-
1
-
-
0033592606
-
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
-
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
-
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
-
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
-
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
-
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
-
-
-
-
-
8
-
-
84879142982
-
-
-
-
-
9
-
-
84879162624
-
-
-
-
-
10
-
-
77954069195
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
-
-
-
24
-
-
0037810449
-
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
-
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
-
26
-
-
0033983822
-
MIPS: A database for genomes and protein sequences
-
Mannhaupt G
-
Mewes H, Frishman D, Gruber C, Geier B, Haase D, Kaps A, Lemcke K, Pfeiffer F, Schuller C, Stocker S, Mannhaupt G MIPS: A database for genomes and protein sequences. Nucleic Acids Res 2000, 28:37-40. Mannhaupt G.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 37-40
-
-
Mewes, H.1
Frishman, D.2
Gruber, C.3
Geier, B.4
Haase, D.5
Kaps, A.6
Lemcke, K.7
Pfeiffer, F.8
Schuller, C.9
Stocker, S.10
-
27
-
-
12344269924
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
36
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman R. Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17(6):520-525.
-
(2001)
Bioinformatics
, vol.17
, Issue.6
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
Brown, P.4
Hastie, T.5
Tibshirani, R.6
Botstein, D.7
Altman, R.8
-
37
-
-
0038237368
-
Estimating dataset size requirements for classifying DNA microarray data
-
Mukherjee S, Tamayo P, Rogers S, Rifkin R, Engle A, Campbell C, Golub T, Mesirov J. Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol 2003, 10(2):119-142.
-
(2003)
J Comput Biol
, vol.10
, Issue.2
, pp. 119-142
-
-
Mukherjee, S.1
Tamayo, P.2
Rogers, S.3
Rifkin, R.4
Engle, A.5
Campbell, C.6
Golub, T.7
Mesirov, J.8
-
38
-
-
29644438050
-
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
|