메뉴 건너뛰기




Volumn 11, Issue 18, 2014, Pages 35-46

Current advances in systems and integrative biology

Author keywords

Computational biology; Data integration; Pathway mapping; Systems biology

Indexed keywords


EID: 84924933259     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.1016/j.csbj.2014.08.007     Document Type: Review
Times cited : (34)

References (123)
  • 1
    • 70449209123 scopus 로고
    • On protein synthesis
    • F.H. Crick On protein synthesis Symp Soc Exp Biol 12 1958 138 163
    • (1958) Symp Soc Exp Biol , vol.12 , pp. 138-163
    • Crick, F.H.1
  • 2
    • 84928398447 scopus 로고    scopus 로고
    • At the dawn of a new revolution in life sciences
    • F. Baluska, and G. Witzany At the dawn of a new revolution in life sciences World J Biol Chem 4 2013 13 15
    • (2013) World J Biol Chem , vol.4 , pp. 13-15
    • Baluska, F.1    Witzany, G.2
  • 3
    • 84871063605 scopus 로고    scopus 로고
    • History of science. The revolution in the life sciences
    • S. Brenner History of science. The revolution in the life sciences Science 338 2012 1427 1428
    • (2012) Science , vol.338 , pp. 1427-1428
    • Brenner, S.1
  • 4
    • 24344466882 scopus 로고    scopus 로고
    • DNA methylation and histone modifications: Teaming up to silence genes
    • F. Fuks DNA methylation and histone modifications: teaming up to silence genes Curr Opin Genet Dev 15 2005 490 495
    • (2005) Curr Opin Genet Dev , vol.15 , pp. 490-495
    • Fuks, F.1
  • 5
    • 84874194072 scopus 로고    scopus 로고
    • DNA methylation: Roles in mammalian development
    • Z.D. Smith, and A. Meissner DNA methylation: roles in mammalian development Nat Rev Genet 14 2013 204 220
    • (2013) Nat Rev Genet , vol.14 , pp. 204-220
    • Smith, Z.D.1    Meissner, A.2
  • 6
    • 77649267695 scopus 로고    scopus 로고
    • Dynamic changes in the human methylome during differentiation
    • L. Laurent, E. Wong, G. Li, T. Huynh, A. Tsirigos, and C.T. Ong Dynamic changes in the human methylome during differentiation Genome Res 20 2010 320 331
    • (2010) Genome Res , vol.20 , pp. 320-331
    • Laurent, L.1    Wong, E.2    Li, G.3    Huynh, T.4    Tsirigos, A.5    Ong, C.T.6
  • 7
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exon-intron structure
    • S. Schwartz, E. Meshorer, and G. Ast Chromatin organization marks exon-intron structure Nat Struct Mol Biol 16 2009 990 995
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 990-995
    • Schwartz, S.1    Meshorer, E.2    Ast, G.3
  • 8
    • 84888865520 scopus 로고    scopus 로고
    • Transgenerational epigenetic inheritance: Focus on soma to germline information transfer
    • A. Sharma Transgenerational epigenetic inheritance: focus on soma to germline information transfer Prog Biophys Mol Biol 113 2013 439 446
    • (2013) Prog Biophys Mol Biol , vol.113 , pp. 439-446
    • Sharma, A.1
  • 10
    • 2342450524 scopus 로고    scopus 로고
    • Molecular evolution of a microRNA cluster
    • A. Tanzer, and P.F. Stadler Molecular evolution of a microRNA cluster J Mol Biol 339 2004 327 335
    • (2004) J Mol Biol , vol.339 , pp. 327-335
    • Tanzer, A.1    Stadler, P.F.2
  • 11
    • 79960918747 scopus 로고    scopus 로고
    • RNA structure and the mechanisms of alternative splicing
    • C.J. McManus, and B.R. Graveley RNA structure and the mechanisms of alternative splicing Curr Opin Genet Dev 21 2011 373 379
    • (2011) Curr Opin Genet Dev , vol.21 , pp. 373-379
    • McManus, C.J.1    Graveley, B.R.2
  • 12
    • 84867623952 scopus 로고    scopus 로고
    • Post-translational modification: Nature's escape from genetic imprisonment and the basis for dynamic information encoding
    • S. Prabakaran, G. Lippens, H. Steen, and J. Gunawardena Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding Wiley Interdiscip Rev Syst Biol Med 4 2012 565 583
    • (2012) Wiley Interdiscip Rev Syst Biol Med , vol.4 , pp. 565-583
    • Prabakaran, S.1    Lippens, G.2    Steen, H.3    Gunawardena, J.4
  • 13
    • 84901409283 scopus 로고    scopus 로고
    • Transcription factors: Specific DNA binding and specific gene regulation
    • A.L. Todeschini, A. Georges, and R.A. Veitia Transcription factors: specific DNA binding and specific gene regulation Trends Genet 30 2014 211 219
    • (2014) Trends Genet , vol.30 , pp. 211-219
    • Todeschini, A.L.1    Georges, A.2    Veitia, R.A.3
  • 14
  • 16
    • 84861664211 scopus 로고    scopus 로고
    • The microbiome as a human organ
    • F. Baquero, and C. Nombela The microbiome as a human organ Clin Microbiol Infect 18 Suppl. 4 2012 2 4
    • (2012) Clin Microbiol Infect , vol.18 , Issue.SUPPL. 4 , pp. 2-4
    • Baquero, F.1    Nombela, C.2
  • 17
    • 0041885325 scopus 로고    scopus 로고
    • Proliferating cell nuclear antigen (PCNA): A dancer with many partners
    • G. Maga, and U. Hubscher Proliferating cell nuclear antigen (PCNA): a dancer with many partners J Cell Sci 116 2003 3051 3060
    • (2003) J Cell Sci , vol.116 , pp. 3051-3060
    • Maga, G.1    Hubscher, U.2
  • 18
    • 33747817940 scopus 로고    scopus 로고
    • Toward a molecular understanding of pleiotropy
    • [1044]
    • X. He, and J. Zhang Toward a molecular understanding of pleiotropy Genetics 173 2006 1885 1891 [1044]
    • (2006) Genetics , vol.173 , pp. 1885-1891
    • He, X.1    Zhang, J.2
  • 19
    • 0027476994 scopus 로고
    • The functional versatility of CREM is determined by its modular structure
    • B.M. Laoide, N.S. Foulkes, F. Schlotter, and P. Sassone-Corsi The functional versatility of CREM is determined by its modular structure EMBO J 12 1993 1179 1191
    • (1993) EMBO J , vol.12 , pp. 1179-1191
    • Laoide, B.M.1    Foulkes, N.S.2    Schlotter, F.3    Sassone-Corsi, P.4
  • 20
    • 34249804498 scopus 로고    scopus 로고
    • Using FlyAtlas to identify better Drosophila melanogaster models of human disease
    • V.R. Chintapalli, J. Wang, and J.A. Dow Using FlyAtlas to identify better Drosophila melanogaster models of human disease Nat Genet 39 2007 715 720
    • (2007) Nat Genet , vol.39 , pp. 715-720
    • Chintapalli, V.R.1    Wang, J.2    Dow, J.A.3
  • 21
    • 84888172561 scopus 로고    scopus 로고
    • Biophysical regulation of epigenetic state and cell reprogramming
    • T.L. Downing, J. Soto, C. Morez, T. Houssin, A. Fritz, and F. Yuan Biophysical regulation of epigenetic state and cell reprogramming Nat Mater 12 2013 1154 1162
    • (2013) Nat Mater , vol.12 , pp. 1154-1162
    • Downing, T.L.1    Soto, J.2    Morez, C.3    Houssin, T.4    Fritz, A.5    Yuan, F.6
  • 23
    • 84874396923 scopus 로고    scopus 로고
    • Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
    • M.E. Price, A.M. Cotton, L.L. Lam, P. Farre, E. Emberly, and C.J. Brown Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array Epigenetics Chromatin 6 2013 4
    • (2013) Epigenetics Chromatin , vol.6 , pp. 4
    • Price, M.E.1    Cotton, A.M.2    Lam, L.L.3    Farre, P.4    Emberly, E.5    Brown, C.J.6
  • 24
    • 26444454986 scopus 로고    scopus 로고
    • A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array
    • J. Harbig, R. Sprinkle, and S.A. Enkemann A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array Nucleic Acids Res 33 2005 e31
    • (2005) Nucleic Acids Res , vol.33 , pp. e31
    • Harbig, J.1    Sprinkle, R.2    Enkemann, S.A.3
  • 25
    • 84877835534 scopus 로고    scopus 로고
    • LSCluster, a large-scale sequence clustering and aligning software for use in partial identity mapping and splice-variant analysis
    • H. Husi, R.J. Skipworth, K.C. Fearon, and J.A. Ross LSCluster, a large-scale sequence clustering and aligning software for use in partial identity mapping and splice-variant analysis J Proteome 84 2013 185 189
    • (2013) J Proteome , vol.84 , pp. 185-189
    • Husi, H.1    Skipworth, R.J.2    Fearon, K.C.3    Ross, J.A.4
  • 26
    • 84868676938 scopus 로고    scopus 로고
    • RNA-seq and microarray complement each other in transcriptome profiling
    • S. Kogenaru, Y. Qing, Y. Guo, and N. Wang RNA-seq and microarray complement each other in transcriptome profiling BMC Genomics 13 2012 629
    • (2012) BMC Genomics , vol.13 , pp. 629
    • Kogenaru, S.1    Qing, Y.2    Guo, Y.3    Wang, N.4
  • 28
    • 0035824631 scopus 로고    scopus 로고
    • Advances in proteome analysis bymass spectrometry
    • T.J. Griffin, and R. Aebersold Advances in proteome analysis bymass spectrometry J Biol Chem 276 2001 45497 45500
    • (2001) J Biol Chem , vol.276 , pp. 45497-45500
    • Griffin, T.J.1    Aebersold, R.2
  • 30
    • 38149060091 scopus 로고    scopus 로고
    • Proteomic profiling using mass spectrometry - Does normalising by total ion current potentially mask some biological differences?
    • D.A. Cairns, D. Thompson, D.N. Perkins, A.J. Stanley, P.J. Selby, and R.E. Banks Proteomic profiling using mass spectrometry - does normalising by total ion current potentially mask some biological differences? Proteomics 8 2008 21 27
    • (2008) Proteomics , vol.8 , pp. 21-27
    • Cairns, D.A.1    Thompson, D.2    Perkins, D.N.3    Stanley, A.J.4    Selby, P.J.5    Banks, R.E.6
  • 31
    • 1442333528 scopus 로고    scopus 로고
    • On the normalization of amass spectrum for comparison of two spectra
    • Z.B. Alfassi On the normalization of amass spectrum for comparison of two spectra J Am Soc Mass Spectrom 15 2004 385 387
    • (2004) J Am Soc Mass Spectrom , vol.15 , pp. 385-387
    • Alfassi, Z.B.1
  • 32
    • 84876573388 scopus 로고    scopus 로고
    • International Nucleotide Sequence Database C. The International Nucleotide Sequence Database Collaboration
    • Y. Nakamura, G. Cochrane, and I. Karsch-Mizrachi International Nucleotide Sequence Database C. The International Nucleotide Sequence Database Collaboration Nucleic Acids Res 41 2013 D21 D24
    • (2013) Nucleic Acids Res , vol.41 , pp. D21-D24
    • Nakamura, Y.1    Cochrane, G.2    Karsch-Mizrachi, I.3
  • 33
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • C. UniProt Update on activities at the Universal Protein Resource (UniProt) in 2013 Nucleic Acids Res 41 2013 D43 D47
    • (2013) Nucleic Acids Res , vol.41 , pp. D43-D47
    • Uniprot, C.1
  • 36
  • 38
    • 38449101120 scopus 로고    scopus 로고
    • Integration of biological networks and gene expression data using Cytoscape
    • M.S. Cline, M. Smoot, E. Cerami, A. Kuchinsky, and N. Landys Integration of biological networks and gene expression data using Cytoscape Nat Protoc 2 2007 2366 2382
    • (2007) Nat Protoc , vol.2 , pp. 2366-2382
    • Cline, M.S.1    Smoot, M.2    Cerami, E.3    Kuchinsky, A.4    Landys, N.5
  • 39
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • R. Edgar, M. Domrachev, and A.E. Lash Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res 30 2002 207 210
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 41
    • 67649354569 scopus 로고    scopus 로고
    • Minimum Information about a Microarray Experiment (MIAME) - Successes, failures, challenges
    • A. Brazma Minimum Information About a Microarray Experiment (MIAME) - successes, failures, challenges Sci World J 9 2009 420 423
    • (2009) Sci World J , vol.9 , pp. 420-423
    • Brazma, A.1
  • 44
    • 76249090489 scopus 로고    scopus 로고
    • BioGPS: An extensible and customizable portal for querying and organizing gene annotation resources
    • C. Wu, C. Orozco, J. Boyer, M. Leglise, J. Goodale, and S. Batalov BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Genome Biol 10 2009
    • (2009) Genome Biol , vol.10
    • Wu, C.1    Orozco, C.2    Boyer, J.3    Leglise, M.4    Goodale, J.5    Batalov, S.6
  • 47
  • 48
    • 84856562355 scopus 로고    scopus 로고
    • The NCBI Taxonomy database
    • S. Federhen The NCBI Taxonomy database Nucleic Acids Res 40 2012 D136 D143
    • (2012) Nucleic Acids Res , vol.40 , pp. D136-D143
    • Federhen, S.1
  • 49
    • 0031114483 scopus 로고    scopus 로고
    • GeneCards: Integrating information about genes, proteins and diseases
    • M. Rebhan, V. Chalifa-Caspi, J. Prilusky, and D. Lancet GeneCards: integrating information about genes, proteins and diseases Trends Genet 13 1997 163
    • (1997) Trends Genet , vol.13 , pp. 163
    • Rebhan, M.1    Chalifa-Caspi, V.2    Prilusky, J.3    Lancet, D.4
  • 56
    • 69749114144 scopus 로고    scopus 로고
    • Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments
    • K. Kandasamy, A. Pandey, and H. Molina Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments Anal Chem 81 2009 7170 7180
    • (2009) Anal Chem , vol.81 , pp. 7170-7180
    • Kandasamy, K.1    Pandey, A.2    Molina, H.3
  • 57
    • 84874584456 scopus 로고    scopus 로고
    • A proteomics search algorithm specifically designed for high resolution tandem mass spectra
    • C.D. Wenger, and J.J. Coon A proteomics search algorithm specifically designed for high resolution tandem mass spectra J Proteome Res 12 2013 1377 1386
    • (2013) J Proteome Res , vol.12 , pp. 1377-1386
    • Wenger, C.D.1    Coon, J.J.2
  • 58
    • 67649400942 scopus 로고    scopus 로고
    • A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    • J. Cox, I. Matic, M. Hilger, N. Nagaraj, M. Selbach, and J.V. Olsen A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics Nat Protoc 4 2009 698 705
    • (2009) Nat Protoc , vol.4 , pp. 698-705
    • Cox, J.1    Matic, I.2    Hilger, M.3    Nagaraj, N.4    Selbach, M.5    Olsen, J.V.6
  • 60
    • 79953267955 scopus 로고    scopus 로고
    • PeakML/mzMatch: A file format, Java library, R library, and tool-chain for mass spectrometry data analysis
    • R.A. Scheltema, A. Jankevics, R.C. Jansen, M.A. Swertz, and R. Breitling PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis Anal Chem 83 2011 2786 2793
    • (2011) Anal Chem , vol.83 , pp. 2786-2793
    • Scheltema, R.A.1    Jankevics, A.2    Jansen, R.C.3    Swertz, M.A.4    Breitling, R.5
  • 61
    • 32444446805 scopus 로고    scopus 로고
    • XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
    • C.A. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal Chem 78 2006 779 787
    • (2006) Anal Chem , vol.78 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3    Abagyan, R.4    Siuzdak, G.5
  • 62
    • 84887006810 scopus 로고
    • A nonlinear mapping for data structure analysis
    • J.W. Sammon A nonlinear mapping for data structure analysis IEEE Trans Comput C 18 1969 401
    • (1969) IEEE Trans Comput , vol.18 C , pp. 401
    • Sammon, J.W.1
  • 63
    • 0000325341 scopus 로고
    • On lines and planes of closest fit to systems of points in space
    • K. Pearson On lines and planes of closest fit to systems of points in space Philos Mag 2 1901 559 572
    • (1901) Philos Mag , vol.2 , pp. 559-572
    • Pearson, K.1
  • 64
    • 34250922831 scopus 로고
    • The varimax criterion for analytic rotation in factor-analysis
    • H.F. Kaiser The varimax criterion for analytic rotation in factor-analysis Psychometrika 23 1958 187 200
    • (1958) Psychometrika , vol.23 , pp. 187-200
    • Kaiser, H.F.1
  • 65
    • 64349124452 scopus 로고    scopus 로고
    • High heritability of metabolomic profiles in families burdened with premature cardiovascular disease
    • S.H. Shah, E.R. Hauser, J.R. Bain, M.J. Muehlbauer, C. Haynes, and R.D. Stevens High heritability of metabolomic profiles in families burdened with premature cardiovascular disease Mol Syst Biol 5 2009 258
    • (2009) Mol Syst Biol , vol.5 , pp. 258
    • Shah, S.H.1    Hauser, E.R.2    Bain, J.R.3    Muehlbauer, M.J.4    Haynes, C.5    Stevens, R.D.6
  • 67
    • 0032213478 scopus 로고    scopus 로고
    • Chaos in the cardiovascular system: An update
    • C.D. Wagner, and P.B. Persson Chaos in the cardiovascular system: an update Cardiovasc Res 40 1998 257 264
    • (1998) Cardiovasc Res , vol.40 , pp. 257-264
    • Wagner, C.D.1    Persson, P.B.2
  • 68
    • 33645762226 scopus 로고
    • A sharper Bonferroni procedure for multiple tests of significance
    • Y. Hochberg A sharper Bonferroni procedure for multiple tests of significance Biometrika 75 1988 800 802
    • (1988) Biometrika , vol.75 , pp. 800-802
    • Hochberg, Y.1
  • 69
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • [Article3]
    • G.K. Smyth Linear models and empirical Bayes methods for assessing differential expression in microarray experiments Stat Appl Genet Mol Biol 3 2004 [Article3]
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 70
    • 64549104807 scopus 로고    scopus 로고
    • ClueGO: A Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
    • G. Bindea, B. Mlecnik, H. Hackl, P. Charoentong, and M. Tosolini ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks Bioinformatics 25 2009 1091 1093
    • (2009) Bioinformatics , vol.25 , pp. 1091-1093
    • Bindea, G.1    Mlecnik, B.2    Hackl, H.3    Charoentong, P.4    Tosolini, M.5
  • 71
    • 84874741556 scopus 로고    scopus 로고
    • CluePedia Cytoscape plugin: Pathway insights using integrated experimental and in silico data
    • G. Bindea, J. Galon, and B. Mlecnik CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data Bioinformatics 29 2013 661 663
    • (2013) Bioinformatics , vol.29 , pp. 661-663
    • Bindea, G.1    Galon, J.2    Mlecnik, B.3
  • 72
    • 84874323682 scopus 로고    scopus 로고
    • KEGGParser: Parsing and editing KEGG pathway maps in Matlab
    • A. Arakelyan, and L. Nersisyan KEGGParser: parsing and editing KEGG pathway maps in Matlab Bioinformatics 29 2013 518 519
    • (2013) Bioinformatics , vol.29 , pp. 518-519
    • Arakelyan, A.1    Nersisyan, L.2
  • 73
    • 77952310528 scopus 로고    scopus 로고
    • A human functional protein interaction network and its application to cancer data analysis
    • G. Wu, X. Feng, and L. Stein A human functional protein interaction network and its application to cancer data analysis Genome Biol 11 2010 R53
    • (2010) Genome Biol , vol.11 , pp. R53
    • Wu, G.1    Feng, X.2    Stein, L.3
  • 74
    • 77951969442 scopus 로고    scopus 로고
    • Metscape: A Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks
    • J. Gao, V.G. Tarcea, A. Karnovsky, B.R. Mirel, and T.E. Weymouth Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks Bioinformatics 26 2010 971 973
    • (2010) Bioinformatics , vol.26 , pp. 971-973
    • Gao, J.1    Tarcea, V.G.2    Karnovsky, A.3    Mirel, B.R.4    Weymouth, T.E.5
  • 76
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical-reactions
    • D.T. Gillespie Exact stochastic simulation of coupled chemical-reactions J Phys Chem 81 1977 2340 2361
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 77
    • 33744899088 scopus 로고    scopus 로고
    • Formal agent-based modelling of intracellular chemical interactions
    • M. Pogson, R. Smallwood, E. Qwarnstrom, and M. Holcombe Formal agent-based modelling of intracellular chemical interactions Biosystems 85 2006 37 45
    • (2006) Biosystems , vol.85 , pp. 37-45
    • Pogson, M.1    Smallwood, R.2    Qwarnstrom, E.3    Holcombe, M.4
  • 78
    • 84872093417 scopus 로고    scopus 로고
    • Analysis of omics data with genome-scale models of metabolism
    • D.R. Hyduke, N.E. Lewis, and B.O. Palsson Analysis of omics data with genome-scale models of metabolism Mol BioSyst 9 2013 167 174
    • (2013) Mol BioSyst , vol.9 , pp. 167-174
    • Hyduke, D.R.1    Lewis, N.E.2    Palsson, B.O.3
  • 79
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • S.A. Becker, and B.O. Palsson Context-specific metabolic networks are consistent with experiments PLoS Comput Biol 4 2008 e1000082
    • (2008) PLoS Comput Biol , vol.4 , pp. e1000082
    • Becker, S.A.1    Palsson, B.O.2
  • 80
    • 84881152495 scopus 로고    scopus 로고
    • COBRApy: COnstraints-Based Reconstruction and Analysis for Python
    • A. Ebrahim, J.A. Lerman, B.O. Palsson, and D.R. Hyduke COBRApy: COnstraints-Based Reconstruction and Analysis for Python BMC Syst Biol 7 2013 74
    • (2013) BMC Syst Biol , vol.7 , pp. 74
    • Ebrahim, A.1    Lerman, J.A.2    Palsson, B.O.3    Hyduke, D.R.4
  • 81
    • 33745619814 scopus 로고    scopus 로고
    • Graph-based analysis and visualization of experimental results with ONDEX
    • J. Kohler, J. Baumbach, J. Taubert, M. Specht, A. Skusa, and A. Ruegg Graph-based analysis and visualization of experimental results with ONDEX Bioinformatics 22 2006 1383 1390
    • (2006) Bioinformatics , vol.22 , pp. 1383-1390
    • Kohler, J.1    Baumbach, J.2    Taubert, J.3    Specht, M.4    Skusa, A.5    Ruegg, A.6
  • 82
    • 79959258968 scopus 로고    scopus 로고
    • Sparse PLS discriminant analysis: Biologically relevant feature selection and graphical displays for multiclass problems
    • K.A. Le Cao, S. Boitard, and P. Besse Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems BMC Bioinforma 12 2011 253
    • (2011) BMC Bioinforma , vol.12 , pp. 253
    • Le Cao, K.A.1    Boitard, S.2    Besse, P.3
  • 83
    • 48449104873 scopus 로고    scopus 로고
    • Overview of mathematical approaches used to model bacterial chemotaxis I: The single cell
    • M.J. Tindall, S.L. Porter, P.K. Maini, G. Gaglia, and J.P. Armitage Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell Bull Math Biol 70 2008 1525 1569
    • (2008) Bull Math Biol , vol.70 , pp. 1525-1569
    • Tindall, M.J.1    Porter, S.L.2    Maini, P.K.3    Gaglia, G.4    Armitage, J.P.5
  • 84
    • 51749113592 scopus 로고    scopus 로고
    • Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    • M.W. Covert, N. Xiao, T.J. Chen, and J.R. Karr Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli Bioinformatics 24 2008 2044 2050
    • (2008) Bioinformatics , vol.24 , pp. 2044-2050
    • Covert, M.W.1    Xiao, N.2    Chen, T.J.3    Karr, J.R.4
  • 86
    • 84864258618 scopus 로고    scopus 로고
    • A whole-cell com- putational model predicts phenotype from genotype
    • J.R. Karr, J.C. Sanghvi, D.N. Macklin, M.V. Gutschow, and B. Bolival Jr. A whole-cell com- putational model predicts phenotype from genotype Cell 150 2012 389 401
    • (2012) Cell , vol.150 , pp. 389-401
    • Karr, J.R.1    Sanghvi, J.C.2    Macklin, D.N.3    Gutschow, M.V.4    Bolival, Jr.B.5
  • 87
    • 84897449198 scopus 로고    scopus 로고
    • Two different network topologies yield bistability in models of mesoderm and anterior mesendoderm specification in amphibians
    • L.E. Brown, J.R. King, and M. Loose Two different network topologies yield bistability in models of mesoderm and anterior mesendoderm specification in amphibians J Theor Biol 353 2014 67 77
    • (2014) J Theor Biol , vol.353 , pp. 67-77
    • Brown, L.E.1    King, J.R.2    Loose, M.3
  • 88
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: A network-based approach to human disease
    • A.L. Barabasi, N. Gulbahce, and J. Loscalzo Network medicine: a network-based approach to human disease Nat Rev Genet 12 2011 56 68
    • (2011) Nat Rev Genet , vol.12 , pp. 56-68
    • Barabasi, A.L.1    Gulbahce, N.2    Loscalzo, J.3
  • 89
    • 79957634007 scopus 로고    scopus 로고
    • Networks medicine: From reductionism to evidence of complex dynamic biomolecular interactions
    • D.H. Roukos Networks medicine: from reductionism to evidence of complex dynamic biomolecular interactions Pharmacogenomics 12 2011 695 698
    • (2011) Pharmacogenomics , vol.12 , pp. 695-698
    • Roukos, D.H.1
  • 90
    • 84887959327 scopus 로고    scopus 로고
    • Network medicine: Finding the links to personalized therapy
    • J.Y. Chen, M. Piquette-Miller, and B.P. Smith Network medicine: finding the links to personalized therapy Clin Pharmacol Ther 94 2013 613 616
    • (2013) Clin Pharmacol Ther , vol.94 , pp. 613-616
    • Chen, J.Y.1    Piquette-Miller, M.2    Smith, B.P.3
  • 91
    • 84861671617 scopus 로고    scopus 로고
    • The spread of neurodegenerative disease
    • J. Hardy, and T. Revesz The spread of neurodegenerative disease N Engl J Med 366 2012 2126 2128
    • (2012) N Engl J Med , vol.366 , pp. 2126-2128
    • Hardy, J.1    Revesz, T.2
  • 93
    • 84863337843 scopus 로고    scopus 로고
    • Alzheimer mechanisms and therapeutic strategies
    • Y. Huang, and L. Mucke Alzheimer mechanisms and therapeutic strategies Cell 148 2012 1204 1222
    • (2012) Cell , vol.148 , pp. 1204-1222
    • Huang, Y.1    Mucke, L.2
  • 94
    • 84868582421 scopus 로고    scopus 로고
    • Alzheimer disease: From inherited to sporadic AD - Crossing the biomarker bridge
    • H. Hampel, and S. Lista Alzheimer disease: from inherited to sporadic AD - crossing the biomarker bridge Nat Rev Neurol 8 2012 598 600
    • (2012) Nat Rev Neurol , vol.8 , pp. 598-600
    • Hampel, H.1    Lista, S.2
  • 96
    • 0035826782 scopus 로고    scopus 로고
    • Practice parameter: Diagnosis of dementia (an evidence-based review). Report of the Quality Standards Subcommittee of the American Academy of Neurology
    • D.S. Knopman, S.T. DeKosky, J.L. Cummings, H. Chui, J. Corey-Bloom, and N. Relkin Practice parameter: diagnosis of dementia (an evidence-based review). Report of the Quality Standards Subcommittee of the American Academy of Neurology Neurology 56 2001 1143 1153
    • (2001) Neurology , vol.56 , pp. 1143-1153
    • Knopman, D.S.1    Dekosky, S.T.2    Cummings, J.L.3    Chui, H.4    Corey-Bloom, J.5    Relkin, N.6
  • 97
    • 79956076567 scopus 로고    scopus 로고
    • Introduction to the recommendations from the National Institute on Aging - Alzheimer's Association workgroups on diagnostic guidelines for Alzheimer's disease
    • C.R. Jack Jr., M.S. Albert, D.S. Knopman, G.M. McKhann, R.A. Sperling, and M.C. Carrillo Introduction to the recommendations from the National Institute on Aging - Alzheimer's Association workgroups on diagnostic guidelines for Alzheimer's disease Alzheimers Dement 7 2011 257 262
    • (2011) Alzheimers Dement , vol.7 , pp. 257-262
    • Jack, Jr.C.R.1    Albert, M.S.2    Knopman, D.S.3    McKhann, G.M.4    Sperling, R.A.5    Carrillo, M.C.6
  • 98
    • 84901621290 scopus 로고    scopus 로고
    • Genetic markers for diagnosis and pathogenesis of Alzheimer's disease
    • D.H. Kim, S.H. Yeo, J.M. Park, J.Y. Choi, T.H. Lee, and S.Y. Park Genetic markers for diagnosis and pathogenesis of Alzheimer's disease Gene 545 2014 185 193
    • (2014) Gene , vol.545 , pp. 185-193
    • Kim, D.H.1    Yeo, S.H.2    Park, J.M.3    Choi, J.Y.4    Lee, T.H.5    Park, S.Y.6
  • 99
  • 100
    • 84859192682 scopus 로고    scopus 로고
    • Inverse association between cancer and Alzheimer's disease: Results from the Framingham Heart Study
    • J.A. Driver, A. Beiser, R. Au, B.E. Kreger, G.L. Splansky, and T. Kurth Inverse association between cancer and Alzheimer's disease: results from the Framingham Heart Study BMJ 344 2012 e1442
    • (2012) BMJ , vol.344 , pp. e1442
    • Driver, J.A.1    Beiser, A.2    Au, R.3    Kreger, B.E.4    Splansky, G.L.5    Kurth, T.6
  • 101
    • 84890190202 scopus 로고    scopus 로고
    • Transcriptional signaling pathways inversely regulated in Alzheimer's disease and glioblastomamultiform
    • T. Liu, D. Ren, X. Zhu, Z. Yin, G. Jin, and Z. Zhao Transcriptional signaling pathways inversely regulated in Alzheimer's disease and glioblastomamultiform Sci Rep 3 2013 3467
    • (2013) Sci Rep , vol.3 , pp. 3467
    • Liu, T.1    Ren, D.2    Zhu, X.3    Yin, Z.4    Jin, G.5    Zhao, Z.6
  • 102
    • 84932196018 scopus 로고    scopus 로고
    • HMGCR is a genetic mod- ifier for risk, age of onset and MCI conversion to Alzheimer's disease in a three cohorts study
    • V. Leduc, L. De Beaumont, L. Theroux, D. Dea, P. Aisen, and R.C. Petersen HMGCR is a genetic mod- ifier for risk, age of onset and MCI conversion to Alzheimer's disease in a three cohorts study Mol Psychiatry 2014
    • (2014) Mol Psychiatry
    • Leduc, V.1    De Beaumont, L.2    Theroux, L.3    Dea, D.4    Aisen, P.5    Petersen, R.C.6
  • 103
    • 84903362440 scopus 로고    scopus 로고
    • Global changes in DNA 1274 methylation and hydroxymethylation in Alzheimer's disease human brain
    • N. Coppieters, B.V. Dieriks, C. Lill, R.L. Faull, M.A. Curtis, and M. Dragunow Global changes in DNA 1274 methylation and hydroxymethylation in Alzheimer's disease human brain Nat Neurosci 35 2014 1334 1344
    • (2014) Nat Neurosci , vol.35 , pp. 1334-1344
    • Coppieters, N.1    Dieriks, B.V.2    Lill, C.3    Faull, R.L.4    Curtis, M.A.5    Dragunow, M.6
  • 104
    • 84904665084 scopus 로고    scopus 로고
    • Histone acetyltransferase p300 mediates histone acetylation of PS1 and BACE1 in a cellular model of Alzheimer's disease
    • X. Lu, Y. Deng, D. Yu, H. Cao, L. Wang, and L. Liu Histone acetyltransferase p300 mediates histone acetylation of PS1 and BACE1 in a cellular model of Alzheimer's disease PLoS One 9 2014 e103067
    • (2014) PLoS One , vol.9 , pp. e103067
    • Lu, X.1    Deng, Y.2    Yu, D.3    Cao, H.4    Wang, L.5    Liu, L.6
  • 105
    • 84893946623 scopus 로고    scopus 로고
    • MicroRNAs in plasma and cerebrospinal fluid as potential markers for Alzheimer's disease
    • T. Kiko, K. Nakagawa, T. Tsuduki, K. Furukawa, H. Arai, and T. Miyazawa MicroRNAs in plasma and cerebrospinal fluid as potential markers for Alzheimer's disease J Alzheimers Dis 39 2014 253 259
    • (2014) J Alzheimers Dis , vol.39 , pp. 253-259
    • Kiko, T.1    Nakagawa, K.2    Tsuduki, T.3    Furukawa, K.4    Arai, H.5    Miyazawa, T.6
  • 106
    • 84864778051 scopus 로고    scopus 로고
    • Target gene repression mediated by miRNAs miR-181c and miR-9 both of which are down-regulated by amyloid-beta
    • N. Schonrock, D.T. Humphreys, T. Preiss, and J. Gotz Target gene repression mediated by miRNAs miR-181c and miR-9 both of which are down-regulated by amyloid-beta J Mol Neurosci 46 2012 324 335
    • (2012) J Mol Neurosci , vol.46 , pp. 324-335
    • Schonrock, N.1    Humphreys, D.T.2    Preiss, T.3    Gotz, J.4
  • 107
    • 84892584524 scopus 로고    scopus 로고
    • CirculatingmiR-125b as a biomarker of Alzheimer's disease
    • L. Tan, J.T. Yu, Q.Y. Liu, M.S. Tan, W. Zhang, and N. Hu CirculatingmiR-125b as a biomarker of Alzheimer's disease J Neurol Sci 336 2014 52 56
    • (2014) J Neurol Sci , vol.336 , pp. 52-56
    • Tan, L.1    Yu, J.T.2    Liu, Q.Y.3    Tan, M.S.4    Zhang, W.5    Hu, N.6
  • 108
    • 84884630099 scopus 로고    scopus 로고
    • Human LilrB2 is a beta-amyloid receptor and its murine homolog PirB regulates synaptic plasticity in an Alzheimer's model
    • T. Kim, G.S. Vidal, M. Djurisic, C.M. William, M.E. Birnbaum, and K.C. Garcia Human LilrB2 is a beta-amyloid receptor and its murine homolog PirB regulates synaptic plasticity in an Alzheimer's model Science 341 2013 1399 1404
    • (2013) Science , vol.341 , pp. 1399-1404
    • Kim, T.1    Vidal, G.S.2    Djurisic, M.3    William, C.M.4    Birnbaum, M.E.5    Garcia, K.C.6
  • 110
    • 84903640571 scopus 로고    scopus 로고
    • Metabolomic study of lipids in serumfor biomarker discovery in Alzheimer's disease using direct infusion mass spectrometry
    • R. Gonzalez-Dominguez, T. Garcia-Barrera, and J.L. Gomez-Ariza Metabolomic study of lipids in serumfor biomarker discovery in Alzheimer's disease using direct infusion mass spectrometry J Pharm Biomed Anal 98c 2014 321 326
    • (2014) J Pharm Biomed Anal , vol.98 C , pp. 321-326
    • Gonzalez-Dominguez, R.1    Garcia-Barrera, T.2    Gomez-Ariza, J.L.3
  • 113
    • 84897045244 scopus 로고    scopus 로고
    • Exploringmitochondrial system properties of neu-rodegenerative diseases through interactome mapping
    • J. Vlasblom, K. Jin, S. Kassir, and M. Babu Exploringmitochondrial system properties of neu-rodegenerative diseases through interactome mapping J Proteome 100 2014 8 24
    • (2014) J Proteome , vol.100 , pp. 8-24
    • Vlasblom, J.1    Jin, K.2    Kassir, S.3    Babu, M.4
  • 114
    • 84890546613 scopus 로고    scopus 로고
    • Systems genetics approaches to understand complex traits
    • M. Civelek, and A.J. Lusis Systems genetics approaches to understand complex traits Nat Rev Genet 15 2014 34 48
    • (2014) Nat Rev Genet , vol.15 , pp. 34-48
    • Civelek, M.1    Lusis, A.J.2
  • 115
    • 84876907931 scopus 로고    scopus 로고
    • Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease
    • B. Zhang, C. Gaiteri, L.G. Bodea, Z. Wang, J. McElwee, and A.A. Podtelezhnikov Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease Cell 153 2013 707 720
    • (2013) Cell , vol.153 , pp. 707-720
    • Zhang, B.1    Gaiteri, C.2    Bodea, L.G.3    Wang, Z.4    McElwee, J.5    Podtelezhnikov, A.A.6
  • 117
    • 84902974185 scopus 로고    scopus 로고
    • Systematic analysis of transcription-level effects of neurodegenerative diseases on human brainmetabolism by a newly reconstructed brain-specific metabolic network
    • M. Sertbas, K. Ulgen, and T. Cakir Systematic analysis of transcription-level effects of neurodegenerative diseases on human brainmetabolism by a newly reconstructed brain-specific metabolic network FEBS Open Biol 4 2014 542 553
    • (2014) FEBS Open Biol , vol.4 , pp. 542-553
    • Sertbas, M.1    Ulgen, K.2    Cakir, T.3
  • 120
    • 84897954630 scopus 로고    scopus 로고
    • Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer's disease
    • D.A. Bennett, L. Yu, and P.L. De Jager Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer's disease Biochem Pharmacol 88 2014 617 630
    • (2014) Biochem Pharmacol , vol.88 , pp. 617-630
    • Bennett, D.A.1    Yu, L.2    De Jager, P.L.3
  • 121
    • 84872335098 scopus 로고    scopus 로고
    • Systems biology approaches and applications in obesity, diabetes, and cardiovascular diseases
    • Q. Meng, V.P. Mäkinen, H. Luk, and X. Yang Systems biology approaches and applications in obesity, diabetes, and cardiovascular diseases Curr Cardiovasc Risk Rep 7 2013 73 83
    • (2013) Curr Cardiovasc Risk Rep , vol.7 , pp. 73-83
    • Meng, Q.1    Mäkinen, V.P.2    Luk, H.3    Yang, X.4
  • 122
    • 67651108806 scopus 로고    scopus 로고
    • The genetics of quantitative traits: Challenges and prospects
    • T.F.C. MacKay, E.A. Stone, and J.F. Ayroles The genetics of quantitative traits: challenges and prospects Nat Rev Genet 10 2009 565 577
    • (2009) Nat Rev Genet , vol.10 , pp. 565-577
    • Mackay, T.F.C.1    Stone, E.A.2    Ayroles, J.F.3
  • 123
    • 0025127467 scopus 로고
    • Capsaicin-sensitive vagal afferents contribute to gastric acid and vascular responses to intracisternal TRH analog
    • H.E. Raybould, P. Holzer, S.N. Reddy, H. Yang, and Y. Tache Capsaicin-sensitive vagal afferents contribute to gastric acid and vascular responses to intracisternal TRH analog Peptides 11 1990 789 795
    • (1990) Peptides , vol.11 , pp. 789-795
    • Raybould, H.E.1    Holzer, P.2    Reddy, S.N.3    Yang, H.4    Tache, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.