PROTEIN INTERACTIONS AND DISEASE

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

[2]  M. Ivan,et al.  Ubiquitination of hypoxia-inducible factor requires direct binding to the β-domain of the von Hippel–Lindau protein , 2000, Nature Cell Biology.

[3]  F. Cohen,et al.  Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.

[4]  B. Berger,et al.  Herpesviral Protein Networks and Their Interaction with the Human Proteome , 2006, Science.

[5]  Zhenran Jiang,et al.  Using Bioinformatics for Drug Target Identification from the Genome , 2005, American journal of pharmacogenomics : genomics-related research in drug development and clinical practice.

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

[7]  David L. Robertson,et al.  Specificity in protein interactions and its relationship with sequence diversity and coevolution , 2007, Proceedings of the National Academy of Sciences.

[8]  Teresa M Przytycka,et al.  Predicting protein domain interactions from coevolution of conserved regions , 2007, Proteins.

[9]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[10]  Stefan Wuchty,et al.  Inferring protein-protein interactions from multiple protein domain combinations. , 2009, Methods in molecular biology.

[11]  Teresa M. Przytycka,et al.  Interrogating domain-domain interactions with parsimony based approaches , 2008, BMC Bioinformatics.

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

[13]  P. Yeyati,et al.  Mechanisms of non-Mendelian inheritance in genetic disease. , 2004, Human molecular genetics.

[14]  Shinichiro Wachi,et al.  Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues , 2005, Bioinform..

[15]  E. Zerhouni The NIH Roadmap , 2003, Science.

[16]  R. Sharan,et al.  Protein networks in disease. , 2008, Genome research.

[17]  Raja Jothi,et al.  Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. , 2006, Journal of molecular biology.

[18]  A. Vazquez,et al.  Epstein–Barr virus and virus human protein interaction maps , 2007, Proceedings of the National Academy of Sciences.

[19]  Benjamin A. Shoemaker,et al.  Finding biologically relevant protein domain interactions: Conserved binding mode analysis , 2006, Protein science : a publication of the Protein Society.

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

[21]  A. Barabasi,et al.  Drug—target network , 2007, Nature Biotechnology.

[22]  Benjamin A. Shoemaker,et al.  Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases , 2007, PLoS Comput. Biol..

[23]  Paul A. Bates,et al.  Global topological features of cancer proteins in the human interactome , 2006, Bioinform..

[24]  F. Collins,et al.  A vision for the future of genomics research , 2003, Nature.

[25]  Yongjin Li,et al.  Discovering disease-genes by topological features in human protein-protein interaction network , 2006, Bioinform..

[26]  Chern-Sing Goh,et al.  Co-evolutionary analysis reveals insights into protein-protein interactions. , 2002, Journal of molecular biology.

[27]  M. Sternberg,et al.  Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. , 2005, Journal of molecular biology.

[28]  R C Punnett Mendelism in Relation to Disease , 1908, Proceedings of the Royal Society of Medicine.

[29]  K. N. Chandrika,et al.  Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets , 2006, Nature Genetics.

[30]  R. Mayeux Mapping the new frontier: complex genetic disorders. , 2005, The Journal of clinical investigation.

[31]  Alfonso Valencia,et al.  TSEMA: interactive prediction of protein pairings between interacting families , 2006, Nucleic Acids Res..

[32]  Alfonso Valencia,et al.  Co‐evolution and co‐adaptation in protein networks , 2008, FEBS letters.

[33]  C R Scriver,et al.  Monogenic traits are not simple: lessons from phenylketonuria. , 1999, Trends in genetics : TIG.

[34]  Yoshihiro Yamanishi,et al.  The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships , 2005, Bioinform..

[35]  A. E. Hirsh,et al.  Coevolution of gene expression among interacting proteins , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Takeshi Kishida,et al.  Von Hippel-Lindau (VHL) disease with pheochromocytoma in the Black Forest region of Germany: evidence for a founder effect , 1995, Human Genetics.

[37]  K. J. Fryxell,et al.  The coevolution of gene family trees. , 1996, Trends in genetics : TIG.

[38]  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.

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

[40]  Mark D'Souza,et al.  Use of contiguity on the chromosome to predict functional coupling , 1998, Silico Biol..

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

[42]  A. Barabasi,et al.  A Protein–Protein Interaction Network for Human Inherited Ataxias and Disorders of Purkinje Cell Degeneration , 2006, Cell.

[43]  G. Cutting,et al.  Variant cystic fibrosis phenotypes in the absence of CFTR mutations. , 2002, The New England journal of medicine.

[44]  D. Botstein,et al.  Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease , 2003, Nature Genetics.

[45]  F. Giorgini,et al.  Connecting the dots in Huntington's disease with protein interaction networks , 2005, Genome Biology.

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

[47]  Jeremy Nathans,et al.  Biochemical defects in ABCR protein variants associated with human retinopathies , 2000, Nature Genetics.

[48]  Steven E. Bayer,et al.  A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. , 1994, Science.

[49]  Peter Grindrod,et al.  Review of uses of network and graph theory concepts within proteomics , 2004, Expert review of proteomics.

[50]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[51]  S. L. Wong,et al.  Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.

[52]  Arun K. Ramani,et al.  Exploiting the co-evolution of interacting proteins to discover interaction specificity. , 2003, Journal of molecular biology.

[53]  Susan Lindquist,et al.  A network of protein interactions determines polyglutamine toxicity. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[54]  H. Lehrach,et al.  A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. , 2004, Molecular cell.

[55]  D. Bentley,et al.  Identification of the breast cancer susceptibility gene BRCA2 , 1995, Nature.

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

[57]  Teresa M. Przytycka,et al.  Predicting protein-protein interaction by searching evolutionary tree automorphism space , 2005, ISMB.

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

[59]  B. Snel,et al.  Predicting disease genes using protein–protein interactions , 2006, Journal of Medical Genetics.

[60]  Benno Schwikowski,et al.  Discovering regulatory and signalling circuits in molecular interaction networks , 2002, ISMB.

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

[62]  Christopher J. Lee,et al.  Inferring protein domain interactions from databases of interacting proteins , 2005, Genome Biology.

[63]  K. Guimaraes,et al.  Predicting domain-domain interactions using a parsimony approach , 2006, Genome Biology.

[64]  Manish S. Shah,et al.  A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes , 1993, Cell.

[65]  Maricel G. Kann,et al.  Protein interactions and disease: computational approaches to uncover the etiology of diseases , 2007, Briefings Bioinform..

[66]  T. Ideker,et al.  Network-based classification of breast cancer metastasis , 2007, Molecular systems biology.

[67]  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.

[68]  L. Tsui,et al.  Erratum: Identification of the Cystic Fibrosis Gene: Genetic Analysis , 1989, Science.

[69]  A. Barabasi,et al.  The human disease network , 2007, Proceedings of the National Academy of Sciences.

[70]  E R McCabe,et al.  Phenotypes of patients with "simple" Mendelian disorders are complex traits: thresholds, modifiers, and systems dynamics. , 2000, American journal of human genetics.

[71]  Martin Scheffner,et al.  Human papillomavirus-induced carcinogenesis and the ubiquitin-proteasome system. , 2003, Seminars in cancer biology.