메뉴 건너뛰기




Volumn 8, Issue , 2013, Pages

The non-negative matrix factorization toolbox for biological data mining

Author keywords

Bi clustering; Classification; Clustering; Feature extraction; Feature selection; Missing values; Non negative matrix factorization

Indexed keywords


EID: 84876097941     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-8-10     Document Type: Article
Times cited : (149)

References (38)
  • 1
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by non-negative matrix factorization
    • Lee DD, Seung S. Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401:788-791.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, S.2
  • 2
    • 1642529511 scopus 로고    scopus 로고
    • Metagenes and molecular pattern discovery using matrix factorization
    • Brunet J, Tamayo P, Golub T, Mesirov J. Metagenes and molecular pattern discovery using matrix factorization. PNAS 2004, 101(12):4164-4169.
    • (2004) PNAS , vol.101 , Issue.12 , pp. 4164-4169
    • Brunet, J.1    Tamayo, P.2    Golub, T.3    Mesirov, J.4
  • 3
    • 34547844077 scopus 로고    scopus 로고
    • Sparse non-negatice matrix factorization via alternating non-negativity-constrained least aquares for microarray data analysis
    • Kim H, Park H. Sparse non-negatice matrix factorization via alternating non-negativity-constrained least aquares for microarray data analysis. SIAM J Matrix Anal Appl 2007, 23(12):1495-1502.
    • (2007) SIAM J Matrix Anal Appl , vol.23 , Issue.12 , pp. 1495-1502
    • Kim, H.1    Park, H.2
  • 4
    • 33645794993 scopus 로고    scopus 로고
    • Biclustering of gene expression data by non-smooth non-negative matrix factorization
    • Pascual-Montano A
    • Carmona-Saez P, Pascual-Marqui RD, Tirado F, Carazo JM, Pascual-Montano A Biclustering of gene expression data by non-smooth non-negative matrix factorization. BMC Bioinformatics 2006, 7:78. Pascual-Montano A.
    • (2006) BMC Bioinformatics , vol.7 , pp. 78
    • Carmona-Saez, P.1    Pascual-Marqui, R.D.2    Tirado, F.3    Carazo, J.M.4
  • 5
    • 33646181805 scopus 로고    scopus 로고
    • LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates
    • Wang G, Kossenkov A, Ochs M. LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates. BMC Bioinformatics 2006, 7:175.
    • (2006) BMC Bioinformatics , vol.7 , pp. 175
    • Wang, G.1    Kossenkov, A.2    Ochs, M.3
  • 6
    • 84864069021 scopus 로고    scopus 로고
    • A new kernel non-negative matrix factorization and its application in microarray data analysis
    • : IEEE CIS Society Piscataway: IEEE Press
    • Li Y, Ngom A. A new kernel non-negative matrix factorization and its application in microarray data analysis. CIBCB 2012, 371-378. : IEEE CIS Society Piscataway: IEEE Press.
    • (2012) CIBCB , pp. 371-378
    • Li, Y.1    Ngom, A.2
  • 7
    • 84879165740 scopus 로고    scopus 로고
  • 8
    • 84879142982 scopus 로고    scopus 로고
  • 9
    • 84879162624 scopus 로고    scopus 로고
  • 10
    • 77954069195 scopus 로고    scopus 로고
    • A flexible R package for nonnegative matrix factorization
    • Gaujoux R, Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics 2010, 11:367. [http://cran.r-project.org/web/packages/NMF].
    • (2010) BMC Bioinformatics , vol.11 , pp. 367
    • Gaujoux, R.1    Seoighe, C.2
  • 11
    • 60149106101 scopus 로고    scopus 로고
    • Non-negative matrix factorization of gene expression profiles: A plug-in for BRB-ArrayTools
    • Qi Q, Zhao Y, Li M, Simon R. non-negative matrix factorization of gene expression profiles: A plug-in for BRB-ArrayTools. Bioinformatics 2009, 25(4):545-547.
    • (2009) Bioinformatics , vol.25 , Issue.4 , pp. 545-547
    • Qi, Q.1    Zhao, Y.2    Li, M.3    Simon, R.4
  • 12
    • 77958479692 scopus 로고    scopus 로고
    • CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data
    • Fertig E, Ding J, Favorov A, Parmigiani G, Ochs M. CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinformatics 2010, 26(21):2792-2793.
    • (2010) Bioinformatics , vol.26 , Issue.21 , pp. 2792-2793
    • Fertig, E.1    Ding, J.2    Favorov, A.3    Parmigiani, G.4    Ochs, M.5
  • 14
    • 84898964201 scopus 로고    scopus 로고
    • Algorithms for non-negative matrix factorization.
    • : Cambridge: MIT Press
    • Lee D, Seung S. Algorithms for non-negative matrix factorization. NIPS 2001, 556-562. : Cambridge: MIT Press.
    • (2001) NIPS , pp. 556-562
    • Lee, D.1    Seung, S.2
  • 15
    • 67349093319 scopus 로고    scopus 로고
    • Nonnegative matrix factorization based on alternating nonnegativity constrained least squares and active set method
    • Kim H, Park H. Nonnegative matrix factorization based on alternating nonnegativity constrained least squares and active set method. SIAM J Matrix Anal Appl 2008, 30(2):713-730.
    • (2008) SIAM J Matrix Anal Appl , vol.30 , Issue.2 , pp. 713-730
    • Kim, H.1    Park, H.2
  • 16
    • 84871617105 scopus 로고    scopus 로고
    • Convex and semi-nonnegative matrix factorizations
    • Ding C, Li T, Jordan MI. Convex and semi-nonnegative matrix factorizations. TPAMI 2010, 32:45-55.
    • (2010) TPAMI , vol.32 , pp. 45-55
    • Ding, C.1    Li, T.2    Jordan, M.I.3
  • 17
    • 85194972808 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani R. Regression shrinkage and selection via the lasso. J R Stat Soc Ser B (Methodol) 1996, 58:267-288.
    • (1996) J R Stat Soc Ser B (Methodol) , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 18
    • 16244401458 scopus 로고    scopus 로고
    • Regularization and variable selection via the elastic Net
    • Zou H, Hastie T. Regularization and variable selection via the elastic Net. J R Stat Soc- Ser B: Stat Methodol 2005, 67(2):301-320.
    • (2005) J R Stat Soc- Ser B: Stat Methodol , vol.67 , Issue.2 , pp. 301-320
    • Zou, H.1    Hastie, T.2
  • 19
    • 33749546310 scopus 로고    scopus 로고
    • Non-negative matrix factorization on kernels
    • Zhang D, Zhou Z, Chen S. Non-negative matrix factorization on kernels. LNCS 2006, 4099:404-412.
    • (2006) LNCS , vol.4099 , pp. 404-412
    • Zhang, D.1    Zhou, Z.2    Chen, S.3
  • 20
    • 33749575326 scopus 로고    scopus 로고
    • Orthogonal nonnegative matrix tri-factorizations for clustering
    • New York: ACM
    • Ding C, Li T, Peng W, Park H. Orthogonal nonnegative matrix tri-factorizations for clustering. KDD 2006, 126-135. New York: ACM.
    • (2006) KDD , pp. 126-135
    • Ding, C.1    Li, T.2    Peng, W.3    Park, H.4
  • 21
    • 85158022027 scopus 로고    scopus 로고
    • Non-negative sparse PCA
    • Cambridge: MIT Press
    • Zass R, Shashua A. Non-negative sparse PCA. NIPS 2006, Cambridge: MIT Press.
    • (2006) NIPS
    • Zass, R.1    Shashua, A.2
  • 22
    • 84879162052 scopus 로고    scopus 로고
  • 24
    • 0037810449 scopus 로고    scopus 로고
    • Subsystem identification through dimensionality reduction of large-scale gene expression data
    • Kim P, Tidor B. Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Res 2003, 13:1706-1718.
    • (2003) Genome Res , vol.13 , pp. 1706-1718
    • Kim, P.1    Tidor, B.2
  • 25
    • 0042121055 scopus 로고    scopus 로고
    • Onto-tools, the toolkit of the modern biologist: onto-express, onto-compare, onto-design and onto-translate
    • Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz S, Tainsky M. Onto-tools, the toolkit of the modern biologist: onto-express, onto-compare, onto-design and onto-translate. Nucleic Acids Res 2003, 31(13):3775-3781.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3775-3781
    • Draghici, S.1    Khatri, P.2    Bhavsar, P.3    Shah, A.4    Krawetz, S.5    Tainsky, M.6
  • 27
    • 12344269924 scopus 로고    scopus 로고
    • GO::TermFinder - open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes
    • Sherlock G
    • Boyle E, Weng S, Gollub J, Jin H, Botstein D, Cherry J, Sherlock G GO::TermFinder - open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 2004, 20:3710-3715. Sherlock G.
    • (2004) Bioinformatics , vol.20 , pp. 3710-3715
    • Boyle, E.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.6
  • 28
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID Bioinformatics resources
    • Huang D
    • Sherman B, Huang D Systematic and integrative analysis of large gene lists using DAVID Bioinformatics resources. Nature Protoc 2009, 4:44-57. Huang D.
    • (2009) Nature Protoc , vol.4 , pp. 44-57
    • Sherman, B.1
  • 29
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang D, Sherman B, Lempicki R. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37:1-13.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang, D.1    Sherman, B.2    Lempicki, R.3
  • 30
    • 27944487902 scopus 로고    scopus 로고
    • Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes
    • McKnight S
    • Tu B, Kudlicki A, Rowicka M, McKnight S Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 2005, 310:1152-1158. McKnight S.
    • (2005) Science , vol.310 , pp. 1152-1158
    • Tu, B.1    Kudlicki, A.2    Rowicka, M.3
  • 31
    • 68949209109 scopus 로고    scopus 로고
    • A core MYC gene expression signature is prominient in basal-like breast cancer but only partially overlaps the core serum response
    • Cole M
    • Chandriani S, Frengen E, Cowling V, Pendergrass S, Perou C, Whitfield M, Cole M A core MYC gene expression signature is prominient in basal-like breast cancer but only partially overlaps the core serum response. PloS ONE 2009, 4(5):e6693. Cole M.
    • (2009) PloS ONE , vol.4 , Issue.5
    • Chandriani, S.1    Frengen, E.2    Cowling, V.3    Pendergrass, S.4    Perou, C.5    Whitfield, M.6
  • 32
    • 71549130141 scopus 로고    scopus 로고
    • Detection of treatment-induced changes in signaling pathways in sastrointestinal stromal tumors using transcripttomic data
    • Godwin A
    • Ochs M, Rink L, Tarn C, Mburu S, Taguchi T, Eisenberg B, Godwin A Detection of treatment-induced changes in signaling pathways in sastrointestinal stromal tumors using transcripttomic data. Cancer Res 2009, 69(23):9125-9132. Godwin A.
    • (2009) Cancer Res , vol.69 , Issue.23 , pp. 9125-9132
    • Ochs, M.1    Rink, L.2    Tarn, C.3    Mburu, S.4    Taguchi, T.5    Eisenberg, B.6
  • 33
    • 0034954414 scopus 로고    scopus 로고
    • Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks
    • Khan J. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 2001, 7(6):673-679.
    • (2001) Nat Med , vol.7 , Issue.6 , pp. 673-679
    • Khan, J.1
  • 34
    • 33646874546 scopus 로고    scopus 로고
    • The molecular portraits of breast tumors are conserved across microarray platforms
    • Hu Z
    • Hu Z The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006, 7:96. Hu Z.
    • (2006) BMC Genomics , vol.7 , pp. 96
  • 35
    • 84881249254 scopus 로고    scopus 로고
    • Classification approach based on non-negative least squares
    • in press
    • Li Y, Ngom A. Classification approach based on non-negative least squares. Neurocomputing 2013,, in press.
    • (2013) Neurocomputing
    • Li, Y.1    Ngom, A.2
  • 38
    • 29644438050 scopus 로고    scopus 로고
    • Statistical comparisons of classifiers over multiple data sets
    • Demsar J. Statistical comparisons of classifiers over multiple data sets. J Mach Learn Res 2006, 7:1-30.
    • (2006) J Mach Learn Res , vol.7 , pp. 1-30
    • Demsar, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.