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Items: 1 to 20 of 239

1.

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
2.

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
3.

A new multiple regression approach for the construction of genetic regulatory networks.

Zhang SQ, Ching WK, Tsing NK, Leung HY, Guo D.

Artif Intell Med. 2010 Feb-Mar;48(2-3):153-60. doi: 10.1016/j.artmed.2009.11.001. Epub 2009 Dec 5.

PMID:
19963359
4.

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
5.

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
6.

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
7.

Structural systems identification of genetic regulatory networks.

Xiong H, Choe Y.

Bioinformatics. 2008 Feb 15;24(4):553-60. doi: 10.1093/bioinformatics/btm623. Epub 2008 Jan 5.

PMID:
18175769
8.

Reconstruction of gene regulatory networks under the finite state linear model.

Ruklisa D, Brazma A, Viksna J.

Genome Inform. 2005;16(2):225-36.

PMID:
16901105
9.

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
10.

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
11.

Bridge and brick network motifs: identifying significant building blocks from complex biological systems.

Huang CY, Cheng CY, Sun CT.

Artif Intell Med. 2007 Oct;41(2):117-27. Epub 2007 Sep 7.

PMID:
17825540
12.

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
13.

Predicting biological system objectives de novo from internal state measurements.

Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA.

BMC Bioinformatics. 2008 Jan 24;9:43. doi: 10.1186/1471-2105-9-43.

14.

A declarative constraint-based method for analyzing discrete genetic regulatory networks.

Corblin F, Tripodi S, Fanchon E, Ropers D, Trilling L.

Biosystems. 2009 Nov;98(2):91-104. doi: 10.1016/j.biosystems.2009.07.007. Epub 2009 Aug 5.

PMID:
19664681
15.

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
16.

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
17.

Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data.

Vu TT, Vohradsky J.

Genomics. 2009 May;93(5):426-33. doi: 10.1016/j.ygeno.2009.01.006. Epub 2009 Feb 5.

18.

Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit.

Eriksson O, Brinne B, Zhou Y, Björkegren J, Tegnér J.

IET Syst Biol. 2009 Mar;3(2):113-29. doi: 10.1049/iet-syb.2007.0028.

PMID:
19292565
19.

A new model for investigating the evolution of transcription control networks.

Jenkins DJ, Stekel DJ.

Artif Life. 2009 Summer;15(3):259-91. doi: 10.1162/artl.2009.Stekel.006.

PMID:
19254178
20.

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