-
1
-
-
0032441150
-
-
M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein, Cluster analysis and display of genome-wide expression patterns, Proc Natl Acad Sci U S A, 95, no. 25, pp. 14 863-14 868, 1998.
-
M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein, "Cluster analysis and display of genome-wide expression patterns," Proc Natl Acad Sci U S A, vol. 95, no. 25, pp. 14 863-14 868, 1998.
-
-
-
-
2
-
-
0345580221
-
Large-scale clustering of cdna-fingerprinting data
-
R. Herwig, A. Poustka, C. Muller, C. Bull, H. Lehrach, and J. O'Brien, "Large-scale clustering of cdna-fingerprinting data," Genome Research, vol. 9, no. 11, pp. 1093-1105, 1999.
-
(1999)
Genome Research
, vol.9
, Issue.11
, pp. 1093-1105
-
-
Herwig, R.1
Poustka, A.2
Muller, C.3
Bull, C.4
Lehrach, H.5
O'Brien, J.6
-
3
-
-
0034782618
-
Model-based clustering and data transformations for gene expression data
-
K. Yeung, C. Fraley, A. Murua, A. Raftery, and W. Ruzzo, "Model-based clustering and data transformations for gene expression data," Bioinformatics, vol. 17, pp. 977-987, 2001.
-
(2001)
Bioinformatics
, vol.17
, pp. 977-987
-
-
Yeung, K.1
Fraley, C.2
Murua, A.3
Raftery, A.4
Ruzzo, W.5
-
4
-
-
0035375137
-
Computational analysis of microarray data
-
J. Quackenbush, "Computational analysis of microarray data," Nat Rev Genet, vol. 2, pp. 418-427.
-
Nat Rev Genet
, vol.2
, pp. 418-427
-
-
Quackenbush, J.1
-
5
-
-
0034565041
-
Click: A clustering algorithm for gene expression analysis
-
R. Shamir and R. Sharan, "Click: A clustering algorithm for gene expression analysis," in Proc Int Conf Intell Syst Mol Biol, vol. 8, 2000, pp. 307-316.
-
(2000)
Proc Int Conf Intell Syst Mol Biol
, vol.8
, pp. 307-316
-
-
Shamir, R.1
Sharan, R.2
-
6
-
-
0141974934
-
Excavator: A computer program for efficiently mining gene expression data
-
D. Xu, V. Olman, L. Wang, and Y. Xu, "Excavator: a computer program for efficiently mining gene expression data," Nucleic Acids Res., vol. 31, no. 19, pp. 5582-5589, 2003.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.19
, pp. 5582-5589
-
-
Xu, D.1
Olman, V.2
Wang, L.3
Xu, Y.4
-
7
-
-
3042686005
-
Bayesian mixture model based clustering of replicated microarray data
-
M. Medvedovic, K. Yeung, and R. Bumgarner, "Bayesian mixture model based clustering of replicated microarray data," Bioinformatics, vol. 20, no. 8, pp. 1222-1232, 2004.
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1222-1232
-
-
Medvedovic, M.1
Yeung, K.2
Bumgarner, R.3
-
8
-
-
0030669030
-
Exploring the metabolic and genetic control of gene expression on a genomic scale
-
J. DeRisi, V. Iyer, and P. Brown, "Exploring the metabolic and genetic control of gene expression on a genomic scale." Science, vol. 278, no. 5338, pp. 680-686, 1997.
-
(1997)
Science
, vol.278
, Issue.5338
, pp. 680-686
-
-
DeRisi, J.1
Iyer, V.2
Brown, P.3
-
9
-
-
0034566246
-
Pattern recognition of genomic features with microarrays: Site typing of mycobacterium tuberculosis strains
-
AAAI Press
-
S. Raychaudhuri, J. M. Stuart, X. Liu, P. M. Small, and R. B. Altman, "Pattern recognition of genomic features with microarrays: Site typing of mycobacterium tuberculosis strains," in Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, 2000, pp. 286-295.
-
(2000)
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
, pp. 286-295
-
-
Raychaudhuri, S.1
Stuart, J.M.2
Liu, X.3
Small, P.M.4
Altman, R.B.5
-
10
-
-
0035755549
-
Analysis of large-scale gene expression data
-
G. Sherlock, "Analysis of large-scale gene expression data," Brief Bioinform, vol. 2, no. 4, pp. 350-362, 2001.
-
(2001)
Brief Bioinform
, vol.2
, Issue.4
, pp. 350-362
-
-
Sherlock, G.1
-
11
-
-
0034602774
-
Knowledge-based analysis of microarray gene expression data by using support vector machines
-
M. P. Brown, W. N. Grundy, D. Lin, N. Cristianini, C. W. Sugnet, T. S. Furey, M. Ares, and D. Haussler, "Knowledge-based analysis of microarray gene expression data by using support vector machines," PNAS, vol. 97, no. 1, pp. 262-267, 2000.
-
(2000)
PNAS
, vol.97
, Issue.1
, pp. 262-267
-
-
Brown, M.P.1
Grundy, W.N.2
Lin, D.3
Cristianini, N.4
Sugnet, C.W.5
Furey, T.S.6
Ares, M.7
Haussler, D.8
-
12
-
-
0035367064
-
Whole-genome expression analysis: Challenges beyond clustering
-
R. Altman and S. Raychaudhuri, "Whole-genome expression analysis: challenges beyond clustering," Current Opinion in Structural Biology, vol. 11, no. 3, pp. 340-347, 2001.
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.3
, pp. 340-347
-
-
Altman, R.1
Raychaudhuri, S.2
-
13
-
-
0036325427
-
Genomics and natural language processing
-
M. Yandell and W. Majoros, "Genomics and natural language processing," Nature Reviews Genetics, vol. 3, pp. 601-610, 2002.
-
(2002)
Nature Reviews Genetics
, vol.3
, pp. 601-610
-
-
Yandell, M.1
Majoros, W.2
-
14
-
-
0342462653
-
A novel method for automatic and reliable functional annotation of proteins
-
W. Fleischmann, S. Möller, A. Gateau, and R. Apweiler, "A novel method for automatic and reliable functional annotation of proteins," in German Conference on Bioinformatics, 1998.
-
(1998)
German Conference on Bioinformatics
-
-
Fleischmann, W.1
Möller, S.2
Gateau, A.3
Apweiler, R.4
-
15
-
-
0036144742
-
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature
-
S. Raychaudhuri, J. Chang, P. Sutphin, and R. Altman, "Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature," Genome Res, vol. 12, pp. 203-214, 2002.
-
(2002)
Genome Res
, vol.12
, pp. 203-214
-
-
Raychaudhuri, S.1
Chang, J.2
Sutphin, P.3
Altman, R.4
-
16
-
-
0031694515
-
Euclid: Automatic classification of proteins in functional classes by their database annotations
-
J. Tamames, C. A. Ouzounis, G. Casari, C. Sander, and A. Valencia, "Euclid: automatic classification of proteins in functional classes by their database annotations," Bioinformatics, vol. 14, no. 6, pp. 542-543, 1998.
-
(1998)
Bioinformatics
, vol.14
, Issue.6
, pp. 542-543
-
-
Tamames, J.1
Ouzounis, C.A.2
Casari, G.3
Sander, C.4
Valencia, A.5
-
17
-
-
0038017587
-
Mining microarray expression data by literature profiling
-
p. RESEARCH0055
-
D. Chaussabel and A. Sher, "Mining microarray expression data by literature profiling," Genome Biology, vol. 3, no. 10, p. RESEARCH0055, 2002.
-
(2002)
Genome Biology
, vol.3
, Issue.10
-
-
Chaussabel, D.1
Sher, A.2
-
18
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
J. Ihmels, G. Friedlander, S. Bergmann, O. Sarig, Y. Ziv, and N. Barkai, "Revealing modular organization in the yeast transcriptional network," Nature Genetics, no. 31, pp. 370-377, 2002.
-
(2002)
Nature Genetics
, Issue.31
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
Barkai, N.6
-
19
-
-
33745496606
-
Clustering genes using gene expression and text literature data
-
Washington, DC, USA: IEEE Computer Society
-
C. Yang, E. Zeng, T. Li, and G. Narasimhan, "Clustering genes using gene expression and text literature data," in CSB '05: Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05). Washington, DC, USA: IEEE Computer Society, 2005, pp. 329-340.
-
(2005)
CSB '05: Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)
, pp. 329-340
-
-
Yang, C.1
Zeng, E.2
Li, T.3
Narasimhan, G.4
-
20
-
-
10244253968
-
Constrained clusters of gene expression profiles with pathological features
-
J. Sese, Y. Kurokawa, M. Monden, K. Kato, and S. Morishita, "Constrained clusters of gene expression profiles with pathological features," Bioinformatics, vol. 20, no. 17, pp. 3137-3145, 2004.
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3137-3145
-
-
Sese, J.1
Kurokawa, Y.2
Monden, M.3
Kato, K.4
Morishita, S.5
-
21
-
-
0042377235
-
Constrained k-means clustering with background knowledge
-
K. Wagsta, C. Cardie, S. Rogers, and S. Schroedl, "Constrained k-means clustering with background knowledge," in Proceedings of 18th International Conference on Machine Learning (ICML-01), 2001, pp. 577-584.
-
(2001)
Proceedings of 18th International Conference on Machine Learning (ICML-01)
, pp. 577-584
-
-
Wagsta, K.1
Cardie, C.2
Rogers, S.3
Schroedl, S.4
-
22
-
-
2542567719
-
Semi-supervised clustering by seeding
-
S. Basu, A. Banerjee, and R. Mooney, "Semi-supervised clustering by seeding," in Proceedings of 19th International Conference on Machine Learning (ICML-02), 2002, pp. 19-26.
-
(2002)
Proceedings of 19th International Conference on Machine Learning (ICML-02)
, pp. 19-26
-
-
Basu, S.1
Banerjee, A.2
Mooney, R.3
-
23
-
-
9444294778
-
From instance-level constraints to space-level constraints: Making the most of prior knowledge in data clustering
-
D. Klein, S. D. Kamvar, and C. D. Manning, "From instance-level constraints to space-level constraints: Making the most of prior knowledge in data clustering." in ICML, 2002, pp. 307-314.
-
(2002)
ICML
, pp. 307-314
-
-
Klein, D.1
Kamvar, S.D.2
Manning, C.D.3
-
24
-
-
84879571292
-
Distance metric learning, with application to clustering with side-information
-
MIT Press
-
E. P. Xing, A. Y. Ng, M. I. Jordan, and S. Russell, "Distance metric learning, with application to clustering with side-information," in Advances in Neural Information Processing Systems, vol. 15. MIT Press, 2003.
-
(2003)
Advances in Neural Information Processing Systems
, vol.15
-
-
Xing, E.P.1
Ng, A.Y.2
Jordan, M.I.3
Russell, S.4
-
25
-
-
21844452080
-
Integrating constraints and metric learning in semi-supervised clustering
-
New York, NY, USA: ACM Press
-
M. Bilenko, S. Basu, and R. J. Mooney, "Integrating constraints and metric learning in semi-supervised clustering," in ICML '04: Proceedings of the twenty-first international conference on Machine learning. New York, NY, USA: ACM Press, 2004, p. 11.
-
(2004)
ICML '04: Proceedings of the twenty-first international conference on Machine learning
, pp. 11
-
-
Bilenko, M.1
Basu, S.2
Mooney, R.J.3
-
26
-
-
33750288047
-
Measuring constraint-set utility for partitional clustering algorithms
-
PKDD, Springer
-
I. Davidson, K. Wagstaff, and S. Basu, "Measuring constraint-set utility for partitional clustering algorithms." in PKDD, ser. Lecture Notes in Computer Science, vol. 4213. Springer, 2006, pp. 115-126.
-
(2006)
ser. Lecture Notes in Computer Science
, vol.4213
, pp. 115-126
-
-
Davidson, I.1
Wagstaff, K.2
Basu, S.3
-
27
-
-
57549092754
-
When is constrained clustering beneficial, and why?
-
K. Wagstaff, S. Basu, and I. Davidson, "When is constrained clustering beneficial, and why?" in AAAI, 2006.
-
(2006)
AAAI
-
-
Wagstaff, K.1
Basu, S.2
Davidson, I.3
-
28
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
T. Ideker, V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood, "Integrated genomic and proteomic analyses of a systematically perturbed metabolic network." Science, vol. 292, no. 5518, pp. 929-934, 2001.
-
(2001)
Science
, vol.292
, Issue.5518
, pp. 929-934
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.A.3
Christmas, R.4
Buhler, J.5
Eng, J.K.6
Bumgarner, R.7
Goodlett, D.R.8
Aebersold, R.9
Hood, L.10
-
29
-
-
0037667290
-
Clustering gene-expression data with repeated measurements
-
K. Y. Yeung, M. Medvedovic, and R. E. Bumgarner, "Clustering gene-expression data with repeated measurements," Genome Biol, vol. 4, p. R34, 2003.
-
(2003)
Genome Biol
, vol.4
-
-
Yeung, K.Y.1
Medvedovic, M.2
Bumgarner, R.E.3
-
30
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization
-
P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher, "Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization." Mol Biol Cell, vol. 9, no. 12, pp. 3273-3297, 1998.
-
(1998)
Mol Biol Cell
, vol.9
, Issue.12
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
31
-
-
0036798238
-
Judging the quality of gene expression-based clustering methods using gene annotation
-
F. Gibbons and F. Roth, "Judging the quality of gene expression-based clustering methods using gene annotation," Genome Research, vol. 12, no. 10, pp. 574-581, 2002.
-
(2002)
Genome Research
, vol.12
, Issue.10
, pp. 574-581
-
-
Gibbons, F.1
Roth, F.2
-
32
-
-
21244496209
-
Meta-clustering of gene expression data and literature-based information
-
P. Glenisson, J. Mathys, and B. D. Moor, "Meta-clustering of gene expression data and literature-based information," SIGKDD Explor. Newsl., vol. 5, no. 2, pp. 101-112, 2003.
-
(2003)
SIGKDD Explor. Newsl
, vol.5
, Issue.2
, pp. 101-112
-
-
Glenisson, P.1
Mathys, J.2
Moor, B.D.3
-
33
-
-
0035031110
-
Linking microarray data to the literature
-
D. Masys, "Linking microarray data to the literature," Nat Genet, vol. 28, pp. 9-10, 2001.
-
(2001)
Nat Genet
, vol.28
, pp. 9-10
-
-
Masys, D.1
-
34
-
-
13444304426
-
Missing value estimation for dna microarray gene expression data: Local least squares imputation
-
H. Kim, G. H. Golub, and H. Park, "Missing value estimation for dna microarray gene expression data: local least squares imputation," Bioinformatics, vol. 21, no. 2, pp. 187-198, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.2
, pp. 187-198
-
-
Kim, H.1
Golub, G.H.2
Park, H.3
-
35
-
-
0035895205
-
Pubmed central: The genbank of the published literature
-
R. J. Roberts, "Pubmed central: The genbank of the published literature," PNAS, vol. 98, pp. 381-382, 2001.
-
(2001)
PNAS
, vol.98
, pp. 381-382
-
-
Roberts, R.J.1
-
36
-
-
0742324218
-
-
E. Hong, R. Balakrishnan, K. Christie, M. Costanzo, S. Dwight, S. Engel, D. Fisk, J. Hirschman, M. Livstone, R. Nash, R. Oughtred, J. Park, M. Skrzypek, B. Starr, R. Andrada, G. Binkley, Q. Dong, B. Hitz, S. Miyasato, M. Schroeder, S. Weng, E. Wong, K. Zhu, K. Dolinski, D. Botstein, and J. Cherry, "Saccharomyces genome database, http://www.yeastgenome.org/."
-
Saccharomyces genome database
-
-
Hong, E.1
Balakrishnan, R.2
Christie, K.3
Costanzo, M.4
Dwight, S.5
Engel, S.6
Fisk, D.7
Hirschman, J.8
Livstone, M.9
Nash, R.10
Oughtred, R.11
Park, J.12
Skrzypek, M.13
Starr, B.14
Andrada, R.15
Binkley, G.16
Dong, Q.17
Hitz, B.18
Miyasato, S.19
Schroeder, M.20
Weng, S.21
Wong, E.22
Zhu, K.23
Dolinski, K.24
Botstein, D.25
Cherry, J.26
more..
-
37
-
-
84950632109
-
Objective criteria for the evaluation of clustering methods
-
W. Rand, "Objective criteria for the evaluation of clustering methods," Journal of the American Statistical Association, vol. 66, no. 336, pp. 846-850, 1971.
-
(1971)
Journal of the American Statistical Association
, vol.66
, Issue.336
, pp. 846-850
-
-
Rand, W.1
-
38
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. the gene ontology consortium
-
M. Ashburner, C. Ball, J. Blake, D. Botstein, H. Butler, J. Cherry, A. Davis, K. Dolinski, S. Dwight, J. Eppig, M. Harris, D. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. Matese, J. Richardson, M. Ringwald, G. Rubin, and G. Sherlock, "Gene ontology: tool for the unification of biology. the gene ontology consortium." Nat Genet, vol. 25, no. 1, pp. 25-9, 2000.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.2
Blake, J.3
Botstein, D.4
Butler, H.5
Cherry, J.6
Davis, A.7
Dolinski, K.8
Dwight, S.9
Eppig, J.10
Harris, M.11
Hill, D.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.16
Richardson, J.17
Ringwald, M.18
Rubin, G.19
Sherlock, G.20
more..
|