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Items: 1 to 20 of 113

1.

Simulating systems genetics data with SysGenSIM.

Pinna A, Soranzo N, Hoeschele I, de la Fuente A.

Bioinformatics. 2011 Sep 1;27(17):2459-62. doi: 10.1093/bioinformatics/btr407. Epub 2011 Jul 6.

2.

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods.

Schaffter T, Marbach D, Floreano D.

Bioinformatics. 2011 Aug 15;27(16):2263-70. doi: 10.1093/bioinformatics/btr373. Epub 2011 Jun 22.

3.

SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies.

Chung RH, Shih CC.

BMC Bioinformatics. 2013 Jun 20;14:199. doi: 10.1186/1471-2105-14-199.

4.

Gene expression complex networks: synthesis, identification, and analysis.

Lopes FM, Cesar RM, Costa Lda F.

J Comput Biol. 2011 Oct;18(10):1353-67. doi: 10.1089/cmb.2010.0118. Epub 2011 May 6.

PMID:
21548810
5.

REVEAL--visual eQTL analytics.

Jäger G, Battke F, Nieselt K.

Bioinformatics. 2012 Sep 15;28(18):i542-i548. doi: 10.1093/bioinformatics/bts382.

6.

SynBioSS: the synthetic biology modeling suite.

Hill AD, Tomshine JR, Weeding EM, Sotiropoulos V, Kaznessis YN.

Bioinformatics. 2008 Nov 1;24(21):2551-3. doi: 10.1093/bioinformatics/btn468. Epub 2008 Aug 30.

7.
8.

WGCNA: an R package for weighted correlation network analysis.

Langfelder P, Horvath S.

BMC Bioinformatics. 2008 Dec 29;9:559. doi: 10.1186/1471-2105-9-559.

9.

PYCHEM: a multivariate analysis package for python.

Jarvis RM, Broadhurst D, Johnson H, O'Boyle NM, Goodacre R.

Bioinformatics. 2006 Oct 15;22(20):2565-6. Epub 2006 Jul 31.

10.

SIMoNe: Statistical Inference for MOdular NEtworks.

Chiquet J, Smith A, Grasseau G, Matias C, Ambroise C.

Bioinformatics. 2009 Feb 1;25(3):417-8. doi: 10.1093/bioinformatics/btn637. Epub 2008 Dec 10.

11.
12.

TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees.

Posada D, Maxwell TJ, Templeton AR.

Bioinformatics. 2005 May 1;21(9):2130-2. Epub 2005 Jan 28.

13.

In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks.

Liu G, Neelamegham S.

Bioinformatics. 2008 Apr 15;24(8):1109-11. doi: 10.1093/bioinformatics/btn061. Epub 2008 Feb 28.

14.

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T.

BMC Bioinformatics. 2005 Jun 1;6:135.

15.

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks.

Verbeke LP, Cloots L, Demeester P, Fostier J, Marchal K.

Bioinformatics. 2013 May 15;29(10):1308-16. doi: 10.1093/bioinformatics/btt142. Epub 2013 Apr 16.

16.

Stochastic simulation GUI for biochemical networks.

Vallabhajosyula RR, Sauro HM.

Bioinformatics. 2007 Jul 15;23(14):1859-61. Epub 2007 Jun 22.

17.

Gene network inference via structural equation modeling in genetical genomics experiments.

Liu B, de la Fuente A, Hoeschele I.

Genetics. 2008 Mar;178(3):1763-76. doi: 10.1534/genetics.107.080069. Epub 2008 Feb 3.

18.

GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

Rigbolt KT, Vanselow JT, Blagoev B.

Mol Cell Proteomics. 2011 Aug;10(8):O110.007450. doi: 10.1074/mcp.O110.007450. Epub 2011 May 20.

19.

Logical modelling of regulatory networks with GINsim 2.3.

Naldi A, Berenguier D, Fauré A, Lopez F, Thieffry D, Chaouiya C.

Biosystems. 2009 Aug;97(2):134-9. doi: 10.1016/j.biosystems.2009.04.008. Epub 2009 May 6.

PMID:
19426782
20.

From genotype to phenotype: computer-based modeling of gene expression with STELLA II.

Hargrove JL, Hulsey MG, Summers AO.

Biotechniques. 1993 Dec;15(6):1096-101.

PMID:
7507334
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