Interpretation of Genomic Variants Using a Unified Biological Network Approach

S Levy, 2007, The diploid genome sequence of an individual human, PLoS Biol, 5, e254, 10.1371/journal.pbio.0050254

DA Wheeler, 2008, The complete genome of an individual by massively parallel DNA sequencing, Nature, 452, 872, 10.1038/nature06884

J Wang, 2008, The diploid genome sequence of an Asian individual, Nature, 456, 60, 10.1038/nature07484

2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534

DG MacArthur, 2012, A systematic survey of loss-of-function variants in human protein-coding genes, Science, 335, 823, 10.1126/science.1215040

PC Ng, 2006, Predicting the effects of amino acid substitutions on protein function, Annu Rev Genomics Hum Genet, 7, 61, 10.1146/annurev.genom.7.080505.115630

X Wang, 2011, Network-based methods for human disease gene prediction, Brief Funct Genomics, 10, 280, 10.1093/bfgp/elr024

KI Goh, 2007, The human disease network, Proc Natl Acad Sci U S A, 104, 8685, 10.1073/pnas.0701361104

H Jeong, 2001, Lethality and centrality in protein networks, Nature, 411, 41, 10.1038/35075138

PM Kim, 2007, Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context, Proc Natl Acad Sci U S A, 104, 20274, 10.1073/pnas.0710183104

Q Cui, 2009, Protein evolution on a human signaling network, BMC Syst Biol, 3, 21, 10.1186/1752-0509-3-21

D Vitkup, 2006, Influence of metabolic network structure and function on enzyme evolution, Genome Biol, 7, R39, 10.1186/gb-2006-7-5-r39

L Montanucci, 2011, Molecular evolution and network-level analysis of the N-glycosylation metabolic pathway across primates, Mol Biol Evol, 28, 813, 10.1093/molbev/msq259

PM Kim, 2006, Relating three-dimensional structures to protein networks provides evolutionary insights, Science, 314, 1938, 10.1126/science.1136174

X Wang, 2012, Three-dimensional reconstruction of protein networks provides insight into human genetic disease, Nat Biotechnol, 30, 159, 10.1038/nbt.2106

CT Saunders, 2002, Evaluation of structural and evolutionary contributions to deleterious mutation prediction, J Mol Biol, 322, 891, 10.1016/S0022-2836(02)00813-6

M Gerstein, 2012, Architecture of the human regulatory network derived from ENCODE data, Nature, 489, 91, 10.1038/nature11245

C Stark, 2006, BioGRID: a general repository for interaction datasets, Nucleic Acids Res, 34, D535, 10.1093/nar/gkj109

BE Hoskins, 2007, Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome, Am J Hum Genet, 80, 800, 10.1086/513322

N Bhardwaj, 2011, Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions, Protein Sci, 20, 1745, 10.1002/pro.710

IA Adzhubei, 2010, A method and server for predicting damaging missense mutations, Nat Methods, 7, 248, 10.1038/nmeth0410-248

P Kumar, 2009, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nat Protoc, 4, 1073, 10.1038/nprot.2009.86

M Kanehisa, 2010, KEGG for representation and analysis of molecular networks involving diseases and drugs, Nucleic Acids Res, 38, D355, 10.1093/nar/gkp896

J Lin, 2010, Understanding protein phosphorylation on a systems level, Brief Funct Genomics, 9, 32, 10.1093/bfgp/elp045

T Korcsmaros, 2010, Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery, Bioinformatics, 26, 2042, 10.1093/bioinformatics/btq310

H Ogata, 1999, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res, 27, 29, 10.1093/nar/27.1.29

G Joshi-Tope, 2005, Reactome: a knowledgebase of biological pathways, Nucleic Acids Res, 33, D428, 10.1093/nar/gki072

K Kandasamy, 2010, NetPath: a public resource of curated signal transduction pathways, Genome Biol, 11, R3, 10.1186/gb-2010-11-1-r3

BY Liao, 2008, Null mutations in human and mouse orthologs frequently result in different phenotypes, Proc Natl Acad Sci U S A, 105, 6987, 10.1073/pnas.0800387105

PD Stenson, 2009, The Human Gene Mutation Database: 2008 update, Genome Med, 1, 13, 10.1186/gm13

P Flicek, 2012, Ensembl 2012, Nucleic Acids Res, 40, D84, 10.1093/nar/gkr991

P Pagel, 2005, The MIPS mammalian protein-protein interaction database, Bioinformatics, 21, 832, 10.1093/bioinformatics/bti115

RD Finn, 2005, iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions, Bioinformatics, 21, 410, 10.1093/bioinformatics/bti011