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Volumn 130, Issue 4, 2011, Pages 465-481

Integrative computational biology for cancer research

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; BIOLOGY; CANCER RESEARCH; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; HIGH THROUGHPUT SEQUENCING; HUMAN; INTEGRATIVE COMPUTATIONAL BIOLOGY; PRIORITY JOURNAL; REVIEW; STANDARD;

EID: 80054867806     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-011-0983-z     Document Type: Review
Times cited : (28)

References (168)
  • 4
    • 43749096790 scopus 로고    scopus 로고
    • Predicting cancer involvement of genes from heterogeneous data
    • Aragues R, Sander C, Oliva B (2008) Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics 9:172
    • (2008) BMC Bioinformatics , vol.9 , pp. 172
    • Aragues, R.1    Sander, C.2    Oliva, B.3
  • 6
    • 77953397764 scopus 로고    scopus 로고
    • Systems medicine: The future of medical genomics and healthcare
    • AuVray C, Chen Z, Hood L (2009) Systems medicine: The future of medical genomics and healthcare. Genome Med 1:2
    • (2009) Genome Med , vol.1 , pp. 2
    • AuVray, C.1    Chen, Z.2    Hood, L.3
  • 7
    • 18044400410 scopus 로고    scopus 로고
    • Information technology to the rescue!
    • Augen J (2001) Information technology to the rescue! Nat Biotechnol 19 Suppl: BE39-40
    • (2001) Nat Biotechnol , vol.19 , Issue.SUPPL.
    • Augen, J.1
  • 8
    • 77957106949 scopus 로고    scopus 로고
    • Avoiding pitfalls in the statistical analysis of heterogeneous tumors
    • Axelrod DE, Miller N, Chapman JA (2009) Avoiding pitfalls in the statistical analysis of heterogeneous tumors. Biomed Inform Insights 2:11-18
    • (2009) Biomed Inform Insights , vol.2 , pp. 11-18
    • Axelrod, D.E.1    Miller, N.2    Chapman, J.A.3
  • 10
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The biomolecular interaction network database
    • DOI 10.1093/nar/gkg056
    • Bader GD, Betel D, Hogue CW (2003) BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res 31:248-250 (Pubitemid 36150376)
    • (2003) Nucleic Acids Research , vol.31 , Issue.1 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.V.3
  • 11
    • 77951163222 scopus 로고    scopus 로고
    • Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology
    • Baggerly KA, Coombes KR (2009) Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology. Ann Appl Stat 3:1309-1334
    • (2009) Ann Appl Stat , vol.3 , pp. 1309-1334
    • Baggerly, K.A.1    Coombes, K.R.2
  • 13
    • 27144486151 scopus 로고    scopus 로고
    • Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
    • DOI 10.1093/nar/gki890
    • Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P (2005) Experimental comparison and cross-validation of the AVymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 33:5914-5923 (Pubitemid 41742611)
    • (2005) Nucleic Acids Research , vol.33 , Issue.18 , pp. 5914-5923
    • Barnes, M.1    Freudenberg, J.2    Thompson, S.3    Aronow, B.4    Pavlidis, P.5
  • 16
    • 11144263678 scopus 로고    scopus 로고
    • Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection
    • DOI 10.1593/neo.04301
    • Blackhall FH, Pintilie M, Wigle D, Jurisica I, Liu N, Radulovitch N, Keshavjee S, Johnston M, Shepherd FA, Tsao M-S (2004) Stability and heterogeneity of expression proWles in lung cancer specimens harvested following surgical resection. Neoplasia 6:761-767 (Pubitemid 40041494)
    • (2004) Neoplasia , vol.6 , Issue.6 , pp. 761-767
    • Blackhall, F.H.1    Pintilie, M.2    Wigle, D.A.3    Jurisica, I.4    Liu, N.5    Radulovich, N.6    Johnston, M.R.7    Keshavjee, S.8    Tsao, M.-S.9
  • 22
    • 18744376914 scopus 로고    scopus 로고
    • Online predicted human interaction database
    • DOI 10.1093/bioinformatics/bti273
    • Brown KR, Jurisica I (2005) Online predicted human interaction database. Bioinformatics 21:2076-2082 (Pubitemid 40668047)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2076-2082
    • Brown, K.R.1    Jurisica, I.2
  • 23
    • 34548855730 scopus 로고    scopus 로고
    • Unequal evolutionary conservation of human protein interactions in interologous networks
    • Brown KR, Jurisica I (2007) Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol 8:R95
    • (2007) Genome Biol , vol.8
    • Brown, K.R.1    Jurisica, I.2
  • 26
    • 79955763421 scopus 로고    scopus 로고
    • Reproducible research concepts and tools for cancer bioinformatics
    • Ochs MF, Cassagrande JT, Davuluri RV (eds) Springer, US
    • Carey VJ, Stodden V (2010) Reproducible research concepts and tools for cancer bioinformatics. In: Ochs MF, Cassagrande JT, Davuluri RV (eds) Biomedical informatics for cancer research. Springer, US, pp 149-175
    • (2010) Biomedical informatics for cancer research. , pp. 149-175
    • Carey, V.J.1    Stodden, V.2
  • 27
    • 25444515422 scopus 로고    scopus 로고
    • RedeWnition of AVymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    • Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z (2005) RedeWnition of AVymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6:107
    • (2005) BMC Bioinformatics , vol.6 , pp. 107
    • Carter, S.L.1    Eklund, A.C.2    Mecham, B.H.3    Kohane, I.S.4    Szallasi, Z.5
  • 30
    • 26844467247 scopus 로고    scopus 로고
    • DiVerences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors
    • Chandran UR, Dhir R, Ma C, Michalopoulos G, Becich M, Gilbertson J (2005) DiVerences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC Cancer 5:45
    • (2005) BMC Cancer , vol.5 , pp. 45
    • Chandran, U.R.1    Dhir, R.2    Ma, C.3    Michalopoulos, G.4    Becich, M.5    Gilbertson, J.6
  • 31
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • DOI 10.1093/bioinformatics/bti722
    • Choi JK, Yu U, Yoo OJ, Kim S (2005) DiVerential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21:4348-4355 (Pubitemid 41782924)
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 41
    • 77957833984 scopus 로고    scopus 로고
    • Cancer biomarkers: Can we turn recent failures into success?
    • Diamandis EP (2010) Cancer biomarkers: Can we turn recent failures into success? J Natl Cancer Inst 102:1462-1467
    • (2010) J Natl Cancer Inst , vol.102 , pp. 1462-1467
    • Diamandis, E.P.1
  • 42
    • 40749107034 scopus 로고    scopus 로고
    • How large a training set is needed to develop a classifier for microarray data?
    • DOI 10.1158/1078-0432.CCR-07-0443
    • Dobbin KK, Zhao Y, Simon RM (2008) How large a training set is needed to develop a classiWer for microarray data? Clin Cancer Res 14:108-114 (Pubitemid 351377984)
    • (2008) Clinical Cancer Research , vol.14 , Issue.1 , pp. 108-114
    • Dobbin, K.K.1    Zhao, Y.2    Simon, R.M.3
  • 43
    • 33846978784 scopus 로고    scopus 로고
    • Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
    • Dupuy A, Simon RM (2007) Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 99:147-157
    • (2007) J Natl Cancer Inst , vol.99 , pp. 147-157
    • Dupuy, A.1    Simon, R.M.2
  • 44
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210 (Pubitemid 34679544)
    • (2002) Nucleic Acids Research , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 45
    • 67650730222 scopus 로고    scopus 로고
    • The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays
    • Eggle D, Debey-Pascher S, Beyer M, Schultze JL (2009) The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays. BMC Bioinformatics 10:186
    • (2009) BMC Bioinformatics , vol.10 , pp. 186
    • Eggle, D.1    Debey-Pascher, S.2    Beyer, M.3    Schultze, J.L.4
  • 46
    • 13444282534 scopus 로고    scopus 로고
    • Outcome signature genes in breast cancer: Is there a unique set?
    • DOI 10.1093/bioinformatics/bth469
    • Ein-Dor L, Kela I, Getz G, Givol D, Domany E (2005) Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics 21:171-178 (Pubitemid 40202018)
    • (2005) Bioinformatics , vol.21 , Issue.2 , pp. 171-178
    • Ein-Dor, L.1    Kela, I.2    Getz, G.3    Givol, D.4    Domany, E.5
  • 47
    • 33645825183 scopus 로고    scopus 로고
    • Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
    • Ein-Dor L, Zuk O, Domany E (2006) Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 103:5923-5928
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5923-5928
    • Ein-Dor, L.1    Zuk, O.2    Domany, E.3
  • 48
    • 24044513966 scopus 로고    scopus 로고
    • Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
    • DOI 10.1038/nmeth785
    • Elias JE, Haas W, Faherty BK, Gygi SP (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2:667-675 (Pubitemid 41223093)
    • (2005) Nature Methods , vol.2 , Issue.9 , pp. 667-675
    • Elias, J.E.1    Haas, W.2    Faherty, B.K.3    Gygi, S.P.4
  • 50
    • 77950789262 scopus 로고    scopus 로고
    • Standards aVecting the consistency of gene expression arrays in clinical applications
    • Enkemann SA (2010) Standards aVecting the consistency of gene expression arrays in clinical applications. Cancer Epidemiol Biomarkers Prev 19:1000-1003
    • (2010) Cancer Epidemiol Biomarkers Prev , vol.19 , pp. 1000-1003
    • Enkemann, S.A.1
  • 52
    • 0033816482 scopus 로고    scopus 로고
    • Laser capture microdissection in pathology
    • Fend F, RaVeld M (2000) Laser capture microdissection in pathology. J Clin Pathol 53:666-672
    • (2000) J Clin Pathol , vol.53 , pp. 666-672
    • Fend, F.1    RaVeld, M.2
  • 54
    • 77953194530 scopus 로고    scopus 로고
    • Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging
    • Fortney K, Kotlyar M, Jurisica I (2010) Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genome Biol 11:R13
    • (2010) Genome Biol , vol.11
    • Fortney, K.1    Kotlyar, M.2    Jurisica, I.3
  • 55
    • 58749098785 scopus 로고    scopus 로고
    • Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates
    • Fujita A, Gomes LR, Sato JR, Yamaguchi R, Thomaz CE, Sogayar MC, Miyano S (2008) Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Syst Biol 2:106
    • (2008) BMC Syst Biol , vol.2 , pp. 106
    • Fujita, A.1    Gomes, L.R.2    Sato, J.R.3    Yamaguchi, R.4    Thomaz, C.E.5    Sogayar, M.C.6    Miyano, S.7
  • 62
    • 68949206409 scopus 로고    scopus 로고
    • Applying mass spectrometry-based proteomics to genetics, genomics and network biology
    • Gstaiger M, Aebersold R (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 10:617-627
    • (2009) Nat Rev Genet , vol.10 , pp. 617-627
    • Gstaiger, M.1    Aebersold, R.2
  • 63
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • DOI 10.1093/molbev/msi072
    • Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22:803-806 (Pubitemid 40471393)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.4 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 64
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • DOI 10.1093/nar/gki033
    • Hamosh A, Scott A, Amberger J, Bocchini C, McKusick V (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514-D517 (Pubitemid 40207927)
    • (2005) Nucleic Acids Research , vol.33 , Issue.DATABASE ISS.
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 67
    • 27544448536 scopus 로고    scopus 로고
    • Implementing the iHOP concept for navigation of biomedical literature
    • DOI 10.1093/bioinformatics/bti1142
    • HoVmann R, Valencia A (2005) Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 Suppl 2: Ii252-ii258 (Pubitemid 41535458)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Hoffmann, R.1    Valencia, A.2
  • 69
    • 2942598149 scopus 로고    scopus 로고
    • PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
    • DOI 10.1002/pmic.200300772
    • Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B (2004) PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4:1551-1561 (Pubitemid 38738314)
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1551-1561
    • Hornbeck, P.V.1    Chabra, I.2    Kornhauser, J.M.3    Skrzypek, E.4    Zhang, B.5
  • 70
    • 32044451325 scopus 로고    scopus 로고
    • Cancer: A Systems Biology disease
    • DOI 10.1016/j.biosystems.2005.05.014, PII S0303264705001176
    • Hornberg JJ, Bruggeman FJ, WesterhoV HV, Lankelma J (2006) Cancer: A systems biology disease. Biosystems 83:81-90 (Pubitemid 43199809)
    • (2006) BioSystems , vol.83 , Issue.2-3 SPEC. ISS. , pp. 81-90
    • Hornberg, J.J.1    Bruggeman, F.J.2    Westerhoff, H.V.3    Lankelma, J.4
  • 72
    • 33845864703 scopus 로고    scopus 로고
    • Computational prediction of cancer-gene function
    • DOI 10.1038/nrc2036, PII NRC2036
    • Hu P, Bader G, Wigle DA, Emili A (2007) Computational prediction of cancer-gene function. Nat Rev Cancer 7:23-34 (Pubitemid 46023413)
    • (2007) Nature Reviews Cancer , vol.7 , Issue.1 , pp. 23-34
    • Hu, P.1    Bader, G.2    Wigle, D.A.3    Emili, A.4
  • 76
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18(Suppl 1):S233-S240 (Pubitemid 41185658)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 78
    • 31144432293 scopus 로고    scopus 로고
    • Literature mining for the biologist: From information retrieval to biological discovery
    • DOI 10.1038/nrg1768, PII NRG1768
    • Jensen LJ, Saric J, Bork P (2006) Literature mining for the biologist: From information retrieval to biological discovery. Nat Rev Genet 7:119-129 (Pubitemid 43128897)
    • (2006) Nature Reviews Genetics , vol.7 , Issue.2 , pp. 119-129
    • Jensen, L.J.1    Saric, J.2    Bork, P.3
  • 79
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • DOI 10.1038/35075138
    • Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42 (Pubitemid 32428180)
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.-L.3    Oltvai, Z.N.4
  • 81
    • 33748706765 scopus 로고    scopus 로고
    • Global topological features of cancer proteins in the human interactome
    • DOI 10.1093/bioinformatics/btl390
    • Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22:2291-2297 (Pubitemid 44390886)
    • (2006) Bioinformatics , vol.22 , Issue.18 , pp. 2291-2297
    • Jonsson, P.F.1    Bates, P.A.2
  • 82
    • 77952107920 scopus 로고    scopus 로고
    • Assessment of tumour hypoxia for prediction of response to therapy and cancer prognosis
    • Jubb AM, BuVa FM, Harris AL (2010) Assessment of tumour hypoxia for prediction of response to therapy and cancer prognosis. J Cell Mol Med 14:18-29
    • (2010) J Cell Mol Med , vol.14 , pp. 18-29
    • Jubb, A.M.1    BuVa, F.M.2    Harris, A.L.3
  • 84
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • DOI 10.1093/bioinformatics/bth351
    • King AD, Przulj N, Jurisica I (2004) Protein complex prediction via cost-based clustering. Bioinformatics 20:3013-3020 (Pubitemid 39619193)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 85
    • 19344375343 scopus 로고    scopus 로고
    • The meaning of systems biology
    • DOI 10.1016/j.cell.2005.05.005, PII S0092867405004472
    • Kirschner MW (2005) The meaning of systems biology. Cell 121:503-504 (Pubitemid 40720002)
    • (2005) Cell , vol.121 , Issue.4 , pp. 503-504
    • Kirschner, M.W.1
  • 86
    • 14344260140 scopus 로고    scopus 로고
    • Multidimensional protein identification technology: Current status and future prospects
    • DOI 10.1586/14789450.2.1.27
    • Kislinger T, Emili A (2005) Multidimensional protein identiWcation technology: Current status and future prospects. Expert Rev Proteomics 2:27-39 (Pubitemid 40292577)
    • (2005) Expert Review of Proteomics , vol.2 , Issue.1 , pp. 27-39
    • Kislinger, T.1    Emili, A.2
  • 88
    • 33144466926 scopus 로고    scopus 로고
    • Predicting protein-protein interactions by association mining
    • DOI 10.1007/s10796-005-6102-8
    • Kotlyar M, Jurisica I (2006) Predicting protein-protein interactions by association mining. Inf Syst Frontiers 8:37-47 (Pubitemid 43269399)
    • (2006) Information Systems Frontiers , vol.8 , Issue.1 , pp. 37-47
    • Kotlyar, M.1    Jurisica, I.2
  • 92
    • 77951094805 scopus 로고    scopus 로고
    • Big science: The cancer genome challenge
    • Ledford H (2010) Big science: The cancer genome challenge. Nature 464:972-974
    • (2010) Nature , vol.464 , pp. 972-974
    • Ledford, H.1
  • 93
    • 70350674928 scopus 로고    scopus 로고
    • Discovering cancer genes by integrating network and functional properties
    • Li L, Zhang K, Lee J, Cordes S, Davis DP, Tang Z (2009) Discovering cancer genes by integrating network and functional properties. BMC Med Genomics 2:61
    • (2009) BMC Med Genomics , vol.2 , pp. 61
    • Li, L.1    Zhang, K.2    Lee, J.3    Cordes, S.4    Davis, D.P.5    Tang, Z.6
  • 96
    • 0037012880 scopus 로고    scopus 로고
    • Specificity and stability in topology of protein networks
    • DOI 10.1126/science.1065103
    • Maslov S, Sneppen K (2002) SpeciWcity and stability in topology of protein networks. Science 296:910-913 (Pubitemid 34464896)
    • (2002) Science , vol.296 , Issue.5569 , pp. 910-913
    • Maslov, S.1    Sneppen, K.2
  • 98
    • 70350638951 scopus 로고    scopus 로고
    • Interaction techniques for selecting and manipulating subgraphs in network visualizations
    • McGuYn M, Jurisica I (2009) Interaction techniques for selecting and manipulating subgraphs in network visualizations. IEEE Trans Vis Comput Graph 15(6):937-944
    • (2009) IEEE Trans Vis Comput Graph , vol.15 , Issue.6 , pp. 937-944
    • McGuYn, M.1    Jurisica, I.2
  • 99
    • 68849092564 scopus 로고    scopus 로고
    • Genomic amplicons target vesicle recycling in breast cancer
    • Mills GB, Jurisica I, Yarden Y, Norman JC (2009) Genomic amplicons target vesicle recycling in breast cancer. J Clin Invest 119:2123-2127
    • (2009) J Clin Invest , vol.119 , pp. 2123-2127
    • Mills, G.B.1    Jurisica, I.2    Yarden, Y.3    Norman, J.C.4
  • 100
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • DOI 10.1126/science.298.5594.824
    • Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: Simple building blocks of complex networks. Science 298:824-827 (Pubitemid 35231534)
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 102
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • DOI 10.1093/bioinformatics/btm019
    • Nacu S, Critchley-Thorne R, Lee P, Holmes S (2007) Gene expression network analysis and applications to immunology. Bioinformatics 23:850-858 (Pubitemid 47049919)
    • (2007) Bioinformatics , vol.23 , Issue.7 , pp. 850-858
    • Nacu, S.1    Critchley-Thorne, R.2    Lee, P.3    Holmes, S.4
  • 104
    • 66149156998 scopus 로고    scopus 로고
    • Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer
    • Nibbe RK, Markowitz S, MyeroV L, Ewing R, Chance MR (2009) Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol Cell Proteomics 8:827-845
    • (2009) Mol Cell Proteomics , vol.8 , pp. 827-845
    • Nibbe, R.K.1    Markowitz, S.2    MyeroV, L.3    Ewing, R.4    Chance, M.R.5
  • 105
    • 76749148657 scopus 로고    scopus 로고
    • An integrative-omics approach to identify functional sub-networks in human colorectal cancer
    • Nibbe RK, Koyuturk M, Chance MR (2010) An integrative-omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol 6:e1000639
    • (2010) PLoS Comput Biol , vol.6
    • Nibbe, R.K.1    Koyuturk, M.2    Chance, M.R.3
  • 106
    • 75249101080 scopus 로고    scopus 로고
    • Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D
    • Niu Y, Otasek D, Jurisica I (2010) Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. Bioinformatics 26:111-119
    • (2010) Bioinformatics , vol.26 , pp. 111-119
    • Niu, Y.1    Otasek, D.2    Jurisica, I.3
  • 109
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • DOI 10.1038/nature03607
    • Palla G, Derenyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435:814-818 (Pubitemid 40839731)
    • (2005) Nature , vol.435 , Issue.7043 , pp. 814-818
    • Palla, G.1    Derenyi, I.2    Farkas, I.3    Vicsek, T.4
  • 110
    • 0031903646 scopus 로고    scopus 로고
    • Phase II study of receptor-enhanced chemosensitivity using recombinant humanized anti-p185(HER2/neu) monoclonal antibody plus cisplatin in patients with HER2/neu-overexpressing metastatic breast cancer refractory to chemotherapy treatment
    • Pegram MD, Lipton A, Hayes DF, Weber BL, Baselga JM, Tripathy D, Baly D, Baughman SA, Twaddell T, Glaspy JA, Slamon DJ (1998) Phase II study of receptor-enhanced chemosensitivity using recombinant humanized anti-p185HER2/neu monoclonal antibody plus cisplatin in patients with HER2/neu-overexpressing metastatic breast cancer refractory to chemotherapy treatment. J Clin Oncol 16:2659-2671 (Pubitemid 28363029)
    • (1998) Journal of Clinical Oncology , vol.16 , Issue.8 , pp. 2659-2671
    • Pegram, M.D.1    Lipton, A.2    Hayes, D.F.3    Weber, B.L.4    Baselga, J.M.5    Tripathy, D.6    Baly, D.7    Baughman, S.A.8    Twaddell, T.9    Glaspy, J.A.10    Slamon, D.J.11
  • 116
    • 33846672214 scopus 로고    scopus 로고
    • Biological network comparison using graphlet degree distribution
    • DOI 10.1093/bioinformatics/btl301
    • Przulj N (2007) Biological network comparison using graphlet degree distribution. Bioinformatics 23:e177-e183 (Pubitemid 46189654)
    • (2007) Bioinformatics , vol.23 , Issue.2
    • Przulj, N.1
  • 117
    • 33645803834 scopus 로고    scopus 로고
    • EYcient estimation of graphlet frequency distributions in protein-protein interaction networks
    • Przulj N, Corneil DG, Jurisica I (2006) EYcient estimation of graphlet frequency distributions in protein-protein interaction networks. Bioinformatics 22:974-980
    • (2006) Bioinformatics , vol.22 , pp. 974-980
    • Przulj, N.1    Corneil, D.G.2    Jurisica, I.3
  • 120
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • DOI 10.1126/science.1073374
    • Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555 (Pubitemid 34971002)
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.-L.5
  • 121
    • 0031114483 scopus 로고    scopus 로고
    • GeneCards: Integrating information about genes, proteins and diseases
    • PII S0168952597011037
    • Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D (1997) GeneCards: Integrating information about genes, proteins and diseases. Trends Genet 13:163 (Pubitemid 127739947)
    • (1997) Trends in Genetics , vol.13 , Issue.4 , pp. 163
    • Rebhan, M.1    Chalifa-Caspi, V.2    Prilusky, J.3    Lancet, D.4
  • 123
    • 20044396570 scopus 로고    scopus 로고
    • Integrative analysis of the cancer transcriptome
    • DOI 10.1038/ng1570
    • Rhodes DR, Chinnaiyan AM (2005) Integrative analysis of the cancer transcriptome. Nat Genet 37 Suppl: S31-37 (Pubitemid 40770401)
    • (2005) Nature Genetics , vol.37 , Issue.6 SUPPL.
    • Rhodes, D.R.1    Chinnaiyan, A.M.2
  • 127
    • 34248591612 scopus 로고    scopus 로고
    • Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer
    • DOI 10.1038/sj.onc.1210422, PII 1210422
    • Roberts PJ, Der CJ (2007) Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer. Oncogene 26:3291-3310 (Pubitemid 46763022)
    • (2007) Oncogene , vol.26 , Issue.22 , pp. 3291-3310
    • Roberts, P.J.1    Der, C.J.2
  • 128
    • 74549117176 scopus 로고    scopus 로고
    • Biomedical text mining and its applications
    • Rodriguez-Esteban R (2009) Biomedical text mining and its applications. PLoS Comput Biol 5:e1000597
    • (2009) PLoS Comput Biol , vol.5
    • Rodriguez-Esteban, R.1
  • 130
    • 33847679625 scopus 로고    scopus 로고
    • Improved precision and accuracy for microarrays using updated probe set deWnitions
    • Sandberg R, Larsson O (2007) Improved precision and accuracy for microarrays using updated probe set deWnitions. BMC Bioinformatics 8:48
    • (2007) BMC Bioinformatics , vol.8 , pp. 48
    • Sandberg, R.1    Larsson, O.2
  • 131
    • 68249142895 scopus 로고    scopus 로고
    • A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research
    • Savas S, Geraci J, Jurisica I, Liu G (2009) A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research. Int J Cancer 125:1257-1265
    • (2009) Int J Cancer , vol.125 , pp. 1257-1265
    • Savas, S.1    Geraci, J.2    Jurisica, I.3    Liu, G.4
  • 133
    • 10344258041 scopus 로고    scopus 로고
    • Targeting the mitogen-activated protein kinase cascade to treat cancer
    • DOI 10.1038/nrc1503
    • Sebolt-Leopold JS, Herrera R (2004) Targeting the mitogen-activated protein kinase cascade to treat cancer. Nat Rev Cancer 4:937-947 (Pubitemid 39626217)
    • (2004) Nature Reviews Cancer , vol.4 , Issue.12 , pp. 937-947
    • Sebolt-Leopold, J.S.1    Herrera, R.2
  • 136
    • 79952146521 scopus 로고    scopus 로고
    • NAViGaTing the microNome-using multiple microRNA prediction databases to identify signaling pathway-associated microRNA
    • Shirdel EA, Xie W, Mak TW, Jurisica I (2011) NAViGaTing the microNome-using multiple microRNA prediction databases to identify signaling pathway-associated microRNA. PLoS One 6(2):e17429
    • (2011) PLoS One , vol.6 , Issue.2
    • Shirdel, E.A.1    Xie, W.2    Mak, T.W.3    Jurisica, I.4
  • 137
    • 65549112480 scopus 로고    scopus 로고
    • Alterations in the TOP2A and HER2 genes: Association with adjuvant anthracycline sensitivity in human breast cancers
    • Slamon DJ, Press MF (2009) Alterations in the TOP2A and HER2 genes: Association with adjuvant anthracycline sensitivity in human breast cancers. J Natl Cancer Inst 101:615-618
    • (2009) J Natl Cancer Inst , vol.101 , pp. 615-618
    • Slamon, D.J.1    Press, M.F.2
  • 138
    • 45749106371 scopus 로고    scopus 로고
    • Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT)
    • DOI 10.1039/b717542f
    • Sodek KL, Evangelou AI, Ignatchenko A, Agochiya M, Brown TJ, Ringuette MJ, Jurisica I, Kislinger T (2008) IdentiWcation of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identiWcation technology (Mud-PIT). Mol Biosyst 4:762-773 (Pubitemid 351871749)
    • (2008) Molecular BioSystems , vol.4 , Issue.7 , pp. 762-773
    • Sodek, K.L.1    Evangelou, A.I.2    Ignatchenko, A.3    Agochiya, M.4    Brown, T.J.5    Ringuette, M.J.6    Jurisica, I.7    Kislinger, T.8
  • 146
    • 75549089911 scopus 로고    scopus 로고
    • Network of Cancer Genes: A web resource to analyze duplicability, orthology and network properties of cancer genes
    • Syed AS, D'Antonio M, Ciccarelli FD (2010) Network of Cancer Genes: A web resource to analyze duplicability, orthology and network properties of cancer genes. Nucleic Acids Res 38:D670-D675
    • (2010) Nucleic Acids Res , vol.38
    • Syed, A.S.1    D'Antonio, M.2    Ciccarelli, F.D.3
  • 153
    • 78149255579 scopus 로고    scopus 로고
    • The Xowvizmenu and parallel scatterplot matrix: Hybrid multidimensional visualizations for network exploration
    • Viau C, McGuYn MJ, Chiricota Y, Jurisica I (2010) The Xowvizmenu and parallel scatterplot matrix: Hybrid multidimensional visualizations for network exploration. Vis Comput Graph IEEE Trans 16:1100-1108
    • (2010) Vis Comput Graph IEEE Trans , vol.16 , pp. 1100-1108
    • Viau, C.1    McGuYn, M.J.2    Chiricota, Y.3    Jurisica, I.4
  • 157
    • 27844594381 scopus 로고    scopus 로고
    • Cross-platform analysis of cancer microarray data improves gene expression based classiWcation of phenotypes
    • Warnat P, Eils R, Brors B (2005) Cross-platform analysis of cancer microarray data improves gene expression based classiWcation of phenotypes. BMC Bioinformatics 6:265
    • (2005) BMC Bioinformatics , vol.6 , pp. 265
    • Warnat, P.1    Eils, R.2    Brors, B.3
  • 159
    • 33746647771 scopus 로고    scopus 로고
    • Topology and weights in a protein domain interaction network - A novel way to predict protein interactions
    • Wuchty S (2006) Topology and weights in a protein domain interaction network-a novel way to predict protein interactions. BMC Genomics 7:122
    • (2006) BMC Genomics , vol.7 , pp. 122
    • Wuchty, S.1
  • 161
    • 33645319955 scopus 로고    scopus 로고
    • Predicting interactions in protein networks by completing defective cliques
    • Yu H, Paccanaro A, Trifonov V, Gerstein M (2006) Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22(7):823-829
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 823-829
    • Yu, H.1    Paccanaro, A.2    Trifonov, V.3    Gerstein, M.4
  • 163
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene co-expression network analysis
    • (article17
    • Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4 (article17)
    • (2005) Stat Appl Genet Mol Biol , pp. 4
    • Zhang, B.1    Horvath, S.2


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