메뉴 건너뛰기




Volumn 1794, Issue 9, 2009, Pages 1280-1287

Know your limits: Assumptions, constraints and interpretation in systems biology

Author keywords

Bioinformatics; Functional genomics; Metadata; Standards; Systems biology

Indexed keywords

BIOPHYSICS; CELL POPULATION; CYTOLOGY; GENE EXPRESSION; GENOMICS; MASS SPECTROMETRY; MICROARRAY ANALYSIS; PRIORITY JOURNAL; REVIEW; SYSTEMS BIOLOGY;

EID: 69449083202     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.05.002     Document Type: Review
Times cited : (6)

References (73)
  • 2
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • Kitano H. Systems biology: a brief overview. Science (New York, N.Y.) 295 (Mar. 2002) 1662-1664
    • (2002) Science (New York, N.Y.) , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 3
    • 5044227742 scopus 로고    scopus 로고
    • The evolution of molecular biology into systems biology
    • Westerhoff H.V., and Palsson B.O. The evolution of molecular biology into systems biology. Nat. Biotech. 22 (Oct. 2004) 1249-1252
    • (2004) Nat. Biotech. , vol.22 , pp. 1249-1252
    • Westerhoff, H.V.1    Palsson, B.O.2
  • 4
    • 30444445381 scopus 로고    scopus 로고
    • Fundamental issues in systems biology
    • O'Malley M.A., and Dupré J. Fundamental issues in systems biology. BioEssays 27 (2005) 1270-1276
    • (2005) BioEssays , vol.27 , pp. 1270-1276
    • O'Malley, M.A.1    Dupré, J.2
  • 6
    • 5044239903 scopus 로고    scopus 로고
    • A partnership between biology and engineering
    • Brent R. A partnership between biology and engineering. Nat. Biotech. 22 (Oct. 2004) 1211-1214
    • (2004) Nat. Biotech. , vol.22 , pp. 1211-1214
    • Brent, R.1
  • 7
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z., Gerstein M., and Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10 (Jan. 2009) 57-63
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 8
    • 38549097071 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • The UniProt Consortium
    • The UniProt Consortium. The Universal Protein Resource (UniProt). Nucl. Acids Res. 36 (Jan. 2008) D190-195
    • (2008) Nucl. Acids Res. , vol.36
  • 16
    • 41549097236 scopus 로고    scopus 로고
    • Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
    • Mueller M., Vizcaíno J.A., Jones P., Côté R., Thorneycroft D., Apweiler R., Hermjakob H., and Martens L. Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics 8 (Mar. 2008) 1138-1148
    • (2008) Proteomics , vol.8 , pp. 1138-1148
    • Mueller, M.1    Vizcaíno, J.A.2    Jones, P.3    Côté, R.4    Thorneycroft, D.5    Apweiler, R.6    Hermjakob, H.7    Martens, L.8
  • 17
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabási A., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5 (Feb. 2004) 101-113
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabási, A.1    Oltvai, Z.N.2
  • 26
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • Jeong H., Tombor B., Albert R., Oltvai Z.N., and Barabasi A. The large-scale organization of metabolic networks. Nature 407 (Oct. 2000) 651-654
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3    Oltvai, Z.N.4    Barabasi, A.5
  • 27
    • 0141596113 scopus 로고    scopus 로고
    • Molecular networks: the top-down view
    • Bray D. Molecular networks: the top-down view. Science 301 (Sep. 2003) 1864-1865
    • (2003) Science , vol.301 , pp. 1864-1865
    • Bray, D.1
  • 29
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: from disarray to consolidation and consensus
    • Allison D.B., Cui X., Page G.P., and Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet. 7 (Jan. 2006) 55-65
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3    Sabripour, M.4
  • 30
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: methodological issues
    • Goeman J.J., and Buhlmann P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23 (Apr. 2007) 980-987
    • (2007) Bioinformatics , vol.23 , pp. 980-987
    • Goeman, J.J.1    Buhlmann, P.2
  • 32
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: current tools, limitations, and open problems
    • Khatri P., and Drǎghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics (Oxford, England) 21 (Sep. 2005) 3587-3595
    • (2005) Bioinformatics (Oxford, England) , vol.21 , pp. 3587-3595
    • Khatri, P.1    Drǎghici, S.2
  • 34
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V., and Mirny L.A. Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. U. S. A. 100 (Oct. 2003) 12123-12128
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 35
    • 11244306358 scopus 로고    scopus 로고
    • Discovering statistically significant biclusters in gene expression data
    • Tanay A., Sharan R., and Shamir R. Discovering statistically significant biclusters in gene expression data. Bioinformatics 18 (Jul. 2002) S136-144
    • (2002) Bioinformatics , vol.18
    • Tanay, A.1    Sharan, R.2    Shamir, R.3
  • 36
    • 34347329333 scopus 로고    scopus 로고
    • In search of the biological significance of modular structures in protein networks
    • Wang Z., and Zhang J. In search of the biological significance of modular structures in protein networks. PLoS Comput. Biol. 3 (Jun. 2007) e107
    • (2007) PLoS Comput. Biol. , vol.3
    • Wang, Z.1    Zhang, J.2
  • 37
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni J.C., Mason C.E., Mane S.M., Stephens M., and Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18 (2008) 1509-1517
    • (2008) Genome Res. , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 38
    • 46249130709 scopus 로고    scopus 로고
    • The beginning of the end for microarrays?
    • Shendure J. The beginning of the end for microarrays?. Nat. Method 5 (Jul. 2008) 585-587
    • (2008) Nat. Method , vol.5 , pp. 585-587
    • Shendure, J.1
  • 44
    • 0036900895 scopus 로고    scopus 로고
    • Fundamentals of experimental design for cDNA microarrays
    • Churchill G.A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32 Suppl. (Dec. 2002) 490-495
    • (2002) Nat. Genet. , vol.32 , Issue.SUPPL , pp. 490-495
    • Churchill, G.A.1
  • 45
    • 0036319960 scopus 로고    scopus 로고
    • Design issues for cDNA microarray experiments
    • Yang Y.H., and Speed T. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3 (2002) 579-588
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 579-588
    • Yang, Y.H.1    Speed, T.2
  • 46
    • 0346733313 scopus 로고    scopus 로고
    • Design considerations for efficient and effective microarray studies
    • Kathleen Kerr M. Design considerations for efficient and effective microarray studies. Biometrics 59 (2003) 822-828
    • (2003) Biometrics , vol.59 , pp. 822-828
    • Kathleen Kerr, M.1
  • 47
    • 0037078982 scopus 로고    scopus 로고
    • Control, exploitation and tolerance of intracellular noise
    • Rao C.V., Wolf D.M., and Arkin A.P. Control, exploitation and tolerance of intracellular noise. Nature 420 (Nov. 2002) 231-237
    • (2002) Nature , vol.420 , pp. 231-237
    • Rao, C.V.1    Wolf, D.M.2    Arkin, A.P.3
  • 48
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: from theories to phenotypes
    • Kaern M., Elston T.C., Blake W.J., and Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6 (Jun. 2005) 451-464
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 451-464
    • Kaern, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 49
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: origins, consequences, and control
    • Raser J.M., and O'Shea E.K. Noise in gene expression: origins, consequences, and control. Science 309 (Sep. 2005) 2010-2013
    • (2005) Science , vol.309 , pp. 2010-2013
    • Raser, J.M.1    O'Shea, E.K.2
  • 54
    • 38349185928 scopus 로고    scopus 로고
    • Effects of molecular memory and bursting on fluctuations in gene expression
    • Pedraza J.M., and Paulsson J. Effects of molecular memory and bursting on fluctuations in gene expression. Science 319 (Jan. 2008) 339-343
    • (2008) Science , vol.319 , pp. 339-343
    • Pedraza, J.M.1    Paulsson, J.2
  • 57
    • 58549108763 scopus 로고    scopus 로고
    • Mapping the gene expression universe
    • Lécuyer E., and Tomancak P. Mapping the gene expression universe. Curr. Opin. Genet. Dev. 18 (Dec. 2008) 506-512
    • (2008) Curr. Opin. Genet. Dev. , vol.18 , pp. 506-512
    • Lécuyer, E.1    Tomancak, P.2
  • 60
    • 34447104600 scopus 로고    scopus 로고
    • Stability and nuclear dynamics of the bicoid morphogen gradient
    • Gregor T., Wieschaus E.F., McGregor A.P., Bialek W., and Tank D.W. Stability and nuclear dynamics of the bicoid morphogen gradient. Cell 130 (Jul. 2007) 141-152
    • (2007) Cell , vol.130 , pp. 141-152
    • Gregor, T.1    Wieschaus, E.F.2    McGregor, A.P.3    Bialek, W.4    Tank, D.W.5
  • 61
    • 0014937223 scopus 로고
    • Central dogma of molecular biology
    • Crick F. Central dogma of molecular biology. Nature 227 (Aug. 1970) 561-563
    • (1970) Nature , vol.227 , pp. 561-563
    • Crick, F.1
  • 63
    • 33745296476 scopus 로고    scopus 로고
    • The multitasking genome
    • Gingeras T.R. The multitasking genome. Nat. Genet. 38 (Jun. 2006) 608-609
    • (2006) Nat. Genet. , vol.38 , pp. 608-609
    • Gingeras, T.R.1
  • 64
    • 34249088350 scopus 로고    scopus 로고
    • Genome-wide transcription and the implications for genomic organization
    • Kapranov P., Willingham A.T., and Gingeras T.R. Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet. 8 (Jun. 2007) 413-423
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 413-423
    • Kapranov, P.1    Willingham, A.T.2    Gingeras, T.R.3
  • 65
    • 60549085054 scopus 로고    scopus 로고
    • Molecular biology: the long and short of RNAs
    • Carninci P. Molecular biology: the long and short of RNAs. Nature 457 (Feb. 2009) 974-975
    • (2009) Nature , vol.457 , pp. 974-975
    • Carninci, P.1
  • 66
    • 33747615285 scopus 로고    scopus 로고
    • Gene expression within a dynamic nuclear landscape
    • Shav-Tal Y., Darzacq X., and Singer R.H. Gene expression within a dynamic nuclear landscape. EMBO J. 25 (Aug. 2006) 3469-3479
    • (2006) EMBO J. , vol.25 , pp. 3469-3479
    • Shav-Tal, Y.1    Darzacq, X.2    Singer, R.H.3
  • 68
    • 37249034083 scopus 로고    scopus 로고
    • Coupling and coordination in gene expression processes: a systems biology view
    • Komili S., and Silver P.A. Coupling and coordination in gene expression processes: a systems biology view. Nat. Rev. Genet. 9 (Jan. 2008) 38-48
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 38-48
    • Komili, S.1    Silver, P.A.2
  • 69
    • 0036499997 scopus 로고    scopus 로고
    • Modeling the heart-from genes to cells to the whole organ
    • Noble D. Modeling the heart-from genes to cells to the whole organ. Science 295 (Mar. 2002) 1678-1682
    • (2002) Science , vol.295 , pp. 1678-1682
    • Noble, D.1
  • 70
  • 73
    • 58149161724 scopus 로고    scopus 로고
    • Genome and proteome annotation: organization, interpretation and integration
    • Reeves G.A., Talavera D., and Thornton J.M. Genome and proteome annotation: organization, interpretation and integration. J. R. Soc. Interface 6 (2009) 129-147
    • (2009) J. R. Soc. Interface , vol.6 , pp. 129-147
    • Reeves, G.A.1    Talavera, D.2    Thornton, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.