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Volumn 5, Issue 2, 2010, Pages

Gene expression prediction by soft integration and the elastic net - Best performance of the DREAM3 gene expression challenge

Author keywords

[No Author keywords available]

Indexed keywords

CALSENILIN; TRANSCRIPTION FACTOR;

EID: 77949535261     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009134     Document Type: Article
Times cited : (23)

References (34)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási A-, Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nature Reviews Genetics 5(2): 101-113.
    • (2004) Nature Reviews Genetics , vol.5 , Issue.2 , pp. 101-113
    • Barabási, A.1    Oltvai, Z.N.2
  • 2
    • 36249019789 scopus 로고    scopus 로고
    • Dialogue on reverse-engineering assessment and methods: The DREAM of high-throughput pathway inference
    • Stolovitzky G, Monroe D, Califano A (2007) Dialogue on reverse-engineering assessment and methods: The DREAM of high-throughput pathway inference. Annals of the New York Academy of Sciences 1115: 1-22.
    • (2007) Annals of the New York Academy of Sciences , vol.1115 , pp. 1-22
    • Stolovitzky, G.1    Monroe, D.2    Califano, A.3
  • 3
    • 63849210631 scopus 로고    scopus 로고
    • Lessons from the DREAM2 challenges: A community effort to assess biological network inference
    • Stolovitzky G, Prill RJ, Califano A (2009) Lessons from the DREAM2 challenges: A community effort to assess biological network inference. Annals of the New York Academy of Sciences 1158: 159-195.
    • (2009) Annals of the New York Academy of Sciences , vol.1158 , pp. 159-195
    • Stolovitzky, G.1    Prill, R.J.2    Califano, A.3
  • 4
    • 77949644952 scopus 로고    scopus 로고
    • Stolovitzky G (2009) DREAM3. PLoS ONE 5(2): doi: 10.1371/journal.pone. 0009202.
    • Stolovitzky G (2009) DREAM3. PLoS ONE 5(2): doi: 10.1371/journal.pone. 0009202.
  • 5
    • 61349180117 scopus 로고    scopus 로고
    • Gene regulatory network inference: Data integration in dynamic models-A review
    • Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R (2009) Gene regulatory network inference: Data integration in dynamic models-A review. BioSystems 96(1): 86-103.
    • (2009) BioSystems , vol.96 , Issue.1 , pp. 86-103
    • Hecker, M.1    Lambeck, S.2    Toepfer, S.3    van Someren, E.4    Guthke, R.5
  • 6
    • 0036271042 scopus 로고    scopus 로고
    • Effective dimensionality of large-scale expression data using principal component analysis
    • Hörnquist M, Hertz J, Wahde M (2002) Effective dimensionality of large-scale expression data using principal component analysis. BioSystems 65(2-3): 147-156.
    • (2002) BioSystems , vol.65 , Issue.2-3 , pp. 147-156
    • Hörnquist, M.1    Hertz, J.2    Wahde, M.3
  • 7
    • 0141987849 scopus 로고    scopus 로고
    • Effective dimensionality for principal component analysis of time series expression data
    • Hörnquist M, Hertz J, Wahde M (2003) Effective dimensionality for principal component analysis of time series expression data. BioSystems 71(3): 311-317.
    • (2003) BioSystems , vol.71 , Issue.3 , pp. 311-317
    • Hörnquist, M.1    Hertz, J.2    Wahde, M.3
  • 8
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology
    • Kitano H (2002) Computational systems biology. Nature 420(6912): 206-210.
    • (2002) Nature , vol.420 , Issue.6912 , pp. 206-210
    • Kitano, H.1
  • 9
    • 54249124501 scopus 로고    scopus 로고
    • Learning biological networks: From modules to dynamics
    • Bonneau R (2008) Learning biological networks: From modules to dynamics. Nature Chemical Biology 4(11): 658-664.
    • (2008) Nature Chemical Biology , vol.4 , Issue.11 , pp. 658-664
    • Bonneau, R.1
  • 10
    • 34249740137 scopus 로고    scopus 로고
    • Reverse engineering of gene regulatory networks
    • Cho K, Choo S, Jung SH, Kim J, Choi H, et al. (2007) Reverse engineering of gene regulatory networks. IET Systems Biology 1(3): 149-163.
    • (2007) IET Systems Biology , vol.1 , Issue.3 , pp. 149-163
    • Cho, K.1    Choo, S.2    Jung, S.H.3    Kim, J.4    Choi, H.5
  • 11
    • 77949481863 scopus 로고    scopus 로고
    • A top-performing algorithm for the DREAM3 gene expression prediction challenge
    • doi: 10.1371/journal.pone.0008944
    • Ruan J (2009) A top-performing algorithm for the DREAM3 gene expression prediction challenge. PLoS ONE 5(2): doi: 10.1371/journal.pone.0008944.
    • (2009) PLoS ONE , vol.5 , Issue.2
    • Ruan, J.1
  • 12
    • 77957226516 scopus 로고    scopus 로고
    • A bias correction for the minimum error rate in cross-validation
    • Tibshirani RJ, Tibshirani R (2009) A bias correction for the minimum error rate in cross-validation. Ann Appl Stat 3(2): 822-829.
    • (2009) Ann Appl Stat , vol.3 , Issue.2 , pp. 822-829
    • Tibshirani, R.J.1    Tibshirani, R.2
  • 13
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • De Jong H (2002) Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology 9(1): 67-103.
    • (2002) Journal of Computational Biology , vol.9 , Issue.1 , pp. 67-103
    • De Jong, H.1
  • 14
    • 0036843965 scopus 로고    scopus 로고
    • Gene networks: How to put the function in genomics
    • Brazhnik P, De La Fuente A, Mendes P (2002) Gene networks: How to put the function in genomics. Trends Biotechnol 20(11): 467-472.
    • (2002) Trends Biotechnol , vol.20 , Issue.11 , pp. 467-472
    • Brazhnik, P.1    De La Fuente, A.2    Mendes, P.3
  • 15
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: From coexpression clustering to reverse engineering
    • D'Haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: From coexpression clustering to reverse engineering. Bioinformatics 16(8): 707-726.
    • (2000) Bioinformatics , vol.16 , Issue.8 , pp. 707-726
    • D'Haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 16
    • 27644508196 scopus 로고    scopus 로고
    • Constructing and analyzing a large-scale gene-to-gene regulatory network-lasso-constrained inference and biological validation
    • Gustafsson M, Hörnquist M, Lombardi A (2005) Constructing and analyzing a large-scale gene-to-gene regulatory network-lasso-constrained inference and biological validation. IEEE/ACM Trans Comput Biol Bioinform 2(3): 254-261.
    • (2005) IEEE/ACM Trans Comput Biol Bioinform , vol.2 , Issue.3 , pp. 254-261
    • Gustafsson, M.1    Hörnquist, M.2    Lombardi, A.3
  • 17
    • 0034760495 scopus 로고    scopus 로고
    • Dynamic models of gene expression and classification
    • Dewey TG, Galas DJ (2001) Dynamic models of gene expression and classification. Functional and Integrative Genomics 1(4): 269-278.
    • (2001) Functional and Integrative Genomics , vol.1 , Issue.4 , pp. 269-278
    • Dewey, T.G.1    Galas, D.J.2
  • 19
    • 68349160767 scopus 로고    scopus 로고
    • Genome-wide system analysis reveals stable yet flexible network dynamics in yeast. IET
    • Gustafsson M, Hörnquist M, Bjorkegren J, Tegner J (2009) Genome-wide system analysis reveals stable yet flexible network dynamics in yeast. IET Syst Biol 3(4): 219-228.
    • (2009) Syst Biol , vol.3 , Issue.4 , pp. 219-228
    • Gustafsson, M.1    Hörnquist, M.2    Bjorkegren, J.3    Tegner, J.4
  • 20
    • 0000270617 scopus 로고
    • The minimum sum of absolute errors regression: A state of the art survey
    • Narula SC, Wellington JF (1982) The minimum sum of absolute errors regression: A state of the art survey. International Statistical Review 50: 317-326.
    • (1982) International Statistical Review , vol.50 , pp. 317-326
    • Narula, S.C.1    Wellington, J.F.2
  • 22
    • 16244401458 scopus 로고    scopus 로고
    • Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society.Series B: Statistical Methodology
    • Zou H, Hastie T (2005) Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society.Series B: Statistical Methodology 67(2): 301-320.
    • (2005) , vol.67 , Issue.2 , pp. 301-320
    • Zou, H.1    Hastie, T.2
  • 26
    • 77949522417 scopus 로고    scopus 로고
    • Friedman J, Hasie T, Tibshirani R (in press) Regularization paths for generalized linear models via coordinate descent. Journal of Statistical Software.
    • Friedman J, Hasie T, Tibshirani R (in press) Regularization paths for generalized linear models via coordinate descent. Journal of Statistical Software.
  • 28
    • 0034616930 scopus 로고    scopus 로고
    • Functional discovery via a compendium of expression profiles
    • Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102(1): 109-126.
    • (2000) Cell , vol.102 , Issue.1 , pp. 109-126
    • Hughes, T.R.1    Marton, M.J.2    Jones, A.R.3    Roberts, C.J.4    Stoughton, R.5
  • 29
    • 21444452397 scopus 로고    scopus 로고
    • Chemogenomic profiling on a genome-wide scale using reverseengineered gene networks
    • Bernardo DD, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, et al. (2005) Chemogenomic profiling on a genome-wide scale using reverseengineered gene networks. Nat Biotechnol 23(3): 377-383.
    • (2005) Nat Biotechnol , vol.23 , Issue.3 , pp. 377-383
    • Bernardo, D.D.1    Thompson, M.J.2    Gardner, T.S.3    Chobot, S.E.4    Eastwood, E.L.5
  • 30
    • 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(1): 207-210.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 31
    • 33846064113 scopus 로고    scopus 로고
    • Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, et al. (2007) NCBI GEO: Mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res 35(SUPPL. 1): D760-D765.
    • Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, et al. (2007) NCBI GEO: Mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res 35(SUPPL. 1): D760-D765.
  • 33
    • 38549135468 scopus 로고    scopus 로고
    • Monteiro PT, Mendes ND, Teixeira MC, D'orey S, Tenreiro S, et al. (2008) YEASTRACT-DISCOVERER: New tools to improve the analysis of transcriptional regulatory associations in saccharomyces cerevisiae. Nucleic Acids Res 36(SUPPL. 1): D132-D136.
    • Monteiro PT, Mendes ND, Teixeira MC, D'orey S, Tenreiro S, et al. (2008) YEASTRACT-DISCOVERER: New tools to improve the analysis of transcriptional regulatory associations in saccharomyces cerevisiae. Nucleic Acids Res 36(SUPPL. 1): D132-D136.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.