-
1
-
-
12344316947
-
A graph-theoretic approach to testing associations between disparate sources of functional genomics data
-
Balasubramanian, R. et al. (2004) A graph-theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics, 20, 3353-3362.
-
(2004)
Bioinformatics
, vol.20
, pp. 3353-3362
-
-
Balasubramanian, R.1
-
2
-
-
0036100113
-
Context-specific Bayesian clustering for gene expression data
-
Barash, Y. and Friedman, N. (2002) Context-specific Bayesian clustering for gene expression data. J. Comput. Biol., 9, 169-191.
-
(2002)
J. Comput. Biol
, vol.9
, pp. 169-191
-
-
Barash, Y.1
Friedman, N.2
-
3
-
-
46749142532
-
ClValid: An R package for cluster validation
-
Brock, G. et al. (2008) clValid: an R package for cluster validation. J. Stat. Softw., 25, 1-22.
-
(2008)
J. Stat. Softw
, vol.25
, pp. 1-22
-
-
Brock, G.1
-
6
-
-
0031858914
-
SGD: Saccharomyces genome database
-
Cherry, J.M. et al. (1998) SGD: Saccharomyces genome database. Nucleic Acids Res., 26, 73-79.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 73-79
-
-
Cherry, J.M.1
-
7
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho, R.J. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
-
(1998)
Mol. Cell
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
-
8
-
-
80053928843
-
Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements
-
Cooke, E.J. et al. (2011) Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. BMC Bioinformatics, 12, 399.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 399
-
-
Cooke, E.J.1
-
9
-
-
33749428430
-
Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes
-
Datta, S. and Datta, S. (2006) Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. BMC Bioinformatics, 7, 397.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 397
-
-
Datta, S.1
Datta, S.2
-
10
-
-
0002629270
-
Maximum likelihood from incomplete data via em Algorithm
-
Dempster, A. et al. (1977) Maximum likelihood from incomplete data via EM Algorithm. J. R. Stat. Soc. Series B Methodol., 39, 1-38.
-
(1977)
J. R. Stat. Soc. Series B Methodol
, vol.39
, pp. 1-38
-
-
Dempster, A.1
-
11
-
-
3142617128
-
Consistency in boosting: Discussion
-
Friedman, J. et al. (2004) Consistency in boosting: discussion. Ann. Stat., 32, 102-107.
-
(2004)
Ann. Stat
, vol.32
, pp. 102-107
-
-
Friedman, J.1
-
12
-
-
77954199057
-
Improved criteria for clustering based on the posterior similarity matrix
-
Fritsch, A. and Ickstadt, K. (2009) Improved criteria for clustering based on the posterior similarity matrix. Bayesian Anal., 4, 367-391.
-
(2009)
Bayesian Anal
, vol.4
, pp. 367-391
-
-
Fritsch, A.1
Ickstadt, K.2
-
13
-
-
77953204308
-
High-resolution transcription atlas of the mitotic cell cycle in budding yeast
-
Granovskaia, M.V. et al. (2010) High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol., 11, R24.
-
(2010)
Genome Biol
, vol.11
-
-
Granovskaia, M.V.1
-
14
-
-
0035531242
-
Modelling heterogeneity with and without the Dirichlet process
-
Green, P. and Richardson, S. (2001) Modelling heterogeneity with and without the Dirichlet process. Scand. J. Stat., 28, 355-375.
-
(2001)
Scand. J. Stat
, vol.28
, pp. 355-375
-
-
Green, P.1
Richardson, S.2
-
15
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
-
16
-
-
0000008146
-
Comparing partitions
-
Hubert, L. and Arabie, P. (1985) Comparing partitions. J. Classif., 2, 193-218.
-
(1985)
J. Classif
, vol.2
, pp. 193-218
-
-
Hubert, L.1
Arabie, P.2
-
17
-
-
66449120271
-
Exploring the human genome with functional maps
-
Huttenhower, C. et al. (2009) Exploring the human genome with functional maps. Genome Res., 19, 1093-1106.
-
(2009)
Genome Res
, vol.19
, pp. 1093-1106
-
-
Huttenhower, C.1
-
18
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
Ideker, T. et al. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292, 929-934.
-
(2001)
Science
, vol.292
, pp. 929-934
-
-
Ideker, T.1
-
19
-
-
0036623091
-
Exact and approximate representations for the sum Dirichlet process
-
Ishwaran, H. and Zarepour, M. (2002) Exact and approximate representations for the sum Dirichlet process. Can. J. Stat., 30, 269-283.
-
(2002)
Can. J. Stat
, vol.30
, pp. 269-283
-
-
Ishwaran, H.1
Zarepour, M.2
-
20
-
-
0034307468
-
Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants
-
Jackson, J.D. and Gorovsky, M.A. (2000) Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants. Nucleic Acids Res., 28, 3811-3816.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 3811-3816
-
-
Jackson, J.D.1
Gorovsky, M.A.2
-
21
-
-
0030478021
-
A likely histone H2A.F/Z variant in Saccharomyces cerevisiae
-
Jackson, J.D. et al. (1996) A likely histone H2A.F/Z variant in Saccharomyces cerevisiae. Trends Biochem. Sci., 21, 466-467.
-
(1996)
Trends Biochem. Sci
, vol.21
, pp. 466-467
-
-
Jackson, J.D.1
-
22
-
-
0142052944
-
A Bayesian networks approach for predicting protein-protein interactions from genomic data
-
Jansen, R. et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 302, 449-453.
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
-
23
-
-
65549161909
-
Gaussian process regression bootstrapping: Exploring the effects of uncertainty in time course data
-
Kirk, P.D. and Stumpf, M.P. (2009) Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. Bioinformatics, 25, 1300-1306.
-
(2009)
Bioinformatics
, vol.25
, pp. 1300-1306
-
-
Kirk, P.D.1
Stumpf, M.P.2
-
24
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
Lee, I. et al. (2004) A probabilistic functional network of yeast genes. Science, 306, 1555-1558.
-
(2004)
Science
, vol.306
, pp. 1555-1558
-
-
Lee, I.1
-
25
-
-
33747875436
-
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
-
Liu, X. et al. (2006) Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. Bioinformatics, 22, 1737-1744.
-
(2006)
Bioinformatics
, vol.22
, pp. 1737-1744
-
-
Liu, X.1
-
26
-
-
34848855728
-
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
-
Liu, X. et al. (2007) Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. BMC Bioinformatics, 8, 283.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 283
-
-
Liu, X.1
-
27
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
Lockhart, D.J. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680.
-
(1996)
Nat. Biotechnol
, vol.14
, pp. 1675-1680
-
-
Lockhart, D.J.1
-
28
-
-
49949096013
-
Gene Ontology term overlap as a measure of gene functional similarity
-
Mistry, M. and Pavlidis, P. (2008) Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics, 9, 327.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 327
-
-
Mistry, M.1
Pavlidis, P.2
-
29
-
-
34548749776
-
Context-sensitive data integration and prediction of biological networks
-
Myers, C.L. and Troyanskaya, O.G. (2007) Context-sensitive data integration and prediction of biological networks. Bioinformatics, 23, 2322-2330.
-
(2007)
Bioinformatics
, vol.23
, pp. 2322-2330
-
-
Myers, C.L.1
Troyanskaya, O.G.2
-
30
-
-
33745113181
-
Discovery of biological networks from diverse functional genomic data
-
Myers, C.L. et al. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol., 6, R114.
-
(2005)
Genome Biol
, vol.6
-
-
Myers, C.L.1
-
32
-
-
77950032550
-
Markov chain sampling methods for Dirichlet process mixture models
-
Neal, R.M. (2000) Markov chain sampling methods for Dirichlet process mixture models. J. Comput. Graph. Stat., 9, 249-265.
-
(2000)
J. Comput. Graph. Stat
, vol.9
, pp. 249-265
-
-
Neal, R.M.1
-
33
-
-
21644433245
-
Normalized random measures driven by increasing additive processes
-
Nieto-Barajas, L. et al. (2004) Normalized random measures driven by increasing additive processes. Ann. Stat., 32, 2343-2360.
-
(2004)
Ann. Stat
, vol.32
, pp. 2343-2360
-
-
Nieto-Barajas, L.1
-
34
-
-
0034841844
-
The tandem affinity purification (TAP) method: A general procedure of protein complex purification
-
Puig, O. et al. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods, 24, 218-229.
-
(2001)
Methods
, vol.24
, pp. 218-229
-
-
Puig, O.1
-
35
-
-
84950632109
-
Objective criteria for the evaluation of clustering methods
-
Rand, W. (1971) Objective criteria for the evaluation of clustering methods. J. Am. Stat. Assoc., 66, 846-850.
-
(1971)
J. Am. Stat. Assoc
, vol.66
, pp. 846-850
-
-
Rand, W.1
-
36
-
-
79955803023
-
The infinite Gaussian mixture model
-
Solla, S.A., Leen, T.K. and Müller, K.-R. (eds.) MIT Press, Cambridge, MA
-
Rasmussen, C.E. (2000) The infinite Gaussian mixture model. In: Solla, S.A., Leen, T.K. and Mü ller, K.-R. (eds.) Advances in Neural Information Processing Systems, Vol. 12. MIT Press, Cambridge, MA, pp. 554-560.
-
(2000)
Advances in Neural Information Processing Systems
, vol.12
, pp. 554-560
-
-
Rasmussen, C.E.1
-
38
-
-
33746067911
-
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
-
Reiss, D.J. et al. (2006) Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics, 7, 280.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 280
-
-
Reiss, D.J.1
-
39
-
-
23444452564
-
Probabilistic model of the human protein-protein interaction network
-
Rhodes, D.R. et al. (2005) Probabilistic model of the human protein-protein interaction network. Nat. Biotechnol., 23, 951-959.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 951-959
-
-
Rhodes, D.R.1
-
40
-
-
0032828715
-
A generic protein purification method for protein complex characterization and proteome exploration
-
Rigaut, G. et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol., 17, 1030-1032.
-
(1999)
Nat. Biotechnol
, vol.17
, pp. 1030-1032
-
-
Rigaut, G.1
-
41
-
-
57249105121
-
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
-
Rogers, S. et al. (2008) Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics, 24, 2894-2900.
-
(2008)
Bioinformatics
, vol.24
, pp. 2894-2900
-
-
Rogers, S.1
-
42
-
-
79958175783
-
Infinite factorization of multiple non-parametric views
-
Rogers, S. et al. (2010) Infinite factorization of multiple non-parametric views. Mach. Learn., 79, 201-226.
-
(2010)
Mach. Learn
, vol.79
, pp. 201-226
-
-
Rogers, S.1
-
43
-
-
80054736950
-
Asymptotic behaviour of the posterior distribution in overfitted mixture models
-
Rousseau, J. and Mengersen, K. (2011) Asymptotic behaviour of the posterior distribution in overfitted mixture models. J. R. Stat. Soc. Series B Stat. Methodol., 73, 689-710.
-
(2011)
J. R. Stat. Soc. Series B Stat. Methodol
, vol.73
, pp. 689-710
-
-
Rousseau, J.1
Mengersen, K.2
-
44
-
-
0034721645
-
Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes
-
Santisteban, M.S. et al. (2000) Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell, 103, 411-422.
-
(2000)
Cell
, vol.103
, pp. 411-422
-
-
Santisteban, M.S.1
-
45
-
-
77954207953
-
Discovering transcriptional modules by Bayesian data integration
-
Savage, R.S. et al. (2010) Discovering transcriptional modules by Bayesian data integration. Bioinformatics, 26, i158-i167.
-
(2010)
Bioinformatics
, vol.26
-
-
Savage, R.S.1
-
46
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena, M. et al. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
-
47
-
-
70449331456
-
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
-
Shen, R. et al. (2009) Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics, 25, 2906-2912.
-
(2009)
Bioinformatics
, vol.25
, pp. 2906-2912
-
-
Shen, R.1
-
48
-
-
0023948705
-
Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
-
Solomon, M.J. et al. (1988)Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell, 53, 937-947.
-
(1988)
Cell
, vol.53
, pp. 937-947
-
-
Solomon, M.J.1
-
49
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark, C. et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stark, C.1
-
50
-
-
77955516707
-
Understanding GPU programming for statistical computation: Studies in massively parallel massive mixtures
-
Suchard, M.A. et al. (2010) Understanding GPU programming for statistical computation: studies in massively parallel massive mixtures. J. Comput. Graph. Stat., 19, 419-438.
-
(2010)
J. Comput. Graph. Stat
, vol.19
, pp. 419-438
-
-
Suchard, M.A.1
-
51
-
-
0038492417
-
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
-
Troyanskaya, O.G. et al. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl Acad. Sci. USA, 100, 8348-8353.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 8348-8353
-
-
Troyanskaya, O.G.1
-
52
-
-
84870277977
-
Bayesian joint modeling of multiple gene networks and diverse genomic data to identify target genes of a transcription factor
-
Wei, P. and Pan, W. (2012) Bayesian joint modeling of multiple gene networks and diverse genomic data to identify target genes of a transcription factor. Ann. Appl. Stat., 6, 334-355.
-
(2012)
Ann. Appl. Stat
, vol.6
, pp. 334-355
-
-
Wei, P.1
Pan, W.2
-
53
-
-
8144227773
-
Combining biological networks to predict genetic interactions
-
Wong, S.L. et al. (2004) Combining biological networks to predict genetic interactions. Proc. Natl Acad. Sci. USA, 101, 15682-15687.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 15682-15687
-
-
Wong, S.L.1
-
54
-
-
0037667290
-
Clustering gene-expression data with repeated measurements
-
Yeung, K.Y. et al. (2003) Clustering gene-expression data with repeated measurements. Genome Biol., 4, R34.
-
(2003)
Genome Biol
, vol.4
-
-
Yeung, K.Y.1
-
55
-
-
80055083654
-
Patient-specific data fusion defines prognostic cancer subtypes
-
Yuan, Y. et al. (2011) Patient-specific data fusion defines prognostic cancer subtypes. PLoS Comput. Biol., 7, e1002227.
-
(2011)
PLoS Comput. Biol
, vol.7
-
-
Yuan, Y.1
|