메뉴 건너뛰기




Volumn 19, Issue 2, 2018, Pages 286-302

Genome, transcriptome and proteome: The rise of omics data and their integration in biomedical sciences

Author keywords

Bioinformatics; Databases; Genomics; Omics; Proteomics; Transcriptomics

Indexed keywords

PROTEOME; TRANSCRIPTOME;

EID: 85052065143     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/BIB/BBW114     Document Type: Article
Times cited : (531)

References (153)
  • 1
    • 0345998876 scopus 로고
    • RNA codewords and protein synthesis the nucleotide sequences of multiple codewords for phenylalanine, serine, leucine, and proline
    • Bernfield MR, Nirenberg MW. RNA codewords and protein synthesis. the nucleotide sequences of multiple codewords for phenylalanine, serine, leucine, and proline. Science 1965;147:479-84
    • (1965) Science , vol.147 , pp. 479-484
    • Bernfield, M.R.1    Nirenberg, M.W.2
  • 2
    • 85052135523 scopus 로고    scopus 로고
    • Genomes. http://www.1000genomes.org/
  • 3
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap project
    • International HapMap Consortium. The International HapMap project. Nature 2003;426:789-96
    • (2003) Nature , vol.426 , pp. 789-796
  • 4
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 2004;431:931-45
    • (2004) Nature , vol.431 , pp. 931-945
  • 5
    • 85052113285 scopus 로고    scopus 로고
    • The First Solution of the Three-Dimensional Molecular Structure of a Protein (1958-1960)
    • HistoryofInformation.com
    • Protein D. The First Solution of the Three-Dimensional Molecular Structure of a Protein (1958-1960). HistoryofInformation.com
    • Protein, D.1
  • 6
    • 77955498814 scopus 로고    scopus 로고
    • The roots of bioinformatics
    • Searls DB. The roots of bioinformatics. PLoS Comput Biol 2010;6:e1000809
    • (2010) PLoS Comput Biol , vol.6
    • Searls, D.B.1
  • 7
    • 85052071367 scopus 로고    scopus 로고
    • Timeline GG. GNN-Genetics and Genomics Timeline
  • 8
    • 0002011401 scopus 로고
    • The chemical basis of morphogenesis
    • Turing AM. The chemical basis of morphogenesis. Philos Trans R Soc Lond 1952;237:37-72
    • (1952) Philos Trans R Soc Lond , vol.237 , pp. 37-72
    • Turing, A.M.1
  • 9
    • 73149086369 scopus 로고
    • An outline of general system theory
    • Von Bertalanffy L. An outline of general system theory. Br J Philos Sci 1950;1:134-65
    • (1950) Br J Philos Sci , vol.1 , pp. 134-165
    • Von Bertalanffy, L.1
  • 10
    • 0038497542 scopus 로고
    • Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid
    • Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953;171:737-8
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, J.D.1    Crick, F.H.2
  • 11
    • 84862908424 scopus 로고    scopus 로고
    • Clinical cancer advances 2011: annual report on progress against cancer from the American Society of Clinical Oncology
    • Vogelzang NJ, Benowitz SI, Adams S, et al. Clinical cancer advances 2011: annual report on progress against cancer from the American Society of Clinical Oncology. J Clin Oncol 2012;30:88-109
    • (2012) J Clin Oncol , vol.30 , pp. 88-109
    • Vogelzang, N.J.1    Benowitz, S.I.2    Adams, S.3
  • 12
    • 84924299916 scopus 로고    scopus 로고
    • Topological sensitivity analysis for systems biology
    • Babtie AC, Kirk P, Stumpf MP. Topological sensitivity analysis for systems biology. Proc Natl Acad Sci USA 2014;111:18507-12
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 18507-18512
    • Babtie, A.C.1    Kirk, P.2    Stumpf, M.P.3
  • 13
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: the reference human genome annotation for the ENCODE project
    • Harrow J, Frankish A, Gonzalez JM, et al. GENCODE: the reference human genome annotation for the ENCODE project. Genome Res 2012;22:1760-74
    • (2012) Genome Res , vol.22 , pp. 1760-1774
    • Harrow, J.1    Frankish, A.2    Gonzalez, J.M.3
  • 15
    • 43049146524 scopus 로고    scopus 로고
    • A HapMap harvest of insights into the genetics of common disease
    • Manolio TA, Brooks LD, Collins FS. A HapMap harvest of insights into the genetics of common disease. J Clin Invest 2008;118:1590-605
    • (2008) J Clin Invest , vol.118 , pp. 1590-1605
    • Manolio, T.A.1    Brooks, L.D.2    Collins, F.S.3
  • 16
    • 33746317014 scopus 로고    scopus 로고
    • Human red blood cell polymorphisms and malaria
    • Williams TN. Human red blood cell polymorphisms and malaria. Curr Opin Microbiol 2006;9:388-94
    • (2006) Curr Opin Microbiol , vol.9 , pp. 388-394
    • Williams, T.N.1
  • 17
    • 70349956433 scopus 로고    scopus 로고
    • Finding the missing heritability of complex diseases
    • Manolio TA, Collins FS, Cox NJ, et al. Finding the missing heritability of complex diseases. Nature 2009;461:747-53
    • (2009) Nature , vol.461 , pp. 747-753
    • Manolio, T.A.1    Collins, F.S.2    Cox, N.J.3
  • 19
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-the next generation
    • Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010;11:31-46
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 20
    • 0036206069 scopus 로고    scopus 로고
    • Guidelines for human gene nomenclature
    • Wain HM, Bruford EA, Lovering RC, et al. Guidelines for human gene nomenclature. Genomics 2002;79:464-70
    • (2002) Genomics , vol.79 , pp. 464-470
    • Wain, H.M.1    Bruford, E.A.2    Lovering, R.C.3
  • 21
    • 84891791841 scopus 로고    scopus 로고
    • The vertebrate genome annotation browser 10 years on
    • Harrow JL, Steward CA, Frankish A, et al. The vertebrate genome annotation browser 10 years on. Nucleic Acids Res 2014;42:D771-9
    • (2014) Nucleic Acids Res , vol.42 , pp. D771-D779
    • Harrow, J.L.1    Steward, C.A.2    Frankish, A.3
  • 22
    • 2342507856 scopus 로고    scopus 로고
    • The challenge of documenting mutation across the genome: the human genome variation society approach
    • Horaitis O, Cotton RG. The challenge of documenting mutation across the genome: the human genome variation society approach. Hum Mutat 2004;23:447-52
    • (2004) Hum Mutat , vol.23 , pp. 447-452
    • Horaitis, O.1    Cotton, R.G.2
  • 24
    • 84877074259 scopus 로고    scopus 로고
    • Overview of DNA microarrays: types, applications, and their future
    • Chapter 22 Unit 22.21
    • Bumgarner R. Overview of DNA microarrays: types, applications, and their future. Curr Protoc Mol Biol 2013;Chapter 22:Unit 22.21
    • (2013) Curr Protoc Mol Biol
    • Bumgarner, R.1
  • 25
    • 85028165246 scopus 로고    scopus 로고
    • Ten years of nextgeneration sequencing technology
    • van Dijk EL, Auger H, Jaszczyszyn Y, et al. Ten years of nextgeneration sequencing technology. Trends Genet 2014;30:418-26
    • (2014) Trends Genet , vol.30 , pp. 418-426
    • van Dijk, E.L.1    Auger, H.2    Jaszczyszyn, Y.3
  • 26
    • 40949127393 scopus 로고    scopus 로고
    • How to interpret a genome-wide association study
    • Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA 2008;299:1335-44
    • (2008) JAMA , vol.299 , pp. 1335-1344
    • Pearson, T.A.1    Manolio, T.A.2
  • 28
    • 1342345645 scopus 로고    scopus 로고
    • 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US);
    • Schneider V.C. The NCBI Handbook [Internet]. 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US); 2013
    • (2013) The NCBI Handbook [Internet]
    • Schneider, V.C.1
  • 29
    • 85052138201 scopus 로고    scopus 로고
    • Pop G. http://www.1000genomes.org/about#ProjectSamples
    • Pop, G.1
  • 30
    • 84943182742 scopus 로고    scopus 로고
    • The UK10K project identifies rare variants in health and disease
    • Consortium UK, Walter K, Min JL, et al. The UK10K project identifies rare variants in health and disease. Nature 2015;526:82-90
    • (2015) Nature , vol.526 , pp. 82-90
    • Consortium, U.K.1    Walter, K.2    Min, J.L.3
  • 31
    • 84940479498 scopus 로고    scopus 로고
    • The DNA of a nation
    • Marx V. The DNA of a nation. Nature 2015;524:503-5
    • (2015) Nature , vol.524 , pp. 503-505
    • Marx, V.1
  • 32
    • 84923762812 scopus 로고    scopus 로고
    • A new initiative on precision medicine
    • Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med 2015;372:793-5
    • (2015) N Engl J Med , vol.372 , pp. 793-795
    • Collins, F.S.1    Varmus, H.2
  • 33
    • 84939599004 scopus 로고    scopus 로고
    • Large-scale metaanalysis of genome-wide association data identifies six new risk loci for Parkinson's disease
    • Nalls MA, Pankratz N, Lill CM, et al. Large-scale metaanalysis of genome-wide association data identifies six new risk loci for Parkinson's disease. Nat Genet 2014;46:989-93
    • (2014) Nat Genet , vol.46 , pp. 989-993
    • Nalls, M.A.1    Pankratz, N.2    Lill, C.M.3
  • 34
    • 34748864128 scopus 로고    scopus 로고
    • A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15
    • Menzel S, Garner C, Gut I, et al. A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15. Nat Genet 2007;39:1197-9
    • (2007) Nat Genet , vol.39 , pp. 1197-1199
    • Menzel, S.1    Garner, C.2    Gut, I.3
  • 35
    • 40349092939 scopus 로고    scopus 로고
    • Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia
    • Uda M, Galanello R, Sanna S, et al. Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia. Proc Natl Acad Sci USA 2008;105:1620-5
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 1620-1625
    • Uda, M.1    Galanello, R.2    Sanna, S.3
  • 36
    • 84868336049 scopus 로고    scopus 로고
    • Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease
    • Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012;491:119-24
    • (2012) Nature , vol.491 , pp. 119-124
    • Jostins, L.1    Ripke, S.2    Weersma, R.K.3
  • 37
    • 85000692305 scopus 로고    scopus 로고
    • An atlas of genetic correlations across human diseases and traits
    • Bulik-Sullivan B, Finucane HK, Anttila V, et al. An atlas of genetic correlations across human diseases and traits. Nat Genet 2015;47:1236-41
    • (2015) Nat Genet , vol.47 , pp. 1236-1241
    • Bulik-Sullivan, B.1    Finucane, H.K.2    Anttila, V.3
  • 38
    • 77952557918 scopus 로고    scopus 로고
    • Missing heritability and strategies for finding the underlying causes of complex disease
    • Eichler EE, Flint J, Gibson G, et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 2010;11:446-50
    • (2010) Nat Rev Genet , vol.11 , pp. 446-450
    • Eichler, E.E.1    Flint, J.2    Gibson, G.3
  • 39
    • 77954140531 scopus 로고    scopus 로고
    • Common SNPs explain a large proportion of the heritability for human height
    • Yang J, Benyamin B, McEvoy BP, et al. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 2010;42:565-9
    • (2010) Nat Genet , vol.42 , pp. 565-569
    • Yang, J.1    Benyamin, B.2    McEvoy, B.P.3
  • 40
    • 84929132687 scopus 로고    scopus 로고
    • Largescale whole-genome sequencing of the Icelandic population
    • Gudbjartsson DF, Helgason H, Gudjonsson SA, et al. Largescale whole-genome sequencing of the Icelandic population. Nat Genet 2015;47:435-44
    • (2015) Nat Genet , vol.47 , pp. 435-444
    • Gudbjartsson, D.F.1    Helgason, H.2    Gudjonsson, S.A.3
  • 41
    • 84880339190 scopus 로고    scopus 로고
    • Use of linkage analysis, genome-wide association studies, and next-generation sequencing in the identification of disease-causing mutations
    • Londin E, Yadav P, Surrey S, et al. Use of linkage analysis, genome-wide association studies, and next-generation sequencing in the identification of disease-causing mutations. Methods Mol Biol 2013;1015:127-46
    • (2013) Methods Mol Biol , vol.1015 , pp. 127-146
    • Londin, E.1    Yadav, P.2    Surrey, S.3
  • 42
    • 84927138651 scopus 로고    scopus 로고
    • A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing
    • Wang Q, Lu Q, Zhao H. A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing. Front Genet 2015;6:149
    • (2015) Front Genet , vol.6 , pp. 149
    • Wang, Q.1    Lu, Q.2    Zhao, H.3
  • 43
    • 34548292504 scopus 로고    scopus 로고
    • PLINK: a tool set for whole-genome association and population-based linkage analyses
    • Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75
    • (2007) Am J Hum Genet , vol.81 , pp. 559-575
    • Purcell, S.1    Neale, B.2    Todd-Brown, K.3
  • 44
    • 34347344976 scopus 로고    scopus 로고
    • A new multipoint method for genome-wide association studies by imputation of genotypes
    • Marchini J, Howie B, Myers S, et al. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 2007;39:906-13
    • (2007) Nat Genet , vol.39 , pp. 906-913
    • Marchini, J.1    Howie, B.2    Myers, S.3
  • 45
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004;5:R80
    • (2004) Genome Biol , vol.5 , pp. R80
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3
  • 46
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-303
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3
  • 47
    • 84965026430 scopus 로고    scopus 로고
    • The European Bioinformatics Institute in 2016: data growth and integration
    • Cook CE, Bergman MT, Finn RD, et al. The European Bioinformatics Institute in 2016: data growth and integration. Nucleic Acids Res 2016;44:D20-6
    • (2016) Nucleic Acids Res , vol.44 , pp. D20-D26
    • Cook, C.E.1    Bergman, M.T.2    Finn, R.D.3
  • 48
    • 84876187089 scopus 로고    scopus 로고
    • Where in the genome are we?. A cautionary tale of database use in genomics research
    • Vaughan LK, Srinivasasainagendra V. Where in the genome are we? A cautionary tale of database use in genomics research. Front Genet 2013;4:38
    • (2013) Front Genet , vol.4 , pp. 38
    • Vaughan, L.K.1    Srinivasasainagendra, V.2
  • 49
    • 84891749517 scopus 로고    scopus 로고
    • The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
    • Kohler S, Doelken SC, Mungall CJ, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 2014;42:D966-74
    • (2014) Nucleic Acids Res , vol.42 , pp. D966-D974
    • Kohler, S.1    Doelken, S.C.2    Mungall, C.J.3
  • 50
    • 84930083227 scopus 로고    scopus 로고
    • Improved genome inference in the MHC using a population reference graph
    • Dilthey A, Cox C, Iqbal Z, et al. Improved genome inference in the MHC using a population reference graph. Nat Genet 2015;47:682-8
    • (2015) Nat Genet , vol.47 , pp. 682-688
    • Dilthey, A.1    Cox, C.2    Iqbal, Z.3
  • 53
    • 46249130709 scopus 로고    scopus 로고
    • The beginning of the end for microarrays?
    • Shendure J. The beginning of the end for microarrays? Nat Methods 2008;5:585-7
    • (2008) Nat Methods , vol.5 , pp. 585-587
    • Shendure, J.1
  • 54
    • 84974604914 scopus 로고    scopus 로고
    • Thermodynamically optimal wholegenome tiling microarray design and validation
    • Cho H, Chou HH. Thermodynamically optimal wholegenome tiling microarray design and validation. BMC Res Notes 2016;9:305
    • (2016) BMC Res Notes , vol.9 , pp. 305
    • Cho, H.1    Chou, H.H.2
  • 55
    • 75949115042 scopus 로고    scopus 로고
    • RNA-Seq: a method for comprehensive transcriptome analysis
    • Chapter 4 Unit 4.11.1-3
    • Nagalakshmi U, Waern K, Snyder M. RNA-Seq: a method for comprehensive transcriptome analysis. Curr Protoc Mol Biol 2010;Chapter 4:Unit 4.11.1-3
    • (2010) Curr Protoc Mol Biol
    • Nagalakshmi, U.1    Waern, K.2    Snyder, M.3
  • 57
    • 84907500627 scopus 로고    scopus 로고
    • RNA-Seq gene profiling-a systematic empirical comparison
    • Fonseca NA, Marioni J, Brazma A. RNA-Seq gene profiling-a systematic empirical comparison. PLoS One 2014;9:e107026
    • (2014) PLoS One , vol.9
    • Fonseca, N.A.1    Marioni, J.2    Brazma, A.3
  • 58
    • 84922715662 scopus 로고    scopus 로고
    • Integromic analysis of genetic variation and gene expression identifies networks for cardiovascular disease phenotypes
    • Yao C, Chen BH, Joehanes R, et al. Integromic analysis of genetic variation and gene expression identifies networks for cardiovascular disease phenotypes. Circulation 2015;131:536-49
    • (2015) Circulation , vol.131 , pp. 536-549
    • Yao, C.1    Chen, B.H.2    Joehanes, R.3
  • 59
    • 84929001104 scopus 로고    scopus 로고
    • Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans
    • Consortium GT. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 2015;348:648-60
    • (2015) Science , vol.348 , pp. 648-660
    • Consortium, G.T.1
  • 60
    • 84885645853 scopus 로고    scopus 로고
    • Transcriptome and genome sequencing uncovers functional variation in humans
    • Lappalainen T, Sammeth M, Friedlander MR, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013;501:506-11
    • (2013) Nature , vol.501 , pp. 506-511
    • Lappalainen, T.1    Sammeth, M.2    Friedlander, M.R.3
  • 61
    • 84921750431 scopus 로고    scopus 로고
    • Genetic variability in the regulation of gene expression in ten regions of the human brain
    • Ramasamy A, Trabzuni D, Guelfi S, et al. Genetic variability in the regulation of gene expression in ten regions of the human brain. Nat Neurosci 2014;17:1418-28
    • (2014) Nat Neurosci , vol.17 , pp. 1418-1428
    • Ramasamy, A.1    Trabzuni, D.2    Guelfi, S.3
  • 62
    • 84885018609 scopus 로고    scopus 로고
    • Systematic identification of trans eQTLs as putative drivers of known disease associations
    • Westra HJ, Peters MJ, Esko T, et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet 2013;45:1238-43
    • (2013) Nat Genet , vol.45 , pp. 1238-1243
    • Westra, H.J.1    Peters, M.J.2    Esko, T.3
  • 63
    • 84929015299 scopus 로고    scopus 로고
    • Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome
    • Rivas MA, Pirinen M, Conrad DF, et al. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 2015;348:666-9
    • (2015) Science , vol.348 , pp. 666-669
    • Rivas, M.A.1    Pirinen, M.2    Conrad, D.F.3
  • 64
    • 84859892863 scopus 로고    scopus 로고
    • MicroRNA profiling: approaches and considerations
    • Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet 2012;13:358-69
    • (2012) Nat Rev Genet , vol.13 , pp. 358-369
    • Pritchard, C.C.1    Cheng, H.H.2    Tewari, M.3
  • 65
    • 84904730206 scopus 로고    scopus 로고
    • Integrative approaches for microRNA target prediction: combining sequence information and the paired mRNA and miRNA expression profiles
    • Naifang S, Minping Q, Minghua D. Integrative approaches for microRNA target prediction: combining sequence information and the paired mRNA and miRNA expression profiles. Curr Bioinform 2013;8:37-45
    • (2013) Curr Bioinform , vol.8 , pp. 37-45
    • Naifang, S.1    Minping, Q.2    Minghua, D.3
  • 66
    • 77954276691 scopus 로고    scopus 로고
    • MAGIA, a web-based tool for miRNA and genes integrated analysis
    • Sales G, Coppe A, Bisognin A, et al. MAGIA, a web-based tool for miRNA and genes integrated analysis. Nucleic Acids Res 2010;38:W352-359
    • (2010) Nucleic Acids Res , vol.38 , pp. W352-359
    • Sales, G.1    Coppe, A.2    Bisognin, A.3
  • 67
    • 34447288056 scopus 로고    scopus 로고
    • Bayesian inference of MicroRNA targets from sequence and expression data
    • Huang JC, Morris QD, Frey BJ. Bayesian inference of MicroRNA targets from sequence and expression data. J Comput Biol 2007;14:550-63
    • (2007) J Comput Biol , vol.14 , pp. 550-563
    • Huang, J.C.1    Morris, Q.D.2    Frey, B.J.3
  • 68
    • 79959997653 scopus 로고    scopus 로고
    • mirConnX: conditionspecific mRNA-microRNA network integrator
    • Huang GT, Athanassiou C, Benos PV. mirConnX: conditionspecific mRNA-microRNA network integrator. Nucleic Acids Res 2011;39:W416-23
    • (2011) Nucleic Acids Res , vol.39 , pp. W416-W423
    • Huang, G.T.1    Athanassiou, C.2    Benos, P.V.3
  • 69
    • 84990848868 scopus 로고    scopus 로고
    • Integrating miRNA and gene expression profiling analysis revealed regulatory networks in gastrointestinal stromal tumors
    • Pantaleo MA, Ravegnini G, Astolfi A, et al. Integrating miRNA and gene expression profiling analysis revealed regulatory networks in gastrointestinal stromal tumors. Epigenomics 2016;8:1347-66
    • (2016) Epigenomics , vol.8 , pp. 1347-1366
    • Pantaleo, M.A.1    Ravegnini, G.2    Astolfi, A.3
  • 70
    • 84990220376 scopus 로고    scopus 로고
    • Integrative analysis of miRNA and mRNA paired expression profiling of primary fibroblast derived from diabetic foot ulcers reveals multiple impaired cellular functions
    • in press
    • Liang L, Stone RC, Stojadinovic O, et al. Integrative analysis of miRNA and mRNA paired expression profiling of primary fibroblast derived from diabetic foot ulcers reveals multiple impaired cellular functions. Wound Repair Regen 2016, in press
    • (2016) Wound Repair Regen
    • Liang, L.1    Stone, R.C.2    Stojadinovic, O.3
  • 71
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: an R package for weighted correlation network analysis
    • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008;9:559
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 72
    • 84931274624 scopus 로고    scopus 로고
    • A survey of human brain transcriptome diversity at the single cell level
    • Darmanis S, Sloan SA, Zhang Y, et al. A survey of human brain transcriptome diversity at the single cell level. Proc Natl Acad Sci USA 2015;112:7285-90
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 7285-7290
    • Darmanis, S.1    Sloan, S.A.2    Zhang, Y.3
  • 73
    • 80055015161 scopus 로고    scopus 로고
    • Temporal dynamics and genetic control of transcription in the human prefrontal cortex
    • Colantuoni C, Lipska BK, Ye T, et al. Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature 2011;478:519-23
    • (2011) Nature , vol.478 , pp. 519-523
    • Colantuoni, C.1    Lipska, B.K.2    Ye, T.3
  • 74
    • 80054993342 scopus 로고    scopus 로고
    • Spatio-temporal transcriptome of the human brain
    • Kang HJ, Kawasawa YI, Cheng F, et al. Spatio-temporal transcriptome of the human brain. Nature 2011;478:483-9
    • (2011) Nature , vol.478 , pp. 483-489
    • Kang, H.J.1    Kawasawa, Y.I.2    Cheng, F.3
  • 75
    • 84938211607 scopus 로고    scopus 로고
    • Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125
    • Giordano D, Pesce A, Boechi L, et al. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. FEBS J 2015;282:2948-65
    • (2015) FEBS J , vol.282 , pp. 2948-2965
    • Giordano, D.1    Pesce, A.2    Boechi, L.3
  • 76
    • 84944165102 scopus 로고    scopus 로고
    • Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0
    • Pible O, Armengaud J. Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0. Proteomics 2015;15:3418-23
    • (2015) Proteomics , vol.15 , pp. 3418-3423
    • Pible, O.1    Armengaud, J.2
  • 77
    • 67349196123 scopus 로고    scopus 로고
    • A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
    • Bell AW, Deutsch EW, Au CE, et al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods 2009;6:423-30
    • (2009) Nat Methods , vol.6 , pp. 423-430
    • Bell, A.W.1    Deutsch, E.W.2    Au, C.E.3
  • 78
    • 79952119025 scopus 로고    scopus 로고
    • Proteomics databases and repositories
    • Martens L. Proteomics databases and repositories. Methods Mol Biol 2011;694:213-27
    • (2011) Methods Mol Biol , vol.694 , pp. 213-227
    • Martens, L.1
  • 80
    • 84976871411 scopus 로고    scopus 로고
    • 2016 update of the PRIDE database and its related tools
    • Vizcaino JA, Csordas A, Del-Toro N, et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res 2016;44:D447-56
    • (2016) Nucleic Acids Res , vol.44 , pp. D447-D456
    • Vizcaino, J.A.1    Csordas, A.2    Del-Toro, N.3
  • 81
    • 78651082595 scopus 로고    scopus 로고
    • mzML-a community standard for mass spectrometry data
    • Martens L, Chambers M, Sturm M, et al. mzML-a community standard for mass spectrometry data. Mol Cell Proteomics 2011;10:R110 000133
    • (2011) Mol Cell Proteomics , vol.10
    • Martens, L.1    Chambers, M.2    Sturm, M.3
  • 82
    • 60549084744 scopus 로고    scopus 로고
    • Managing the data explosio. A report on the HUPO-PSI workshop. August 2008, Amsterdam, The Netherlands
    • Orchard S, Hoogland C, Bairoch A, et al. Managing the data explosion. A report on the HUPO-PSI workshop. August 2008, Amsterdam, The Netherlands. Proteomics 2009;9: 499-501
    • (2009) Proteomics , vol.9 , pp. 499-501
    • Orchard, S.1    Hoogland, C.2    Bairoch, A.3
  • 83
    • 84920070787 scopus 로고    scopus 로고
    • Making proteomics data accessible and reusable: current state of proteomics databases and repositories
    • Perez-Riverol Y, Alpi E, Wang R, et al. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 2015;15:930-49
    • (2015) Proteomics , vol.15 , pp. 930-949
    • Perez-Riverol, Y.1    Alpi, E.2    Wang, R.3
  • 84
    • 84891796097 scopus 로고    scopus 로고
    • ProteomeXchange provides globally coordinated proteomics data submission and dissemination
    • Vizcaino JA, Deutsch EW, Wang R, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 2014;32:223-6
    • (2014) Nat Biotechnol , vol.32 , pp. 223-226
    • Vizcaino, J.A.1    Deutsch, E.W.2    Wang, R.3
  • 85
    • 58149213932 scopus 로고    scopus 로고
    • Literature-curated protein interaction datasets
    • Cusick ME, Yu H, Smolyar A, et al. Literature-curated protein interaction datasets. Nat Methods 2009;6:39-46
    • (2009) Nat Methods , vol.6 , pp. 39-46
    • Cusick, M.E.1    Yu, H.2    Smolyar, A.3
  • 86
    • 84859609641 scopus 로고    scopus 로고
    • Analyzing protein-protein interaction networks
    • Koh GC, Porras P, Aranda B, et al. Analyzing protein-protein interaction networks. J Proteome Res 2012;11:2014-31
    • (2012) J Proteome Res , vol.11 , pp. 2014-2031
    • Koh, G.C.1    Porras, P.2    Aranda, B.3
  • 87
    • 84891799734 scopus 로고    scopus 로고
    • The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases
    • Orchard S, Ammari M, Aranda B, et al. The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 2014;42:D358-63
    • (2014) Nucleic Acids Res , vol.42 , pp. D358-D363
    • Orchard, S.1    Ammari, M.2    Aranda, B.3
  • 89
    • 84862642360 scopus 로고    scopus 로고
    • Molecular interaction databases
    • Orchard S. Molecular interaction databases. Proteomics 2012;12:1656-62
    • (2012) Proteomics , vol.12 , pp. 1656-1662
    • Orchard, S.1
  • 90
    • 84941051170 scopus 로고    scopus 로고
    • STRING v10: protein-protein interaction networks, integrated over the tree of life
    • Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015;43:D447-52
    • (2015) Nucleic Acids Res , vol.43 , pp. D447-D452
    • Szklarczyk, D.1    Franceschini, A.2    Wyder, S.3
  • 91
    • 0037012884 scopus 로고    scopus 로고
    • Proteomics. Public-private group maps out initiatives
    • Kaiser J. Proteomics. Public-private group maps out initiatives. Science 2002;296:827
    • (2002) Science , vol.296 , pp. 827
    • Kaiser, J.1
  • 92
    • 35348976204 scopus 로고    scopus 로고
    • Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions
    • Kerrien S, Orchard S, Montecchi-Palazzi L, et al. Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 2007;5:44
    • (2007) BMC Biol , vol.5 , pp. 44
    • Kerrien, S.1    Orchard, S.2    Montecchi-Palazzi, L.3
  • 93
    • 84859208501 scopus 로고    scopus 로고
    • Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
    • Orchard S, Kerrien S, Abbani S, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods 2012;9:345-50
    • (2012) Nat Methods , vol.9 , pp. 345-350
    • Orchard, S.1    Kerrien, S.2    Abbani, S.3
  • 94
    • 79959846617 scopus 로고    scopus 로고
    • PSICQUIC and PSISCORE: accessing and scoring molecular interactions
    • Aranda B, Blankenburg H, Kerrien S, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods 2011;8:528-9
    • (2011) Nat Methods , vol.8 , pp. 528-529
    • Aranda, B.1    Blankenburg, H.2    Kerrien, S.3
  • 95
    • 84881183501 scopus 로고    scopus 로고
    • Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis
    • Li W, Chen L, He W, et al. Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis. PLoS One 2013;8:e71191
    • (2013) PLoS One , vol.8
    • Li, W.1    Chen, L.2    He, W.3
  • 96
    • 84926486250 scopus 로고    scopus 로고
    • Computational analysis of the LRRK2 interactome
    • Manzoni C, Denny P, Lovering RC, et al. Computational analysis of the LRRK2 interactome. PeerJ 2015;3:e778
    • (2015) PeerJ , vol.3 , pp. e778
    • Manzoni, C.1    Denny, P.2    Lovering, R.C.3
  • 97
    • 84856918212 scopus 로고    scopus 로고
    • HIPPIE: Integrating protein interaction networks with experiment based quality scores
    • Schaefer MH, Fontaine JF, Vinayagam A, et al. HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One 2012;7:e31826
    • (2012) PLoS One , vol.7
    • Schaefer, M.H.1    Fontaine, J.F.2    Vinayagam, A.3
  • 98
    • 77954269901 scopus 로고    scopus 로고
    • The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
    • Warde-Farley D, Donaldson SL, Comes O, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 2010;38:W214-20
    • (2010) Nucleic Acids Res , vol.38 , pp. W214-W220
    • Warde-Farley, D.1    Donaldson, S.L.2    Comes, O.3
  • 99
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: a hub for protein information
    • UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res 2015;43:D204-12
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-D212
  • 100
    • 84897102242 scopus 로고    scopus 로고
    • Bias tradeoffs in the creation and analysis of protein-protein interaction networks
    • Gillis J, Ballouz S, Pavlidis P. Bias tradeoffs in the creation and analysis of protein-protein interaction networks. J Proteomics 2014;100:44-54
    • (2014) J Proteomics , vol.100 , pp. 44-54
    • Gillis, J.1    Ballouz, S.2    Pavlidis, P.3
  • 101
    • 84928081356 scopus 로고    scopus 로고
    • Clinical proteomics: promises, challenges and limitations of affinity arrays
    • Betzen C, Alhamdani MS, Lueong S, et al. Clinical proteomics: promises, challenges and limitations of affinity arrays. Proteomics Clin Appl 2015;9:342-7
    • (2015) Proteomics Clin Appl , vol.9 , pp. 342-347
    • Betzen, C.1    Alhamdani, M.S.2    Lueong, S.3
  • 102
    • 84926147304 scopus 로고    scopus 로고
    • Selecting causal genes from genome-wide association studies via functionally coherent subnetworks
    • Tasan M, Musso G, Hao T, et al. Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nat Methods 2015;12:154-9
    • (2015) Nat Methods , vol.12 , pp. 154-159
    • Tasan, M.1    Musso, G.2    Hao, T.3
  • 103
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 104
    • 84976907502 scopus 로고    scopus 로고
    • KEGG as a reference resource for gene and protein annotation
    • Kanehisa M, Sato Y, Kawashima M, et al. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016;44:D457-462
    • (2016) Nucleic Acids Res , vol.44 , pp. D457-462
    • Kanehisa, M.1    Sato, Y.2    Kawashima, M.3
  • 105
    • 84891753483 scopus 로고    scopus 로고
    • The Reactome pathway knowledgebase
    • Croft D, Mundo AF, Haw R, et al. The Reactome pathway knowledgebase. Nucleic Acids Res 2014;42:D472-7
    • (2014) Nucleic Acids Res , vol.42 , pp. D472-D477
    • Croft, D.1    Mundo, A.F.2    Haw, R.3
  • 106
    • 78651332286 scopus 로고    scopus 로고
    • Pathway Commons, a web resource for biological pathway data
    • Cerami EG, Gross BE, Demir E, et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 2011;39:D685-690
    • (2011) Nucleic Acids Res , vol.39 , pp. D685-690
    • Cerami, E.G.1    Gross, B.E.2    Demir, E.3
  • 107
    • 46049087782 scopus 로고    scopus 로고
    • The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    • Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 2008;9:326-32
    • (2008) Brief Bioinform , vol.9 , pp. 326-332
    • Wingender, E.1
  • 108
    • 45549107329 scopus 로고    scopus 로고
    • Use and misuse of the gene ontology annotations
    • Rhee SY, Wood V, Dolinski K, et al. Use and misuse of the gene ontology annotations. Nat Rev Genet 2008;9:509-15
    • (2008) Nat Rev Genet , vol.9 , pp. 509-515
    • Rhee, S.Y.1    Wood, V.2    Dolinski, K.3
  • 109
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009;37:1-13
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 110
    • 79959923522 scopus 로고    scopus 로고
    • g:Profiler-a web server for functional interpretation of gene lists (2011 update)
    • Reimand J, Arak T, Vilo J. g:Profiler-a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res 2011;39:W307-15
    • (2011) Nucleic Acids Res , vol.39 , pp. W307-W315
    • Reimand, J.1    Arak, T.2    Vilo, J.3
  • 111
    • 84938748671 scopus 로고    scopus 로고
    • FunRich: An open access standalone functional enrichment and interaction network analysis tool
    • Pathan M, Keerthikumar S, Ang CS, et al. FunRich: An open access standalone functional enrichment and interaction network analysis tool. Proteomics 2015;15:2597-601
    • (2015) Proteomics , vol.15 , pp. 2597-2601
    • Pathan, M.1    Keerthikumar, S.2    Ang, C.S.3
  • 112
    • 84880617636 scopus 로고    scopus 로고
    • WEB-based GEne SeT analysis toolkit (WebGestalt): update 2013
    • Wang J, Duncan D, Shi Z, et al. WEB-based GEne SeT analysis toolkit (WebGestalt): update 2013. Nucleic Acids Res 2013;41:W77-83
    • (2013) Nucleic Acids Res , vol.41 , pp. W77-83
    • Wang, J.1    Duncan, D.2    Shi, Z.3
  • 113
    • 84874969184 scopus 로고    scopus 로고
    • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
    • Mi H, Muruganujan A, Thomas PD. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 2013;41:D377-86
    • (2013) Nucleic Acids Res , vol.41 , pp. D377-D386
    • Mi, H.1    Muruganujan, A.2    Thomas, P.D.3
  • 114
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: current tools, limitations, and open problems
    • Khatri P, Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005;21:3587-95
    • (2005) Bioinformatics , vol.21 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 115
    • 84865790047 scopus 로고    scopus 로고
    • An integrated Encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. An integrated Encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74
    • (2012) Nature , vol.489 , pp. 57-74
  • 116
    • 84899633396 scopus 로고    scopus 로고
    • Defining functional DNA elements in the human genome
    • Kellis M, Wold B, Snyder MP, et al. Defining functional DNA elements in the human genome. Proc Natl Acad Sci USA 2014;111:6131-8
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 6131-6138
    • Kellis, M.1    Wold, B.2    Snyder, M.P.3
  • 117
    • 84891767304 scopus 로고    scopus 로고
    • DrugBank 4.0: shedding new light on drug metabolism
    • Law V, Knox C, Djoumbou Y, et al. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res 2014;42:D1091-7
    • (2014) Nucleic Acids Res , vol.42 , pp. D1091-D1097
    • Law, V.1    Knox, C.2    Djoumbou, Y.3
  • 118
    • 84899149579 scopus 로고    scopus 로고
    • Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network
    • Roider HG, Pavlova N, Kirov I, et al. Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. BMC Bioinformatics 2014;15:68
    • (2014) BMC Bioinformatics , vol.15 , pp. 68
    • Roider, H.G.1    Pavlova, N.2    Kirov, I.3
  • 119
    • 33644876210 scopus 로고    scopus 로고
    • DrugBank: a comprehensive resource for in silico drug discovery and exploration
    • Wishart DS, Knox C, Guo AC, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006;34:D668-72
    • (2006) Nucleic Acids Res , vol.34 , pp. D668-D672
    • Wishart, D.S.1    Knox, C.2    Guo, A.C.3
  • 120
    • 33749335282 scopus 로고    scopus 로고
    • The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease
    • Lamb J, Crawford ED, Peck D, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006;313:1929-35
    • (2006) Science , vol.313 , pp. 1929-1935
    • Lamb, J.1    Crawford, E.D.2    Peck, D.3
  • 121
    • 84944145290 scopus 로고    scopus 로고
    • Connectivity Map-based discovery of parbendazole reveals targetable human osteogenic pathway
    • Brum AM, van de Peppel J, van der Leije CS, et al. Connectivity Map-based discovery of parbendazole reveals targetable human osteogenic pathway. Proc Natl Acad Sci USA 2015;112:12711-6
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 12711-12716
    • Brum, A.M.1    van Peppel, J.2    van der Leije, C.S.3
  • 122
    • 84902075817 scopus 로고    scopus 로고
    • Drug-repurposing identified the combination of Trolox C and Cytisine for the treatment of type 2 diabetes
    • Jin L, Tu J, Jia J, et al. Drug-repurposing identified the combination of Trolox C and Cytisine for the treatment of type 2 diabetes. J Transl Med 2014;12:153
    • (2014) J Transl Med , vol.12 , pp. 153
    • Jin, L.1    Tu, J.2    Jia, J.3
  • 123
    • 84876148784 scopus 로고    scopus 로고
    • HMDB 3.0-the human metabolome database in 2013
    • Wishart DS, Jewison T, Guo AC, et al. HMDB 3.0-the human metabolome database in 2013. Nucleic Acids Res 2013;41:D801-7
    • (2013) Nucleic Acids Res , vol.41 , pp. D801-D807
    • Wishart, D.S.1    Jewison, T.2    Guo, A.C.3
  • 124
    • 32444432587 scopus 로고    scopus 로고
    • METLIN: a metabolite mass spectral database
    • Smith CA, O'Maille G, Want EJ, et al. METLIN: a metabolite mass spectral database. Ther Drug Monit 2005;27:747-51
    • (2005) Ther Drug Monit , vol.27 , pp. 747-751
    • Smith, C.A.1    O'Maille, G.2    Want, E.J.3
  • 125
    • 84876560030 scopus 로고    scopus 로고
    • MetaboLights-an openaccess general-purpose repository for metabolomics studies and associated meta-data
    • Haug K, Salek RM, Conesa P, et al. MetaboLights-an openaccess general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res 2013;41:D781-6
    • (2013) Nucleic Acids Res , vol.41 , pp. D781-D786
    • Haug, K.1    Salek, R.M.2    Conesa, P.3
  • 126
    • 34547778398 scopus 로고    scopus 로고
    • The metabolomics standards initiative
    • MSI Board Menbers, Sansone SA, Fan T, et al. The metabolomics standards initiative. Nat Biotechnol 2007;25:846-8
    • (2007) Nat Biotechnol , vol.25 , pp. 846-848
    • Sansone, S.A.1    Fan, T.2
  • 127
    • 84944278465 scopus 로고    scopus 로고
    • COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
    • Salek RM, Neumann S, Schober D, et al. COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics 2015;11:1587-97
    • (2015) Metabolomics , vol.11 , pp. 1587-1597
    • Salek, R.M.1    Neumann, S.2    Schober, D.3
  • 128
    • 85039998984 scopus 로고    scopus 로고
    • Analytical methods in untargeted metabolomics: state of the art in 2015
    • Alonso A, Marsal S, Julia A. Analytical methods in untargeted metabolomics: state of the art in 2015. Front Bioeng Biotechnol 2015;3:23
    • (2015) Front Bioeng Biotechnol , vol.3 , pp. 23
    • Alonso, A.1    Marsal, S.2    Julia, A.3
  • 129
    • 84966348806 scopus 로고    scopus 로고
    • Advantages and pitfalls of mass spectrometry based metabolome profiling in systems biology
    • Aretz I, Meierhofer D. Advantages and pitfalls of mass spectrometry based metabolome profiling in systems biology. Int J Mol Sci 2016;17:632
    • (2016) Int J Mol Sci , vol.17 , pp. 632
    • Aretz, I.1    Meierhofer, D.2
  • 130
    • 74449085466 scopus 로고    scopus 로고
    • Mass-spectrometrybased metabolomics: limitations and recommendations for future progress with particular focus on nutrition research
    • Scalbert A, Brennan L, Fiehn O, et al. Mass-spectrometrybased metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics 2009;5:435-58
    • (2009) Metabolomics , vol.5 , pp. 435-458
    • Scalbert, A.1    Brennan, L.2    Fiehn, O.3
  • 131
    • 84883310696 scopus 로고    scopus 로고
    • Plasma lipidomic profile signature of hypertension in Mexican American families: specific role of diacylglycerols
    • Kulkarni H, Meikle PJ, Mamtani M, et al. Plasma lipidomic profile signature of hypertension in Mexican American families: specific role of diacylglycerols. Hypertension 2013;62:621-6
    • (2013) Hypertension , vol.62 , pp. 621-626
    • Kulkarni, H.1    Meikle, P.J.2    Mamtani, M.3
  • 132
    • 84947465966 scopus 로고    scopus 로고
    • Highly-accurate metabolomic detection of early-stage ovarian cancer
    • Gaul DA, Mezencev R, Long TQ, et al. Highly-accurate metabolomic detection of early-stage ovarian cancer. Sci Rep 2015;5:16351
    • (2015) Sci Rep , vol.5 , pp. 16351
    • Gaul, D.A.1    Mezencev, R.2    Long, T.Q.3
  • 133
    • 84883577718 scopus 로고    scopus 로고
    • Analysis tool web services from the EMBL-EBI
    • McWilliam H, Li W, Uludag M, et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res 2013;41:W597-600
    • (2013) Nucleic Acids Res , vol.41 , pp. W597-600
    • McWilliam, H.1    Li, W.2    Uludag, M.3
  • 134
    • 84858292659 scopus 로고    scopus 로고
    • Treatable inborn errors of metabolism causing intellectual disability: a systematic literature review
    • van Karnebeek CD, Stockler S. Treatable inborn errors of metabolism causing intellectual disability: a systematic literature review. Mol Genet Metab 2012;105:368-81
    • (2012) Mol Genet Metab , vol.105 , pp. 368-381
    • van Karnebeek, C.D.1    Stockler, S.2
  • 135
    • 84941365835 scopus 로고    scopus 로고
    • Genomic, proteomic, and metabolomic data integration strategies
    • Wanichthanarak K, Fahrmann JF, Grapov D. Genomic, proteomic, and metabolomic data integration strategies. Biomark Insights 2015;10:1-6
    • (2015) Biomark Insights , vol.10 , pp. 1-6
    • Wanichthanarak, K.1    Fahrmann, J.F.2    Grapov, D.3
  • 136
    • 84899530032 scopus 로고    scopus 로고
    • Principles and methods of integrative genomic analyses in cancer
    • Kristensen VN, Lingjaerde OC, Russnes HG, et al. Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer 2014;14:299-313
    • (2014) Nat Rev Cancer , vol.14 , pp. 299-313
    • Kristensen, V.N.1    Lingjaerde, O.C.2    Russnes, H.G.3
  • 137
    • 84991314240 scopus 로고    scopus 로고
    • Public data and open source tools for multi-assay genomic investigation of disease
    • Kannan L, Ramos M, Re A, et al. Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform 2016;17:603-15
    • (2016) Brief Bioinform , vol.17 , pp. 603-615
    • Kannan, L.1    Ramos, M.2    Re, A.3
  • 138
    • 84946571753 scopus 로고    scopus 로고
    • The consensus molecular subtypes of colorectal cancer
    • Guinney J, Dienstmann R, Wang X, et al. The consensus molecular subtypes of colorectal cancer. Nat Med 2015;21:1350-6
    • (2015) Nat Med , vol.21 , pp. 1350-1356
    • Guinney, J.1    Dienstmann, R.2    Wang, X.3
  • 139
    • 84961262989 scopus 로고    scopus 로고
    • Translating RNA sequencing into clinical diagnostics: opportunities and challenges
    • Byron SA, Van Keuren-Jensen KR, Engelthaler DM, et al. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet 2016;17:257-71
    • (2016) Nat Rev Genet , vol.17 , pp. 257-271
    • Byron, S.A.1    Van Keuren-Jensen, K.R.2    Engelthaler, D.M.3
  • 140
    • 84899847372 scopus 로고    scopus 로고
    • Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver
    • Wu P, Zhang H, Lin W, et al. Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver. J Proteome Res 2014;13:2409-19
    • (2014) J Proteome Res , vol.13 , pp. 2409-2419
    • Wu, P.1    Zhang, H.2    Lin, W.3
  • 141
    • 84971281712 scopus 로고    scopus 로고
    • Systematic integration of molecular profiles identifies miR-22 as a regulator of lipid and folate metabolism in breast cancer cells
    • Koufaris C, Valbuena GN, Pomyen Y, et al. Systematic integration of molecular profiles identifies miR-22 as a regulator of lipid and folate metabolism in breast cancer cells. Oncogene 2015;35:2766-76
    • (2015) Oncogene , vol.35 , pp. 2766-2776
    • Koufaris, C.1    Valbuena, G.N.2    Pomyen, Y.3
  • 142
    • 84862186859 scopus 로고    scopus 로고
    • The BioSample Database (BioSD) at the European Bioinformatics Institute
    • Gostev M, Faulconbridge A, Brandizi M, et al. The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res 2012;40:D64-70
    • (2012) Nucleic Acids Res , vol.40 , pp. D64-70
    • Gostev, M.1    Faulconbridge, A.2    Brandizi, M.3
  • 143
    • 84962292552 scopus 로고    scopus 로고
    • GeneAnalytics: an integrative gene set analysis tool for next generation sequencing, RNAseq and microarray data
    • Ben-Ari Fuchs S, Lieder I, Stelzer G, et al. GeneAnalytics: an integrative gene set analysis tool for next generation sequencing, RNAseq and microarray data. Omics 2016;20:139-51
    • (2016) Omics , vol.20 , pp. 139-151
    • Ben-Ari Fuchs, S.1    Lieder, I.2    Stelzer, G.3
  • 144
    • 84937705886 scopus 로고    scopus 로고
    • BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
    • Kartashov AV, Barski A. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome Biol 2015;16:158
    • (2015) Genome Biol , vol.16 , pp. 158
    • Kartashov, A.V.1    Barski, A.2
  • 145
    • 84979970983 scopus 로고    scopus 로고
    • European open science cloud
    • European open science cloud. Nat Genet 2016;48:821
    • (2016) Nat Genet , vol.48 , pp. 821
  • 146
    • 84930324062 scopus 로고    scopus 로고
    • Cell-based screening: extracting meaning from complex data
    • Finkbeiner S, Frumkin M, Kassner PD. Cell-based screening: extracting meaning from complex data. Neuron 2015;86:160-74
    • (2015) Neuron , vol.86 , pp. 160-174
    • Finkbeiner, S.1    Frumkin, M.2    Kassner, P.D.3
  • 147
    • 84881613658 scopus 로고    scopus 로고
    • Global proteome analysis of the NCI-60 cell line panel
    • Gholami AM, Hahne H, Wu Z, et al. Global proteome analysis of the NCI-60 cell line panel. Cell Rep 2013;4:609-20
    • (2013) Cell Rep , vol.4 , pp. 609-620
    • Gholami, A.M.1    Hahne, H.2    Wu, Z.3
  • 148
    • 84954328682 scopus 로고    scopus 로고
    • Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures
    • Modelska A, Quattrone A, Re A. Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. Brief Bioinform 2015;16:1000-7
    • (2015) Brief Bioinform , vol.16 , pp. 1000-1007
    • Modelska, A.1    Quattrone, A.2    Re, A.3
  • 149
    • 23844523425 scopus 로고    scopus 로고
    • Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology
    • Wild CP. Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiol Biomarkers Prev 2005;14:1847-50
    • (2005) Cancer Epidemiol Biomarkers Prev , vol.14 , pp. 1847-1850
    • Wild, C.P.1
  • 150
    • 85031678782 scopus 로고    scopus 로고
    • A review of instrumental variable estimators for Mendelian randomization
    • Burgess S, Small DS, Thompson SG. A review of instrumental variable estimators for Mendelian randomization. Stat Methods Med Res 2015, DOI: 10.1177/0962280215597579
    • (2015) Stat Methods Med Res
    • Burgess, S.1    Small, D.S.2    Thompson, S.G.3
  • 151
    • 50849101381 scopus 로고    scopus 로고
    • Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays
    • Homer N, Szelinger S, Redman M, et al. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet 2008;4:e1000167
    • (2008) PLoS Genet , vol.4
    • Homer, N.1    Szelinger, S.2    Redman, M.3
  • 152
    • 84992561367 scopus 로고    scopus 로고
    • An overview of human genetic priv
    • Shi X, Wu X. An overview of human genetic privacy. Ann N Y Acad Sci 2016, DOI: 10.1111/nyas.13211. 153
    • (2016) Ann N Y Acad Sci
    • Shi, X.1    Wu, X.2
  • 153
    • 84946711117 scopus 로고    scopus 로고
    • Big data in biomedicine: 4 big questions
    • Bender E. Big data in biomedicine: 4 big questions. Nature 2015;527:S19
    • (2015) Nature , vol.527 , pp. S19
    • Bender, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.