997, Genome informatics. Workshop on Genome Informatics.
[12] Gapped BLAST and PSI-BLAST: A new , 1997 .
[13] Amos Bairoch,et al. The PROSITE database, its status in 1997 , 1997, Nucleic Acids Res..
[14] C. Chothia,et al. Intermediate sequences increase the detection of homology between sequences. , 1997, Journal of molecular biology.
[15] D. Lipman,et al. A genomic perspective on protein families. , 1997, Science.
[16] A. Valencia,et al. Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes , 1997, Journal of Molecular Evolution.
[17] Jun Zhu,et al. Bayesian adaptive sequence alignment algorithms , 1998, Bioinform..
[18] Michael Ruogu Zhang,et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.
[19] J A Eisen,et al. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. , 1998, Genome research.
[20] S. Michnick,et al. Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[21] 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.
[22] Mark Gerstein,et al. Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence , 1998, Bioinform..
[23] B. Snel,et al. Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.
[24] J. Claverie,et al. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. , 1999, Genome research.
[25] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[26] 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.
[27] P. Brown,et al. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[28] D. Eisenberg,et al. A combined algorithm for genome-wide prediction of protein function , 1999, Nature.
[29] Masaru Tomita,et al. E-CELL: software environment for whole-cell simulation , 1999, Bioinform..
[30] 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.
[31] E. Sprinzak,et al. Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. , 1999, Genome research.
[32] Anton J. Enright,et al. Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.
[33] Jérôme Gouzy,et al. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons , 2000, Nucleic Acids Res..
[34] James R. Knight,et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.
[35] B. Palsson,et al. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[36] Yudong D. He,et al. Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.
[37] R. Overbeek,et al. Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[38] Julio Collado-Vides,et al. RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12 , 2000, Nucleic Acids Res..
[39] Michael Y. Galperin,et al. The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..
[40] Warren C. Lathe,et al. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. , 2000, Genome research.
[41] Michal Linial,et al. Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..
[42] B. Schwikowski,et al. A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.
[43] D. Eisenberg,et al. Protein function in the post-genomic era , 2000, Nature.
[44] G. Odell,et al. The segment polarity network is a robust developmental module , 2000, Nature.
[45] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[46] W. Grundy,et al. Combining Microarray Expression Data and Phylogenetic Profiles to Learn Gene Functional Categories Using Support Vector Machines , 2000, RECOMB 2000.
[47] P. Brown,et al. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. , 2000, Molecular biology of the cell.
[48] G. Church,et al. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.
[49] Sarah A. Teichmann,et al. Computing protein function , 2000, Nature Biotechnology.
[50] F. Cohen,et al. Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.
[51] Anton J. Enright,et al. GeneRAGE: a robust algorithm for sequence clustering and domain detection , 2000, Bioinform..
[52] L. Aravind. Guilt by association: contextual information in genome analysis. , 2000, Genome research.
[53] Rithy K. Roth,et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays , 2000, Nature Biotechnology.
[54] Michael Y. Galperin,et al. Who's your neighbor? New computational approaches for functional genomics , 2000, Nature Biotechnology.
[55] C. Chothia,et al. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. , 2001, Journal of molecular biology.
[56] H. Bussemaker,et al. Regulatory element detection using correlation with expression , 2001, Nature Genetics.
[57] M. Pellegrini,et al. Computational method to assign microbial genes to pathways , 2001, Journal of cellular biochemistry. Supplement.
[58] T. Takagi,et al. Assessment of prediction accuracy of protein function from protein–protein interaction data , 2001, Yeast.
[59] S. Salzberg,et al. Prediction of operons in microbial genomes. , 2001, Nucleic acids research.
[60] Julio Collado-Vides,et al. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 , 2001, Nucleic Acids Res..
[61] Gary D Bader,et al. BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.
[62] Yudong D. He,et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.
[63] M. Gerstein,et al. Global Analysis of Protein Activities Using Proteome Chips , 2001, Science.
[64] Todd,et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning , 2002, Nature Medicine.
[65] E. Marcotte,et al. Predicting functional linkages from gene fusions with confidence. , 2002, Applied bioinformatics.
[66] Nicola J. Rinaldi,et al. Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.
[67] Ioannis Xenarios,et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..
[68] Ji Huang,et al. [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.
[69] P. Bork,et al. Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.
[70] Peer Bork,et al. Recent improvements to the SMART domain-based sequence annotation resource , 2002, Nucleic Acids Res..
[71] E. Gilles,et al. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors , 2002, Nature Biotechnology.
[72] Chern-Sing Goh,et al. Co-evolutionary analysis reveals insights into protein-protein interactions. , 2002, Journal of molecular biology.
[73] Charles DeLisi,et al. Predictome: a database of putative functional links between proteins , 2002, Nucleic Acids Res..
[74] Owen White,et al. The TIGRFAMs database of protein families , 2003, Nucleic Acids Res..
[75] Cathy H. Wu,et al. Protein family classification and functional annotation , 2003, Comput. Biol. Chem..
[76] Arun K. Ramani,et al. Exploiting the co-evolution of interacting proteins to discover interaction specificity. , 2003, Journal of molecular biology.
[77] Terri K. Attwood,et al. PRINTS and its automatic supplement, prePRINTS , 2003, Nucleic Acids Res..
[78] Edward M Marcotte,et al. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages , 2003, Nature Biotechnology.
[79] Alessandro Vespignani,et al. Global protein function prediction from protein-protein interaction networks , 2003, Nature Biotechnology.
[80] Alex Bateman,et al. The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..
[81] Simon Kasif,et al. Identification of functional links between genes using phylogenetic profiles , 2003, Bioinform..
[82] Eric C. Rouchka,et al. Gibbs Recursive Sampler: finding transcription factor binding sites , 2003, Nucleic Acids Res..
[83] Christian von Mering,et al. STRING: a database of predicted functional associations between proteins , 2003, Nucleic Acids Res..