-
1
-
-
0034710924
-
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
-
Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A. 2000;97(22):12182-6.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, Issue.22
, pp. 12182-12186
-
-
Butte, A.J.1
Tamayo, P.2
Slonim, D.3
Golub, T.R.4
Kohane, I.S.5
-
2
-
-
34848903220
-
From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data
-
Opgen-Rhein R, Strimmer K. From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Syst Biol. 2007;1:37.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 37
-
-
Opgen-Rhein, R.1
Strimmer, K.2
-
3
-
-
79952635505
-
Principles and strategies for developing network models in cancer
-
Pe'er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell. 2011;144(6):864-73.
-
(2011)
Cell
, vol.144
, Issue.6
, pp. 864-873
-
-
Pe'er, D.1
Hacohen, N.2
-
4
-
-
84856083002
-
Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut
-
Shulzhenko N, Morgun A, Hsiao W, Battle M, Yao M, Gavrilova O, Orandle M, Mayer L, Macpherson AJ, McCoy KD, et al. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nat Med. 2011;17(12):1585-93.
-
(2011)
Nat Med
, vol.17
, Issue.12
, pp. 1585-1593
-
-
Shulzhenko, N.1
Morgun, A.2
Hsiao, W.3
Battle, M.4
Yao, M.5
Gavrilova, O.6
Orandle, M.7
Mayer, L.8
Macpherson, A.J.9
McCoy, K.D.10
-
5
-
-
33947305781
-
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Favera RD, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinf. 2006;7 Suppl 1:S7.
-
(2006)
BMC Bioinf
, vol.7
, pp. S7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Favera, R.D.6
Califano, A.7
-
6
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science. 2003;302(5643):249-55.
-
(2003)
Science
, vol.302
, Issue.5643
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
7
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004;5(2):101-13.
-
(2004)
Nat Rev Genet
, vol.5
, Issue.2
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
8
-
-
70249134919
-
Molecular networks as sensors and drivers of common human diseases
-
Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009;461(7261):218-23.
-
(2009)
Nature
, vol.461
, Issue.7261
, pp. 218-223
-
-
Schadt, E.E.1
-
9
-
-
78649976005
-
An integrated approach to uncover drivers of cancer
-
Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D. An integrated approach to uncover drivers of cancer. Cell. 2010;143(6):1005-17.
-
(2010)
Cell
, vol.143
, Issue.6
, pp. 1005-1017
-
-
Akavia, U.D.1
Litvin, O.2
Kim, J.3
Sanchez-Garcia, F.4
Kotliar, D.5
Causton, H.C.6
Pochanard, P.7
Mozes, E.8
Garraway, L.A.9
Pe'er, D.10
-
10
-
-
85027917673
-
Investigating a holobiont: Microbiota perturbations and transkingdom networks
-
Greer R, Dong X, Morgun A, Shulzhenko N. Investigating a holobiont: Microbiota perturbations and transkingdom networks. Gut Microbes. 2016;7(2):126-35.
-
(2016)
Gut Microbes
, vol.7
, Issue.2
, pp. 126-135
-
-
Greer, R.1
Dong, X.2
Morgun, A.3
Shulzhenko, N.4
-
11
-
-
43149125186
-
A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
-
Keller MP, Choi Y, Wang P, Davis DB, Rabaglia ME, Oler AT, Stapleton DS, Argmann C, Schueler KL, Edwards S, et al. A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Genome Res. 2008;18(5):706-16.
-
(2008)
Genome Res
, vol.18
, Issue.5
, pp. 706-716
-
-
Keller, M.P.1
Choi, Y.2
Wang, P.3
Davis, D.B.4
Rabaglia, M.E.5
Oler, A.T.6
Stapleton, D.S.7
Argmann, C.8
Schueler, K.L.9
Edwards, S.10
-
12
-
-
84992113655
-
Akkermansia muciniphila mediates negative effects of IFNg on glucose metabolism
-
Greer RL, Dong X, Zielke R, Vasquez-Perez S, Peremyslova E, Sikora AE, Morgun A, Shulzhenko N. Akkermansia muciniphila mediates negative effects of IFNg on glucose metabolism. Nat Commun. 2016;7:13329. doi: 10.1038/ncomms13329.
-
(2016)
Nat Commun
, vol.7
, pp. 13329
-
-
Greer, R.L.1
Dong, X.2
Zielke, R.3
Vasquez-Perez, S.4
Peremyslova, E.5
Sikora, A.E.6
Morgun, A.7
Shulzhenko, N.8
-
13
-
-
84947552418
-
Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks
-
Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut. 2015;64(11):1732-43. doi: 10.1136/gutjnl-2014-308820.
-
(2015)
Gut
, vol.64
, Issue.11
, pp. 1732-1743
-
-
Morgun, A.1
Dzutsev, A.2
Dong, X.3
Greer, R.L.4
Sexton, D.J.5
Ravel, J.6
Schuster, M.7
Hsiao, W.8
Matzinger, P.9
Shulzhenko, N.10
-
14
-
-
75149195336
-
The transcriptional network for mesenchymal transformation of brain tumours
-
Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, et al. The transcriptional network for mesenchymal transformation of brain tumours. Nature. 2010;463(7279):318-25.
-
(2010)
Nature
, vol.463
, Issue.7279
, pp. 318-325
-
-
Carro, M.S.1
Lim, W.K.2
Alvarez, M.J.3
Bollo, R.J.4
Zhao, X.5
Snyder, E.Y.6
Sulman, E.P.7
Anne, S.L.8
Doetsch, F.9
Colman, H.10
-
15
-
-
84925435486
-
Integration of genomic data enables selective discovery of breast cancer drivers
-
Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia UD, Chen BJ, Saucedo-Cuevas L, Rodriguez Barrueco R, Llobet-Navas D, et al. Integration of genomic data enables selective discovery of breast cancer drivers. Cell. 2014;159(6):1461-75.
-
(2014)
Cell
, vol.159
, Issue.6
, pp. 1461-1475
-
-
Sanchez-Garcia, F.1
Villagrasa, P.2
Matsui, J.3
Kotliar, D.4
Castro, V.5
Akavia, U.D.6
Chen, B.J.7
Saucedo-Cuevas, L.8
Rodriguez Barrueco, R.9
Llobet-Navas, D.10
-
16
-
-
84878571547
-
Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer
-
Mine KL, Shulzhenko N, Yambartsev A, Rochman M, Sanson GF, Lando M, Varma S, Skinner J, Volfovsky N, Deng T, et al. Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer. Nat Commun. 2013;4:1806.
-
(2013)
Nat Commun
, vol.4
, pp. 1806
-
-
Mine, K.L.1
Shulzhenko, N.2
Yambartsev, A.3
Rochman, M.4
Sanson, G.F.5
Lando, M.6
Varma, S.7
Skinner, J.8
Volfovsky, N.9
Deng, T.10
-
17
-
-
77649295233
-
An introduction to causal inference
-
Pearl J. An introduction to causal inference. Int J Biostat. 2010;6(2):Article 7.
-
(2010)
Int J Biostat
, vol.6
, Issue.2
-
-
Pearl, J.1
-
18
-
-
0003398906
-
Causality: models, reasoning and inference
-
Cambridge: Cambridge Univ Press
-
Pearl J. Causality: models, reasoning and inference, vol. 29. Cambridge: Cambridge Univ Press; 2000.
-
(2000)
, vol.29
-
-
Pearl, J.1
-
19
-
-
0004261364
-
The direction of time
-
Oakland: Univ of California Press
-
Reichenbach H. The direction of time, vol. 65. Oakland: Univ of California Press; 1991.
-
(1991)
, vol.65
-
-
Reichenbach, H.1
-
20
-
-
84870004702
-
Building complex networks through classical and Bayesian statistics-A comparison
-
In: XI brazilian meeting on bayesian statistics: EBEB 2012, 2012, Amparo-SP. arXiv:14092833
-
Thomas LD, Fossaluza V, Yambartsev A. Building complex networks through classical and Bayesian statistics-A comparison. In: XI brazilian meeting on bayesian statistics: EBEB 2012, 2012, Amparo-SP. AIP Conference Proceedings. arXiv:14092833. 2012;1490:323-31.
-
(2012)
AIP Conference Proceedings
, vol.1490
, pp. 323-331
-
-
Thomas, L.D.1
Fossaluza, V.2
Yambartsev, A.3
-
21
-
-
79961200389
-
GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods
-
Schaffter T, Marbach D, Floreano D. GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics. 2011;27(16):2263-70.
-
(2011)
Bioinformatics
, vol.27
, Issue.16
, pp. 2263-2270
-
-
Schaffter, T.1
Marbach, D.2
Floreano, D.3
-
22
-
-
84992096963
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57(1):289-300.
-
(1995)
J R Stat Soc Ser B
, vol.57
, Issue.1
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
23
-
-
0036020944
-
Operating characteristics and extensions of the false discovery rate procedure
-
Genovese C, Wasserman L. Operating characteristics and extensions of the false discovery rate procedure. J R Stat Soc Series B Stat Methodology. 2002;64(3):499-517.
-
(2002)
J R Stat Soc Series B Stat Methodology
, vol.64
, Issue.3
, pp. 499-517
-
-
Genovese, C.1
Wasserman, L.2
-
24
-
-
1542784653
-
Empirical Bayes analysis of a microarray experiment
-
Efron B, Tibshirani R, Storey JD, Tusher V. Empirical Bayes analysis of a microarray experiment. J Am Stat Assoc. 2001;96(456):1151-60.
-
(2001)
J Am Stat Assoc
, vol.96
, Issue.456
, pp. 1151-1160
-
-
Efron, B.1
Tibshirani, R.2
Storey, J.D.3
Tusher, V.4
-
25
-
-
0036020892
-
A direct approach to false discovery rates
-
Storey JD. A direct approach to false discovery rates. J R Stat Soc Series B Stat Methodology. 2002;64(3):479-98.
-
(2002)
J R Stat Soc Series B Stat Methodology
, vol.64
, Issue.3
, pp. 479-498
-
-
Storey, J.D.1
-
26
-
-
0345822598
-
The positive false discovery rate: A Bayesian interpretation and the q-value
-
Storey JD. The positive false discovery rate: A Bayesian interpretation and the q-value. Ann Stat. 2003;31(6):2013-35.
-
(2003)
Ann Stat
, vol.31
, Issue.6
, pp. 2013-2035
-
-
Storey, J.D.1
-
27
-
-
0035733108
-
The control of the false discovery rate in multiple testing under dependency
-
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Annals of statistics 2001:1165-1188.
-
(2001)
Annals of statistics
, pp. 1165-1188
-
-
Benjamini, Y.1
Yekutieli, D.2
-
28
-
-
79960563628
-
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
-
Skinner J, Kotliarov Y, Varma S, Mine KL, Yambartsev A, Simon R, Huyen Y, Morgun A. Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview. BMC Bioinf. 2011;12:286.
-
(2011)
BMC Bioinf
, vol.12
, pp. 286
-
-
Skinner, J.1
Kotliarov, Y.2
Varma, S.3
Mine, K.L.4
Yambartsev, A.5
Simon, R.6
Huyen, Y.7
Morgun, A.8
|