-
1
-
-
15944399178
-
Sparse graphical models for exploring gene expression data
-
A. Dobra, C. Hans, B. Jones, J. Nevins, G. Yao, andM.West, "Sparse graphical models for exploring gene expression data, " Journal of Multivariate Analysis, vol. 90, no. 1, pp. 196-212, 2004.
-
(2004)
Journal of Multivariate Analysis
, vol.90
, Issue.1
, pp. 196-212
-
-
Dobra, A.1
Hans, C.2
Jones, B.3
Nevins, J.4
Yao, G.5
West, M.6
-
2
-
-
73149097219
-
Regularized estimation of large-scale gene association networks using graphical gaussian models
-
N. Krämer, J. Schäfer, and A. Boulesteix, "Regularized estimation of large-scale gene association networks using graphical gaussian models, " BMC Bioinformatics, vol. 10, no. 1, p. 384, 2009.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.1
, pp. 384
-
-
Krämer, N.1
Schäfer, J.2
Boulesteix, A.3
-
3
-
-
0001038826
-
Covariance selection
-
A. P. Dempster, "Covariance selection, " Biometrics, vol. 28, no. 1, pp. 157-175, 1972.
-
(1972)
Biometrics
, vol.28
, Issue.1
, pp. 157-175
-
-
Dempster, A.P.1
-
4
-
-
33747163541
-
High-dimensional graphs and variable selection with the lasso
-
N.Meinshausen and P. Buhlmann, "High-dimensional graphs and variable selection with the lasso, " The Annals of Statistics, vol. 34, no. 3, pp. 1436-1462, 2006.
-
(2006)
The Annals of Statistics
, vol.34
, Issue.3
, pp. 1436-1462
-
-
Meinshausen, N.1
Buhlmann, P.2
-
5
-
-
33947115409
-
Model selection and estimation in the gaussian graphical model
-
M. Yuan and Y. Lin, "Model selection and estimation in the gaussian graphical model, " Biometrika, vol. 94, no. 1, p. 19, 2007.
-
(2007)
Biometrika
, vol.94
, Issue.1
, pp. 19
-
-
Yuan, M.1
Lin, Y.2
-
6
-
-
45849134070
-
Sparse inverse covariance estimation with the lasso
-
J. Friedman, T. Hastie, and R. Tibshirani, "Sparse inverse covariance estimation with the lasso, " Biostatistics, vol. 9, no. 3, pp. 432-441, 2007.
-
(2007)
Biostatistics
, vol.9
, Issue.3
, pp. 432-441
-
-
Friedman, J.1
Hastie, T.2
Tibshirani, R.3
-
7
-
-
77951455815
-
High-dimensional ising model selection using l1-regularized logistic regression
-
P. Ravikumar, M. Wainwright, and J. Lafferty, "High-dimensional ising model selection using l1-regularized logistic regression, " The Annals of Statistics, vol. 38, no. 3, pp. 1287-1319, 2010.
-
(2010)
The Annals of Statistics
, vol.38
, Issue.3
, pp. 1287-1319
-
-
Ravikumar, P.1
Wainwright, M.2
Lafferty, J.3
-
9
-
-
50649089207
-
Rna-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
J. Marioni, C. Mason, S. Mane, M. Stephens, and Y. Gilad, "Rna-seq: An assessment of technical reproducibility and comparison with gene expression arrays, " Genome Research, vol. 18, no. 9, pp. 1509-1517, 2008.
-
(2008)
Genome Research
, vol.18
, Issue.9
, pp. 1509-1517
-
-
Marioni, J.1
Mason, C.2
Mane, S.3
Stephens, M.4
Gilad, Y.5
-
10
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mrna-seq experiments
-
J.Bullard, E. Purdom, K. Hansen, and S. Dudoit, "Evaluation of statistical methods for normalization and differential expression in mrna-seq experiments, " BMC Bioinformatics, vol. 11, no. 1, p. 94, 2010.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.1
, pp. 94
-
-
Bullard, J.1
Purdom, E.2
Hansen, K.3
Dudoit, S.4
-
11
-
-
84866634300
-
Normalization, testing, and false discovery rate estimation for rna-sequencing data
-
J. Li, D. Witten, I. Johnstone, and R. Tibshirani, "Normalization, testing, and false discovery rate estimation for rna-sequencing data, " Biostatistics, 2011.
-
(2011)
Biostatistics
-
-
Li, J.1
Witten, D.2
Johnstone, I.3
Tibshirani, R.4
-
12
-
-
0347444723
-
Micrornas: Genomics, biogenesis, mechanism, and function
-
D. P. Bartel, "Micrornas: Genomics, biogenesis, mechanism, and function, " Cell, vol. 116, no. 2, pp. 281-297, 2004.
-
(2004)
Cell
, vol.116
, Issue.2
, pp. 281-297
-
-
Bartel, D.P.1
-
13
-
-
64549119707
-
Statistical inferences for isoform expression in rna-seq
-
H. Jiang and W. Wong, "Statistical inferences for isoform expression in rna-seq, " Bioinformatics, vol. 25, no. 8, pp. 1026-1032, 2009.
-
(2009)
Bioinformatics
, vol.25
, Issue.8
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.2
-
14
-
-
85052549687
-
A two-parameter generalized poisson model to improve the analysis of rna-seq data
-
S. Srivastava and L. Chen, "A two-parameter generalized poisson model to improve the analysis of rna-seq data, " Nucleic Acids Research, vol. 38, no. 17, p. e170, 2010.
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.17
-
-
Srivastava, S.1
Chen, L.2
-
15
-
-
77953176036
-
A scaling normalization method for differential expression analysis of rna-seq data
-
M. Robinson and A. Oshlack, "A scaling normalization method for differential expression analysis of rna-seq data, " Genome Biol, vol. 11, no. 3, p. R25, 2010.
-
(2010)
Genome Biol
, vol.11
, Issue.3
-
-
Robinson, M.1
Oshlack, A.2
-
16
-
-
77958471357
-
Differential expression analysis for sequence count data
-
S. Anders and W. Huber, "Differential expression analysis for sequence count data, " Genome Biol, vol. 11, no. 10, p. R106, 2010.
-
(2010)
Genome Biol
, vol.11
, Issue.10
-
-
Anders, S.1
Huber, W.2
-
17
-
-
70450277253
-
The nonparanormal: Semiparametric estimation of high dimensional undirected graphs
-
H. Liu, J. Lafferty, and L.Wasserman, "The nonparanormal: Semiparametric estimation of high dimensional undirected graphs, " The Journal of Machine Learning Research, vol. 10, pp. 2295-2328, 2009.
-
(2009)
The Journal of Machine Learning Research
, vol.10
, pp. 2295-2328
-
-
Liu, H.1
Lafferty, J.2
Wasserman, L.3
-
18
-
-
84857070635
-
Copula gaussian graphical models and their application to modeling functional disability data
-
A. Dobra and A. Lenkoski, "Copula gaussian graphical models and their application to modeling functional disability data, " The Annals of Applied Statistics, vol. 5, no. 2A, pp. 969-993, 2011.
-
(2011)
The Annals of Applied Statistics
, vol.5
, Issue.2 A
, pp. 969-993
-
-
Dobra, A.1
Lenkoski, A.2
-
19
-
-
84883365004
-
-
Arxiv preprint arXiv:1206.6488
-
H. Liu, F. Han, M. Yuan, J. Lafferty, and L.Wasserman, "The nonparanormal skeptic, " Arxiv preprint arXiv:1206.6488, 2012.
-
(2012)
The Nonparanormal Skeptic
-
-
Liu, H.1
Han, F.2
Yuan, M.3
Lafferty, J.4
Wasserman, L.5
-
20
-
-
84873376907
-
Regularized rank-based estimation of high-dimensional nonparanormal graphical models
-
L. Xue and H. Zou, "Regularized rank-based estimation of high-dimensional nonparanormal graphical models, " Forthcoming in Ann. Statist, 2012.
-
(2012)
Forthcoming in Ann. Statist
-
-
Xue, L.1
Zou, H.2
-
22
-
-
21844520724
-
Bayesian graphical models for discrete data
-
D. Madigan, J. York, and D. Allard, "Bayesian graphical models for discrete data, " International Statistical Review/Revue Internationale de Statistique, vol. 63, no. 2, pp. 215-232, 1995.
-
(1995)
International Statistical Review/Revue Internationale de Statistique
, vol.63
, Issue.2
, pp. 215-232
-
-
Madigan, D.1
York, J.2
Allard, D.3
-
23
-
-
0004047518
-
-
USA: Oxford University Press
-
S. Lauritzen, Graphical Models., USA: Oxford University Press, 1996, vol. 17.
-
(1996)
Graphical Models
, vol.17
-
-
Lauritzen, S.1
-
25
-
-
65749118363
-
Graphical models, exponential families, and variational inference
-
M. Wainwright and M. Jordan, "Graphical models, exponential families, and variational inference, " Foundations and Trends in Machine Learning, vol. 1, no. 1-2, pp. 1-305, 2008.
-
(2008)
Foundations and Trends in Machine Learning
, vol.1
, Issue.1-2
, pp. 1-305
-
-
Wainwright, M.1
Jordan, M.2
-
26
-
-
0000913755
-
Spatial interaction and the statistical analysis of lattice systems
-
J. Besag, "Spatial interaction and the statistical analysis of lattice systems, " Journal of the Royal Statistical Society. Series B (Methodological), vol. 36, no. 2, pp. 192-236, 1974.
-
(1974)
Journal of the Royal Statistical Society. Series B (Methodological)
, vol.36
, Issue.2
, pp. 192-236
-
-
Besag, J.1
-
27
-
-
84877773753
-
Graphical models via generalized linear models
-
E. Yang, P. Ravikumar, G. Allen, and Z. Liu, "Graphical models via generalized linear models, " Advances in Neural Information Processing Systems, vol. 25, pp. 1367-1375, 2012.
-
(2012)
Advances in Neural Information Processing Systems
, vol.25
, pp. 1367-1375
-
-
Yang, E.1
Ravikumar, P.2
Allen, G.3
Liu, Z.4
-
29
-
-
84946357749
-
An efficient method of estimating seemingly unrelated regressions and tests for aggregation bias
-
A. Zellner, "An efficient method of estimating seemingly unrelated regressions and tests for aggregation bias, " Journal of the American Statistical Association, vol. 57, no. 298, pp. 348-368, 1962.
-
(1962)
Journal of the American Statistical Association
, vol.57
, Issue.298
, pp. 348-368
-
-
Zellner, A.1
-
30
-
-
0031489565
-
A graphical characterization of lattice conditional independencemodels
-
S. A. Andersson, D. Madigan, M. D. Perlman, and C. M. Triggs, "A graphical characterization of lattice conditional independencemodels, " Annals of Mathematics and Artificial Intelligence, vol. 21, no. 1, pp. 27-50, 1997.
-
(1997)
Annals of Mathematics and Artificial Intelligence
, vol.21
, Issue.1
, pp. 27-50
-
-
Andersson, S.A.1
Madigan, D.2
Perlman, M.D.3
Triggs, C.M.4
-
32
-
-
84860635352
-
On learning discrete graphical models using group-sparse regularization
-
A. Jalali, P. Ravikumar, V. Vasuki, S. Sanghavi, U. ECE, and U. CS, "On learning discrete graphical models using group-sparse regularization, " in Proceedings of the International Conference on Artificial Intelligence and Statistics (AISTATS), 2011.
-
(2011)
Proceedings of the International Conference on Artificial Intelligence and Statistics (AISTATS)
-
-
Jalali, A.1
Ravikumar, P.2
Vasuki, V.3
Sanghavi, S.4
-
33
-
-
77950537175
-
Regularization paths for generalized linear models via coordinate descent
-
J. Friedman, T. Hastie, and R. Tibshirani, "Regularization paths for generalized linear models via coordinate descent, " Journal of Statistical Software, vol. 33, no. 1, p. 1, 2010.
-
(2010)
Journal of Statistical Software
, vol.33
, Issue.1
, pp. 1
-
-
Friedman, J.1
Hastie, T.2
Tibshirani, R.3
-
34
-
-
77958487535
-
Stability selection
-
N.Meinshausen and P. Buhlmann, "Stability selection, " Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol. 72, no. 4, pp. 417-473, 2010.
-
(2010)
Journal of the Royal Statistical Society: Series B (Statistical Methodology)
, vol.72
, Issue.4
, pp. 417-473
-
-
Meinshausen, N.1
Buhlmann, P.2
-
35
-
-
0037238291
-
An em algorithm for multivariate poisson distribution and related models
-
D. Karlis, "An em algorithm for multivariate poisson distribution and related models, " Journal of Applied Statistics, vol. 30, no. 1, pp. 63-77, 2003.
-
(2003)
Journal of Applied Statistics
, vol.30
, Issue.1
, pp. 63-77
-
-
Karlis, D.1
-
36
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by rna-seq
-
A. Mortazavi, B. Williams, K. McCue, L. Schaeffer, and B. Wold, "Mapping and quantifying mammalian transcriptomes by rna-seq, " Nature Methods, vol. 5, no. 7, pp. 621-628, 2008.
-
(2008)
Nature Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
37
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
J. Leek, R. Scharpf, H. Bravo, D. Simcha, B. Langmead, W. Johnson, D. Geman, K. Baggerly, and R. Irizarry, "Tackling the widespread and critical impact of batch effects in high-throughput data, " Nature Reviews Genetics, vol. 11, no. 10, pp. 733-739, 2010.
-
(2010)
Nature Reviews Genetics
, vol.11
, Issue.10
, pp. 733-739
-
-
Leek, J.1
Scharpf, R.2
Bravo, H.3
Simcha, D.4
Langmead, B.5
Johnson, W.6
Geman, D.7
Baggerly, K.8
Irizarry, R.9
-
38
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas Research Network, "Comprehensive molecular portraits of human breast tumours, " Nature, vol. 490, no. 7418, pp. 61-70, 2012.
-
(2012)
Nature
, vol.490
, Issue.7418
, pp. 61-70
-
-
-
39
-
-
0038483826
-
Emergence of scaling in random networks
-
5439
-
A. Barabási and R. Albert, "Emergence of scaling in random networks, " Science, vol. 286, no. 5439, p. 509, 1999.
-
(1999)
Science
, vol.286
, pp. 509
-
-
Barabási, A.1
Albert, R.2
-
40
-
-
36849078711
-
Let-7 regulates self renewal and tumorigenicity of breast cancer cells
-
Dec
-
F. Yu, H. Yao, P. Zhu, X. Zhang, Q. Pan, C. Gong, Y. Huang, X. Hu, F. Su, J. Lieberman, and E. Song, "Let-7 regulates self renewal and tumorigenicity of breast cancer cells, " Cell, vol. 131, no. 6, pp. 1109-1123, Dec. 2007.
-
(2007)
Cell
, vol.131
, Issue.6
, pp. 1109-1123
-
-
Yu, F.1
Yao, H.2
Zhu, P.3
Zhang, X.4
Pan, Q.5
Gong, C.6
Huang, Y.7
Hu, X.8
Su, F.9
Lieberman, J.10
Song, E.11
-
41
-
-
79851479816
-
MicroRNA expression analysis in triple-negative (ER, PR and Her2/neu) breast cancer
-
Feb
-
J. Radojicic, A. Zaravinos, T. Vrekoussis, M. Kafousi, D. A. Spandidos, and E. N. Stathopoulos, "MicroRNA expression analysis in triple-negative (ER, PR and Her2/neu) breast cancer, " Cell Cycle (Georgetown, Tex.), vol. 10, no. 3, pp. 507-517, Feb. 2011.
-
(2011)
Cell Cycle (Georgetown, Tex.)
, vol.10
, Issue.3
, pp. 507-517
-
-
Radojicic, J.1
Zaravinos, A.2
Vrekoussis, T.3
Kafousi, M.4
Spandidos, D.A.5
Stathopoulos, E.N.6
-
42
-
-
77950665077
-
Therapeutic silencing of miR-10b inhibits metastasis in a mouse mammary tumor model
-
Apr
-
L. Ma, F. Reinhardt, E. Pan, J. Soutschek, B. Bhat, E. G. Marcusson, J. Teruya-Feldstein, G. W. Bell, and R. A. Weinberg, "Therapeutic silencing of miR-10b inhibits metastasis in a mouse mammary tumor model, " Nature Biotechnology, vol. 28, no. 4, pp. 341-347, Apr. 2010.
-
(2010)
Nature Biotechnology
, vol.28
, Issue.4
, pp. 341-347
-
-
Ma, L.1
Reinhardt, F.2
Pan, E.3
Soutschek, J.4
Bhat, B.5
Marcusson, E.G.6
Teruya-Feldstein, J.7
Bell, G.W.8
Weinberg, R.A.9
-
43
-
-
78549249846
-
Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor alpha in breast cancer cells
-
Nov
-
P. de Souza Rocha Simonini, A. Breiling, N. Gupta, M. Malekpour, M. Youns, R. Omranipour, F.Malekpour, S. Volinia, C. M. Croce, H. Najmabadi, S. Diederichs, O. Sahin, D.Mayer, F.Lyko, J.D. Hoheisel, and Y. Riazalhosseini, "Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor alpha in breast cancer cells, " Cancer Research, vol. 70, no. 22, pp. 9175-9184, Nov. 2010.
-
(2010)
Cancer Research
, vol.70
, Issue.22
, pp. 9175-9184
-
-
De Souza, R.S.P.1
Breiling, A.2
Gupta, N.3
Malekpour, M.4
Youns, M.5
Omranipour, R.6
Malekpour, F.7
Volinia, S.8
Croce, C.M.9
Najmabadi, H.10
Diederichs, S.11
Sahin, O.12
Mayer, D.13
Lyko, F.14
Hoheisel, J.D.15
Riazalhosseini, Y.16
-
44
-
-
22844440427
-
Identification of hundreds of conserved and nonconserved human micrornas
-
I. Bentwich, A. Avniel, Y. Karov, R. Aharonov, S. Gilad, O. Barad, A. Barzilai, P. Einat, U. Einav, and E. Meiri et al., "Identification of hundreds of conserved and nonconserved human micrornas, " Nature Genetics, vol. 37, no. 7, pp. 766-770, 2005
-
(2005)
Nature Genetics
, vol.37
, Issue.7
, pp. 766-770
-
-
Bentwich, I.1
Avniel, A.2
Karov, Y.3
Aharonov, R.4
Gilad, S.5
Barad, O.6
Barzilai, A.7
Einat, P.8
Einav, U.9
Meiri Et Al., E.10
|