-
1
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The gene ontology consortium
-
Ashburner, M., C. Ball, J. Blake, D. Botstein, H. Butler, J. Cherry, A. Davis, K. Dolinski, S. Dwight, J. Eppig, et al. (2000): "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium." Nature Genetics, 25, 25-29.
-
(2000)
Nature Genetics
, vol.25
, 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
-
2
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Y. Hochberg (1995): "Controlling the false discovery rate: a practical and powerful approach to multiple testing," J. Roy. Statist. Soc. Ser. B, 57, 289-300.
-
(1995)
J. Roy. Statist. Soc. Ser. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
3
-
-
0035149551
-
Remodeling of yeast genome expression in response to environmental changes
-
Causton, H., B. Ren, S. Koh, C. Harbison, E. Kanin, E. Jennings, T. Lee, H. True, E. Lander, and R. Young (2001): "Remodeling of Yeast Genome Expression in Response to Environmental Changes," Molecular Biology Of The Cell, 12, 323-337.
-
(2001)
Molecular Biology of the Cell
, vol.12
, pp. 323-337
-
-
Causton, H.1
Ren, B.2
Koh, S.3
Harbison, C.4
Kanin, E.5
Jennings, E.6
Lee, T.7
True, H.8
Lander, E.9
Young, R.10
-
4
-
-
33947153898
-
Estimation of a covariance matrix with zeros
-
Chaudhuri, S., M. Drton, and T. Richardson (2007): "Estimation of a covariance matrix with zeros," Biometrika, 94, 199-216.
-
(2007)
Biometrika
, vol.94
, pp. 199-216
-
-
Chaudhuri, S.1
Drton, M.2
Richardson, T.3
-
7
-
-
0002403935
-
Block-relaxation algorithms in statistics
-
Springer-Verlag
-
de Leeuw, J. (1994): "Block-relaxation algorithms in statistics," in Information System and Data Analysis, Springer-Verlag, 308-325.
-
(1994)
Information System and Data Analysis
, pp. 308-325
-
-
De Leeuw, J.1
-
8
-
-
35348890683
-
On testing the significance of sets of genes
-
Efron, B. and R. Tibshirani (2007): "On testing the significance of sets of genes," Annals of Applied Statistics, 1, 107-129.
-
(2007)
Annals of Applied Statistics
, vol.1
, pp. 107-129
-
-
Efron, B.1
Tibshirani, R.2
-
10
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown (2000): "Genomic expression programs in the response of yeast cells to environmental changes," Mol Bio Cell, 11, 4241-4257.
-
(2000)
Mol Bio Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
11
-
-
0036728274
-
The genomics of yeast responses to environmental stress and starvation
-
Gasch, A. P. and M. Werner-Washburne (2002): "The genomics of yeast responses to environmental stress and starvation," Funct. Integr. Genomics, 2, 181-192.
-
(2002)
Funct. Integr. Genomics
, vol.2
, pp. 181-192
-
-
Gasch, A.P.1
Werner-Washburne, M.2
-
12
-
-
0010774684
-
Concavity and estimation
-
Haberman, S. (1989): "Concavity and Estimation," Annals of Statistics, 17, 1631-1661.
-
(1989)
Annals of Statistics
, vol.17
, pp. 1631-1661
-
-
Haberman, S.1
-
13
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C., D. Gordon, T. Lee, N. Rinaldi, K. Macisaac, T. Danford, N. Hannett, J. Tagne, D. Reynolds, J. Yoo, et al. (2004): "Transcriptional regulatory code of a eukaryotic genome," Nature, 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.1
Gordon, D.2
Lee, T.3
Rinaldi, N.4
MacIsaac, K.5
Danford, T.6
Hannett, N.7
Tagne, J.8
Reynolds, D.9
Yoo, J.10
-
14
-
-
33745242945
-
Functional hierarchical models for identifying genes with different time-course expression profiles
-
Hong, F. and H. Li (2006): "Functional Hierarchical Models for Identifying Genes with Different Time-Course Expression Profiles," Biometrics, 62, 534-544.
-
(2006)
Biometrics
, vol.62
, pp. 534-544
-
-
Hong, F.1
Li, H.2
-
15
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker, T., O. Ozier, B. Schwikowski, and A. Siegel (2002): "Discovering regulatory and signalling circuits in molecular interaction networks," Bioinformatics, 18, S233-S240.
-
(2002)
Bioinformatics
, vol.18
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.4
-
16
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
Ideker, T., V. Thorsson, J. Ranish, R. Christmas, J. Buhler, J. Eng, R. Bumgarner, D. Goodlett, R. Aebersold, and L. Hood (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
Thorsson, V.2
Ranish, J.3
Christmas, R.4
Buhler, J.5
Eng, J.6
Bumgarner, R.7
Goodlett, D.8
Aebersold, R.9
Hood, L.10
-
17
-
-
33947524259
-
Estimating high-dimensional directed acyclic graphs with the PC-algorithm
-
Kalisch, M. and P. B̈uhlmann (2007): "Estimating high-dimensional directed acyclic graphs with the PC-algorithm," The Journal of Machine Learning Research, 8, 613-636.
-
(2007)
The Journal of Machine Learning Research
, vol.8
, pp. 613-636
-
-
Kalisch, M.1
B̈uhlmann, P.2
-
18
-
-
0035032570
-
Statistical design and the analysis of gene expression microarray data
-
DOI 10.1017/S0016672301005055
-
Kerr, M. and A. Churchill (2001a): "Statistical design and the analysis of gene expression microarray data," Genetics Research, 77, 123-128. (Pubitemid 32390329)
-
(2001)
Genetical Research
, vol.77
, Issue.2
, pp. 123-128
-
-
Kathleen Kerr, M.1
Churchill, G.A.2
-
19
-
-
0000884487
-
Experimental design for gene expression microarrays
-
Kerr, M. and G. Churchill (2001b): "Experimental design for gene expression microarrays," Biostatistics, 2, 183-201.
-
(2001)
Biostatistics
, vol.2
, pp. 183-201
-
-
Kerr, M.1
Churchill, G.2
-
21
-
-
41549138299
-
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae
-
Lee, I., Z. Li, and E. Marcotte (2007): "An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae," PLoS ONE, 2, e988.
-
(2007)
PLoS ONE
, vol.2
-
-
Lee, I.1
Li, Z.2
Marcotte, E.3
-
22
-
-
84950419603
-
Newton-Raphson and em algorithms for linear mixed-effects models for repeated-measures data
-
Lindstrom, M. J. and D. M. Bates (1988): "Newton-Raphson and EM algorithms for linear mixed-effects models for repeated-measures data," Journal of the American Statistical Association, 83, 1014-1022.
-
(1988)
Journal of the American Statistical Association
, vol.83
, pp. 1014-1022
-
-
Lindstrom, M.J.1
Bates, D.M.2
-
24
-
-
34250407557
-
A trace inequality of John von Neumann
-
Mirsky, L. (1975): "A trace inequality of John von Neumann," Monatshefte f̈ur Mathematik, 79, 303-306.
-
(1975)
Monatshefte f̈ur Mathematik
, vol.79
, pp. 303-306
-
-
Mirsky, L.1
-
25
-
-
0000416018
-
A general procedure for obtaining maximum likelihood estimates in generalized regression models
-
Oberhofer, W. and J. Kmenta (1974): "A General Procedure for Obtaining Maximum Likelihood Estimates in Generalized Regression Models." Econometrica, 42, 579-590
-
(1974)
Econometrica
, vol.42
, pp. 579-590
-
-
Oberhofer, W.1
Kmenta, J.2
-
26
-
-
14644430468
-
Calculating the statistical significance of changes in pathway activity from gene expression data
-
Rahnenf̈uhrer, J., F. S. Domingues, J. Maydt, and T. Lengauer (2004): "Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data," Statistical Applications in Genetics and Molecular Biology, 3, 1055.
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
, pp. 1055
-
-
Rahnenf̈uhrer, J.1
Domingues, F.S.2
Maydt, J.3
Lengauer, T.4
-
28
-
-
41949107946
-
MMG: A probabilistic tool to identify submodules of metabolic pathways
-
Sanguinetti, G., J. Noirel, and P. Wright (2008): "MMG: a probabilistic tool to identify submodules of metabolic pathways," Bioinformatics, 24, 1078-1084.
-
(2008)
Bioinformatics
, vol.24
, pp. 1078-1084
-
-
Sanguinetti, G.1
Noirel, J.2
Wright, P.3
-
29
-
-
0004242197
-
-
New York: John Wiley & Sons, Inc
-
Searle, S. R. (1971): Linear Models, New York: John Wiley & Sons, Inc.
-
(1971)
Linear Models
-
-
Searle, S.R.1
-
30
-
-
61749083981
-
Analysis of gene sets based on the underlying regulatory network
-
Shojaie, A. and G. Michailidis (2009): "Analysis of Gene Sets Based on the Underlying Regulatory Network," Journal of Computational Biology, 16, 407-426.
-
(2009)
Journal of Computational Biology
, vol.16
, pp. 407-426
-
-
Shojaie, A.1
Michailidis, G.2
-
31
-
-
77953107844
-
Penalized Likelihood Methods for Estimation of sparse high dimensional directed acyclic graphs
-
(to appear)
-
Shojaie, A. and G. Michailidis (2010): "Penalized Likelihood Methods for Estimation of sparse high dimensional directed acyclic graphs," Biometrika (to appear).
-
(2010)
Biometrika
-
-
Shojaie, A.1
Michailidis, G.2
-
32
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A., P. Tamayo, V. Mootha, S. Mukherjee, B. Ebert, M. Gillette, A. Paulovich, S. Pomeroy, T. Golub, E. Lander, et al. (2005): "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles," Proceedings of the National Academy of Sciences, 102, 15545-15550.
-
(2005)
Proceedings of the National Academy of Sciences
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.3
Mukherjee, S.4
Ebert, B.5
Gillette, M.6
Paulovich, A.7
Pomeroy, S.8
Golub, T.9
Lander, E.10
-
33
-
-
26444608611
-
Discovering statistically significant pathways in expression profiling studies
-
Tian, L., S. A. Greenberg, S. W. Kong, J. Altschuler, I. S. Kohane, and P. J. Park (2005): "Discovering statistically significant pathways in expression profiling studies," Proceedings of the National Academy of Sciences, 102, 13544-13549.
-
(2005)
Proceedings of the National Academy of Sciences
, vol.102
, pp. 13544-13549
-
-
Tian, L.1
Greenberg, S.A.2
Kong, S.W.3
Altschuler, J.4
Kohane, I.S.5
Park, P.J.6
-
34
-
-
38849163722
-
Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model
-
Wei, P. and W. Pan (2008): "Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model," Bioinformatics, 24, 404-411.
-
(2008)
Bioinformatics
, vol.24
, pp. 404-411
-
-
Wei, P.1
Pan, W.2
-
35
-
-
34547844074
-
A Markov random field model for network-based analysis of genomic data
-
Wei, Z. and H. Li (2007): "A Markov random field model for network-based analysis of genomic data," Bioinformatics, 23, 1537-1544.
-
(2007)
Bioinformatics
, vol.23
, pp. 1537-1544
-
-
Wei, Z.1
Li, H.2
-
36
-
-
42649117688
-
A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
-
Wei, Z. and H. Li (2008): "A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data," Annals of Applied Statistics, 2, 408-429.
-
(2008)
Annals of Applied Statistics
, vol.2
, pp. 408-429
-
-
Wei, Z.1
Li, H.2
-
37
-
-
0036319960
-
Design issues for cDNA microarray experiments
-
Yang, Y. and T. Speed (2002): "Design issues for cDNA microarray experiments," Nature reviews. Genetics(Print), 3, 579-588.
-
(2002)
Nature Reviews. Genetics(Print)
, vol.3
, pp. 579-588
-
-
Yang, Y.1
Speed, T.2
-
38
-
-
34248546301
-
A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors
-
Yoneya, T. and H. Mamitsuka (2007): "A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors," Bioinformatics, 23, 842-849.
-
(2007)
Bioinformatics
, vol.23
, pp. 842-849
-
-
Yoneya, T.1
Mamitsuka, H.2
|