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Items: 1 to 20 of 262

1.

Reverse engineering of gene networks with LASSO and nonlinear basis functions.

Gustafsson M, Hörnquist M, Lundström J, Björkegren J, Tegnér J.

Ann N Y Acad Sci. 2009 Mar;1158:265-75. doi: 10.1111/j.1749-6632.2008.03764.x.

PMID:
19348648
2.

Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge.

Marbach D, Mattiussi C, Floreano D.

Ann N Y Acad Sci. 2009 Mar;1158:102-13. doi: 10.1111/j.1749-6632.2008.03945.x.

PMID:
19348636
3.

A gene network simulator to assess reverse engineering algorithms.

Di Camillo B, Toffolo G, Cobelli C.

Ann N Y Acad Sci. 2009 Mar;1158:125-42. doi: 10.1111/j.1749-6632.2008.03756.x.

PMID:
19348638
4.

Inferring gene networks: dream or nightmare?

Baralla A, Mentzen WI, de la Fuente A.

Ann N Y Acad Sci. 2009 Mar;1158:246-56. doi: 10.1111/j.1749-6632.2008.04099.x.

PMID:
19348646
5.

Reverse engineering genetic networks using evolutionary computation.

Noman N, Iba H.

Genome Inform. 2005;16(2):205-14.

PMID:
16901103
6.

Inference of regulatory gene interactions from expression data using three-way mutual information.

Watkinson J, Liang KC, Wang X, Zheng T, Anastassiou D.

Ann N Y Acad Sci. 2009 Mar;1158:302-13. doi: 10.1111/j.1749-6632.2008.03757.x.

PMID:
19348651
7.

Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data.

Shimamura T, Imoto S, Yamaguchi R, Miyano S.

Genome Inform. 2007;19:142-53.

PMID:
18546512
8.

Computational methods for discovering gene networks from expression data.

Lee WP, Tzou WS.

Brief Bioinform. 2009 Jul;10(4):408-23. doi: 10.1093/bib/bbp028. Review.

PMID:
19505889
9.

Inferring gene networks: dream or nightmare?

Scheinine A, Mentzen WI, Fotia G, Pieroni E, Maggio F, Mancosu G, de la Fuente A.

Ann N Y Acad Sci. 2009 Mar;1158:287-301. doi: 10.1111/j.1749-6632.2008.04100.x.

PMID:
19348650
10.

List-decoding methods for inferring polynomials in finite dynamical gene network models.

Dingel J, Milenkovic O.

Bioinformatics. 2009 Jul 1;25(13):1686-93. doi: 10.1093/bioinformatics/btp281. Epub 2009 Apr 28.

PMID:
19401400
11.

Replaying the evolutionary tape: biomimetic reverse engineering of gene networks.

Marbach D, Mattiussi C, Floreano D.

Ann N Y Acad Sci. 2009 Mar;1158:234-45. doi: 10.1111/j.1749-6632.2008.03944.x.

PMID:
19348645
12.

Reverse-engineering transcriptional modules from gene expression data.

Michoel T, De Smet R, Joshi A, Marchal K, Van de Peer Y.

Ann N Y Acad Sci. 2009 Mar;1158:36-43. doi: 10.1111/j.1749-6632.2008.03943.x.

PMID:
19348630
13.

A network inference workflow applied to virulence-related processes in Salmonella typhimurium.

Taylor RC, Singhal M, Weller J, Khoshnevis S, Shi L, McDermott J.

Ann N Y Acad Sci. 2009 Mar;1158:143-58. doi: 10.1111/j.1749-6632.2008.03762.x.

PMID:
19348639
14.

Network inference by combining biologically motivated regulatory constraints with penalized regression.

Parisi F, Koeppl H, Naef F.

Ann N Y Acad Sci. 2009 Mar;1158:114-24. doi: 10.1111/j.1749-6632.2008.03751.x.

PMID:
19348637
15.

Reverse engineering cellular networks.

Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A.

Nat Protoc. 2006;1(2):662-71.

PMID:
17406294
16.

Learning regulatory programs that accurately predict differential expression with MEDUSA.

Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C.

Ann N Y Acad Sci. 2007 Dec;1115:178-202. Epub 2007 Oct 12.

PMID:
17934055
17.

Lessons from the DREAM2 Challenges.

Stolovitzky G, Prill RJ, Califano A.

Ann N Y Acad Sci. 2009 Mar;1158:159-95. doi: 10.1111/j.1749-6632.2009.04497.x.

PMID:
19348640
18.

Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm.

Wang M, Augusto Benedito V, Xuechun Zhao P, Udvardi M.

Mol Biosyst. 2010 Jun;6(6):988-98. doi: 10.1039/b917571g. Epub 2010 Feb 19.

PMID:
20485743
19.

Fast calculation of pairwise mutual information for gene regulatory network reconstruction.

Qiu P, Gentles AJ, Plevritis SK.

Comput Methods Programs Biomed. 2009 May;94(2):177-80. doi: 10.1016/j.cmpb.2008.11.003. Epub 2009 Jan 22.

PMID:
19167129
20.

Inferring gene regulatory networks from time series data using the minimum description length principle.

Zhao W, Serpedin E, Dougherty ER.

Bioinformatics. 2006 Sep 1;22(17):2129-35. Epub 2006 Jul 15.

PMID:
16845143

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