Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

[1]  E. Lander,et al.  Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. , 1989, Genetics.

[2]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[3]  B. Rost,et al.  Adaptation of protein surfaces to subcellular location. , 1998, Journal of molecular biology.

[4]  K. Nakai,et al.  PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. , 1999, Trends in biochemical sciences.

[5]  D. Wallace.  Mitochondrial diseases in man and mouse. , 1999, Science.

[6]  M. Gerstein,et al.  A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. , 2000, Journal of molecular biology.

[7]  S. Brunak,et al.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. , 2000, Journal of molecular biology.

[8]  L. Aravind.  Guilt by association: contextual information in genome analysis. , 2000, Genome research.

[9]  Trevor Hastie,et al.  The Elements of Statistical Learning , 2001 .

[10]  Zhirong Sun,et al.  Support vector machine approach for protein subcellular localization prediction , 2001, Bioinform..

[11]  Jean Rossier,et al.  Systematic identification of mitochondrial proteins by LC-MS/MS. , 2002, Analytical chemistry.

[12]  Stefan Fritz,et al.  Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. , 2002, Molecular biology of the cell.

[13]  André Boorsma,et al.  Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state , 2002, Genome Biology.

[14]  M. Gerstein,et al.  Subcellular localization of the yeast proteome. , 2002, Genes & development.

[15]  Ronald W. Davis,et al.  Systematic screen for human disease genes in yeast , 2002, Nature Genetics.

[16]  Antoine Margeot,et al.  Genome‐wide analysis of mRNAs targeted to yeast mitochondria , 2002, EMBO reports.

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

[18]  J. Ott,et al.  Mathematical multi-locus approaches to localizing complex human trait genes , 2003, Nature Reviews Genetics.

[19]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[20]  Eric S. Lander,et al.  Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

[22]  C. Jacq,et al.  The role of the 3' untranslated region in mRNA sorting to the vicinity of mitochondria is conserved from yeast to human cells. , 2003, Molecular biology of the cell.

[23]  Albert Sickmann,et al.  The proteome of Saccharomyces cerevisiae mitochondria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Marjan S. Bolouri,et al.  Integrated Analysis of Protein Composition, Tissue Diversity, and Gene Regulation in Mouse Mitochondria , 2003, Cell.

[25]  Benedikt Westermann,et al.  'Omics' of the mitochondrion , 2003, Nature Biotechnology.

[26]  Robert W. Taylor,et al.  The epidemiology of mitochondrial disorders--past, present and future. , 2004, Biochimica et biophysica acta.

[27]  Eoin Fahy,et al.  MitoProteome: mitochondrial protein sequence database and annotation system , 2004, Nucleic Acids Res..

[28]  F. Legeai,et al.  Predotar: A tool for rapidly screening proteomes for N‐terminal targeting sequences , 2004, Proteomics.

[29]  Gary D Bader,et al.  Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.

[30]  A. Kastaniotis,et al.  The Yeast Mitochondrial Proteome, a Study of Fermentative and Respiratory Growth* , 2004, Journal of Biological Chemistry.

[31]  Razvan C. Bunescu,et al.  Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome , 2005, Genome Biology.

[32]  Harvey J. Greenberg,et al.  Reconstruction and Functional Characterization of the Human Mitochondrial Metabolic Network Based on Proteomic and Biochemical Data* , 2004, Journal of Biological Chemistry.

[33]  J. Rothberg,et al.  Gaining confidence in high-throughput protein interaction networks , 2004, Nature Biotechnology.

[34]  Ronald J. Moore,et al.  Integrative Analysis of the Mitochondrial Proteome in Yeast , 2004, PLoS biology.

[35]  Michael E Phelps,et al.  Systems Biology and New Technologies Enable Predictive and Preventative Medicine , 2004, Science.

[36]  D. Wallace.  A Mitochondrial Paradigm of Metabolic and Degenerative Diseases, Aging, and Cancer: A Dawn for Evolutionary Medicine , 2005, Annual review of genetics.

[37]  J. Martinou,et al.  Building the mitochondrial proteome , 2005, Expert review of proteomics.

[38]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..

[39]  John R Yates,et al.  Protein identification using 2D-LC-MS/MS. , 2005, Methods.

[40]  Joshua L. Heazlewood,et al.  AMPDB: the Arabidopsis Mitochondrial Protein Database , 2004, Nucleic Acids Res..

[41]  D. Rebholz-Schuhmann,et al.  Facts from Text—Is Text Mining Ready to Deliver? , 2005, PLoS biology.

[42]  Xiaohui S. Xie,et al.  Disease gene discovery through integrative genomics. , 2005, Annual review of genomics and human genetics.

[43]  Chittibabu Guda,et al.  TARGET: a new method for predicting protein subcellular localization in eukaryotes , 2005, Bioinform..

[44]  C. Saccone,et al.  The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae. , 2006, Mitochondrion.

[45]  Sarah Calvo,et al.  Systematic identification of human mitochondrial disease genes through integrative genomics , 2006, Nature Genetics.

[46]  Thomas Meitinger,et al.  MitoP2: the mitochondrial proteome database—now including mouse data , 2005, Nucleic Acids Res..

[47]  R. Aebersold,et al.  Mass Spectrometry and Protein Analysis , 2006, Science.

[48]  Frank Dudbridge,et al.  Detecting multiple associations in genome-wide studies , 2006, Human Genomics.

[49]  Gopal R. Gopinath,et al.  Reactome: a knowledge base of biologic pathways and processes , 2007, Genome Biology.

[50]  Hans-Werner Mewes,et al.  MPact: the MIPS protein interaction resource on yeast , 2005, Nucleic Acids Res..

[51]  C. Wijmenga,et al.  Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. , 2006, American journal of human genetics.

[52]  D. Chan.  Mitochondria: Dynamic Organelles in Disease, Aging, and Development , 2006, Cell.

[53]  D. Kell.  Systems biology, metabolic modelling and metabolomics in drug discovery and development. , 2006, Drug discovery today.

[54]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[55]  J. Nicholson.  Global systems biology, personalized medicine and molecular epidemiology , 2006, Molecular systems biology.

[56]  Sarah Calvo,et al.  MPV17 encodes an inner mitochondrial membrane protein and is mutated in infantile hepatic mitochondrial DNA depletion , 2006, Nature Genetics.

[57]  Neema Jamshidi,et al.  Systems biology of SNPs , 2006, Molecular systems biology.

[58]  Peer Bork,et al.  Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle , 2006, PLoS genetics.

[59]  Paul Horton,et al.  Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .

[60]  Christian von Mering,et al.  STRING 7—recent developments in the integration and prediction of protein interactions , 2006, Nucleic Acids Res..

[61]  Balázs Papp,et al.  Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling. , 2007, Genome research.

[62]  Y. Umezawa,et al.  A genetic method to identify mitochondrial proteins in living mammalian cells. , 2007, Methods in molecular biology.

[63]  Marni J. Falk,et al.  Mitochondrial Disease: A Practical Approach for Primary Care Physicians , 2007, Pediatrics.

[64]  Hagit Shatkay,et al.  SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. , 2007, Bioinformatics.

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

[66]  Kenta Nakai,et al.  Computational prediction of subcellular localization. , 2007, Methods in molecular biology.

[67]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[68]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[69]  Simon C. Potter,et al.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls , 2007, Nature.

[70]  B. Palsson,et al.  Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome. , 2007, Molecular genetics and metabolism.

[71]  S. Kaech,et al.  Convergence of multiple signaling pathways is required to coordinately up-regulate mtDNA and mitochondrial biogenesis during T cell activation. , 2007, Mitochondrion.

[72]  Kriston L. McGary,et al.  Open Access Method , 2007 .

[73]  S. Carr,et al.  A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology , 2008, Cell.

[74]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[75]  Lars M Steinmetz,et al.  Systematic screens for human disease genes, from yeast to human and back. , 2008, Molecular bioSystems.

[76]  K. Conley,et al.  Mitochondrial function in vivo: spectroscopy provides window on cellular energetics. , 2008, Methods.

[77]  Kara Dolinski,et al.  The BioGRID Interaction Database: 2008 update , 2008, Nucleic Acids Res..

[78]  Leonid Kruglyak,et al.  The road to genome-wide association studies , 2008, Nature Reviews Genetics.

[79]  K. Mossman.  The Wellcome Trust Case Control Consortium, U.K. , 2008 .

[80]  Weidong Tian,et al.  Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function , 2008, Genome Biology.

[81]  Lukas N. Mueller,et al.  An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. , 2008, Journal of proteome research.

[82]  Werner J H Koopman,et al.  Computer-assisted live cell analysis of mitochondrial membrane potential, morphology and calcium handling. , 2008, Methods.

[83]  M. Hild,et al.  Identification of novel modulators of mitochondrial function by a genome-wide RNAi screen in Drosophila melanogaster. , 2007, Genome research.

[84]  Dietrich Rebholz-Schuhmann,et al.  Integrating protein-protein interactions and text mining for protein function prediction , 2008, BMC Bioinformatics.

[85]  S. Horvath,et al.  Variations in DNA elucidate molecular networks that cause disease , 2008, Nature.