An evolutionary and structural characterization of mammalian protein complex organization
暂无分享,去创建一个
Dmitrij Frishman | Florian Blöchl | Sonja Althammer | Pawel Smialowski | Matthias Oesterheld | Fabian J Theis | Andreas Ruepp | Philip Wong | Philipp Pagel | Normann Strack | D. Frishman | N. Strack | M. Oesterheld | A. Ruepp | and D. Kirschner | P. Pagel | Philip Wong | S. Althammer | P. Smialowski | F. Blöchl | Thorsten Schmidt | Thorsten Schmidt | Andrea Hildebrand | Andreas Kirschner | Bernd Geissler | Andrea Hildebrand | Bernd Geissler | Matthias Oesterheld
[1] R. Guigó,et al. Are splicing mutations the most frequent cause of hereditary disease? , 2005, FEBS letters.
[2] Nikolay V Dokholyan,et al. Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. , 2008, Molecular biology and evolution.
[3] Hunter B. Fraser,et al. Using protein complexes to predict phenotypic effects of gene mutation , 2007, Genome Biology.
[4] Liran Carmel,et al. Widespread positive selection in synonymous sites of mammalian genes. , 2007, Molecular biology and evolution.
[5] Eugene V Koonin,et al. Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution , 2008, Biology Direct.
[6] Cathy H. Wu,et al. The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..
[7] Joshua B Plotkin,et al. Assessing the determinants of evolutionary rates in the presence of noise. , 2007, Molecular biology and evolution.
[8] Hans-Werner Mewes,et al. MPact: the MIPS protein interaction resource on yeast , 2005, Nucleic Acids Res..
[9] Alex Bateman,et al. Reuse of structural domain–domain interactions in protein networks , 2007, BMC Bioinformatics.
[10] Eugene V Koonin,et al. Evolutionary systems biology: links between gene evolution and function. , 2006, Current opinion in biotechnology.
[11] Joachim Nickel,et al. Structure Analysis of Bone Morphogenetic Protein-2 Type I Receptor Complexes Reveals a Mechanism of Receptor Inactivation in Juvenile Polyposis Syndrome* , 2008, Journal of Biological Chemistry.
[12] S. Yi,et al. Understanding relationship between sequence and functional evolution in yeast proteins , 2007, Genetica.
[13] C. Schein. Controlling oligomerization of pharmaceutical proteins. , 1994, Pharmaceutica acta Helvetiae.
[14] Maria Victoria Schneider,et al. MINT: a Molecular INTeraction database. , 2002, FEBS letters.
[15] Thomas Wilhelm,et al. Physical and Functional Modularity of the Protein Network in Yeast* , 2003, Molecular & Cellular Proteomics.
[16] Peer Bork,et al. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..
[17] A. E. Hirsh,et al. Adjusting for selection on synonymous sites in estimates of evolutionary distance. , 2005, Molecular biology and evolution.
[18] Albert Sickmann,et al. Multiple pathways for sorting mitochondrial precursor proteins , 2008, EMBO reports.
[19] Adam J. Smith,et al. The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..
[20] Piero Fariselli,et al. eSLDB: eukaryotic subcellular localization database , 2006, Nucleic Acids Res..
[21] Frederick P. Roth,et al. Predicting co-complexed protein pairs using genomic and proteomic data integration , 2004, BMC Bioinformatics.
[22] Ian M. Donaldson,et al. The Biomolecular Interaction Network Database and related tools 2005 update , 2004, Nucleic Acids Res..
[23] J. Xie,et al. Parkinson's Disease Brain Mitochondrial Complex I Has Oxidatively Damaged Subunits and Is Functionally Impaired and Misassembled , 2006, The Journal of Neuroscience.
[24] Dmitrij Frishman,et al. Conservation of protein-protein interactions - lessons from ascomycota. , 2004, Trends in genetics : TIG.
[25] David K. Smith,et al. Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota , 2006, Journal of Molecular Evolution.
[26] B. Friguet,et al. Mitochondrial protein quality control: Implications in ageing , 2008, Biotechnology journal.
[27] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[28] Derek E. Wildman,et al. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences , 2007, Source Code for Biology and Medicine.
[29] Robert D. Finn,et al. iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions , 2005, Bioinform..
[30] Limsoon Wong,et al. Using indirect protein interactions for the prediction of Gene Ontology functions , 2007, BMC Bioinformatics.
[31] Robert B. Russell,et al. 3did: interacting protein domains of known three-dimensional structure , 2004, Nucleic Acids Res..
[32] Claus O. Wilke,et al. Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution , 2008, Cell.
[33] N. Friedman,et al. Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.
[34] PagelPhilipp,et al. The MIPS mammalian protein--protein interaction database , 2005 .
[35] Shoshana J. Wodak,et al. CYGD: the Comprehensive Yeast Genome Database , 2004, Nucleic Acids Res..
[36] Nikolay V Dokholyan,et al. The Coordinated Evolution of Yeast Proteins Is Constrained by Functional Modularity , 2022 .
[37] Sarah A Teichmann,et al. Evolution of protein complexes by duplication of homomeric interactions , 2007, Genome Biology.
[38] C. Pál,et al. An integrated view of protein evolution , 2006, Nature Reviews Genetics.
[39] See-Kiong Ng,et al. Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. , 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.
[40] Roded Sharan,et al. Identification of conserved protein complexes based on a model of protein network evolution , 2007, Bioinform..
[41] Pierre Baldi,et al. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles , 2002, Proteins.
[42] D. Niu,et al. Selection for the miniaturization of highly expressed genes. , 2007, Biochemical and biophysical research communications.
[43] Hunter B. Fraser,et al. Modularity and evolutionary constraint on proteins , 2005, Nature Genetics.
[44] Igor Jurisica,et al. Protein complex prediction via cost-based clustering , 2004, Bioinform..
[45] Hanah Margalit,et al. Characterization and prediction of protein–protein interactions within and between complexes , 2006, Proceedings of the National Academy of Sciences.
[46] Stephen J. Elledge,et al. Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening , 2008, Science.
[47] Philip M. Kim,et al. Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.
[48] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[49] S. Teichmann,et al. Assembly reflects evolution of protein complexes , 2008, Nature.
[50] Nagiza F. Samatova,et al. From pull-down data to protein interaction networks and complexes with biological relevance. , 2008, Bioinformatics.
[51] Martijn A. Huynen,et al. From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism , 2007, PLoS Comput. Biol..
[52] Peter Tompa,et al. Structural disorder promotes assembly of protein complexes , 2007, BMC Structural Biology.
[53] P. Carroad,et al. Estimation of diffusion coefficients of proteins , 1980 .
[54] R. Schwartz,et al. Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. , 2001, Genome research.
[55] Thomas Wilhelm,et al. Dynamic simulation of protein complex formation on a genomic scale , 2005, Bioinform..
[56] Y. Zhang,et al. IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..
[57] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[58] 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.
[59] G. Wagner,et al. The road to modularity , 2007, Nature Reviews Genetics.
[60] Alan F. Scott,et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..
[61] Dmitrij Frishman,et al. The MIPS mammalian protein?Cprotein interaction database , 2005, Bioinform..
[62] Hans-Werner Mewes,et al. CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..
[63] Dmitrij Frishman,et al. PROMPT: a protein mapping and comparison tool , 2006, BMC Bioinformatics.
[64] J. McInerney,et al. The causes of protein evolutionary rate variation. , 2006, Trends in ecology & evolution.
[65] Andreas Prlic,et al. Ensembl 2007 , 2006, Nucleic Acids Res..
[66] William Stafford Noble,et al. Predicting Co-Complexed Protein Pairs from Heterogeneous Data , 2008, PLoS Comput. Biol..
[67] Pall I. Olason,et al. A human phenome-interactome network of protein complexes implicated in genetic disorders , 2007, Nature Biotechnology.
[68] Araxi O. Urrutia,et al. The signature of selection mediated by expression on human genes. , 2003, Genome research.
[69] I. Jurisica,et al. Unequal evolutionary conservation of human protein interactions in interologous networks , 2007, Genome Biology.
[70] Dmitrij Frishman,et al. MIPS: analysis and annotation of proteins from whole genomes in 2005 , 2005, Nucleic Acids Res..
[71] K. Sneppen,et al. Specificity and Stability in Topology of Protein Networks , 2002, Science.
[72] Dmitrij Frishman,et al. MIPS: analysis and annotation of proteins from whole genomes in 2005 , 2006, Nucleic Acids Res..
[73] I. Tetko,et al. MitoP2: An Integrative Tool for the Analysis of the Mitochondrial Proteome , 2008, Molecular biotechnology.
[74] J. Echave,et al. Quaternary structure constraints on evolutionary sequence divergence. , 2006, Molecular biology and evolution.
[75] Caroline C. Friedel,et al. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast , 2008, RECOMB.
[76] Eduardo P C Rocha,et al. The quest for the universals of protein evolution. , 2006, Trends in genetics : TIG.
[77] Shigehiko Kanaya,et al. Development and implementation of an algorithm for detection of protein complexes in large interaction networks , 2006, BMC Bioinformatics.
[78] Dmitrij Frishman,et al. Designability, aggregation propensity and duplication of disease-associated proteins. , 2005, Protein engineering, design & selection : PEDS.
[79] A. E. Hirsh,et al. Evolutionary Rate in the Protein Interaction Network , 2002, Science.
[80] M. Vidal,et al. Effect of sampling on topology predictions of protein-protein interaction networks , 2005, Nature Biotechnology.
[81] Wen-Lian Hsu,et al. Protein subcellular localization prediction based on compartment-specific features and structure conservation , 2007, BMC Bioinformatics.
[82] Ioannis Xenarios,et al. DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..
[83] Jason E Stajich,et al. An Introduction to BioPerl. , 2007, Methods in molecular biology.
[84] Barbara Imperiali,et al. Protein Oligomerization: How and Why , 2005 .
[85] T. Chatila,et al. FOXP3 is a homo-oligomer and a component of a supramolecular regulatory complex disabled in the human XLAAD/IPEX autoimmune disease. , 2007, International immunology.
[86] Burkhard Rost,et al. Protein–Protein Interactions More Conserved within Species than across Species , 2006, PLoS Comput. Biol..
[87] Sergei Maslov,et al. Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size , 2008, Molecular systems biology.
[88] R. Tsien,et al. Specificity and Stability in Topology of Protein Networks , 2022 .
[89] Jianzhi Zhang,et al. Null mutations in human and mouse orthologs frequently result in different phenotypes , 2008, Proceedings of the National Academy of Sciences.
[90] Gary D. Bader,et al. An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.