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Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference

Minh Quach, Nicolas Brunel, and Florence d'Alché-Buc

Bioinformatics (Oxford, England) 23 (23), 3209-16 (01 Dec 2007)

info:pmid/18042557 | info:doi/10.1093/bioinformatics/btm510

Posted by hpshanahan and 2 others to systems biology time-series on Thu Aug 28 2008 at 16:51 UTC | info | related

Inferring gene regulatory networks from temporal expression profiles under time-delay and noise

Computational Biology and Chemistry 31 (4), 239 (2007)

info:doi/10.1016/j.compbiolchem.2007.03.013

Posted by hpshanahan to systems biology time-series on Thu Aug 28 2008 at 16:49 UTC | info | related

Constructing transcriptional regulatory networks

Alexandre Blais and Brian David Dynlacht

Genes & development. 19 (13), 1499-1511 (01 Jul 2005)

info:pmid/15998805 | info:doi/10.1101/gad.1325605

Posted by hpshanahan and 1 other to systems biology network transcription motif search on Wed Jul 16 2008 at 13:41 UTC | info | related

Yeast systems biology to unravel the network of life

R Mustacchi, S Hohman, and J Nielsen

Yeast 23 (3), 227 (2006)

info:doi/10.1002/yea.1357

Posted by hpshanahan to yeast systems biology on Wed Jul 16 2008 at 13:21 UTC | info | related

Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks

Adriano V Werhli, Marco Grzegorczyk, and Dirk Husmeier

Bioinformatics (Oxford, England) 22 (20), 2523-31 (15 Oct 2006)

info:pmid/16844710 | info:doi/10.1093/bioinformatics/btl391

Posted by hpshanahan and 2 others to systems biology partial correlation on Mon Jul 14 2008 at 14:42 UTC | info | related

Reverse engineering gene networks using singular value decomposition and robust regression

M Yeung, J Tegner, and J Collins

Proceedings of the National Academy of Sciences 99 (9), 6163 (30 Apr 2002)

info:doi/10.1073/pnas.092576199

Posted by hpshanahan and 1 other to time-series systems biology on Sun Jul 13 2008 at 19:42 UTC | info | related

Integration of Known Transcription Factor Binding Site Information and Gene Expression Data to Advance from Co-Expression to Co-Regulation

Maarten Clements et al.

Genomics, Proteomics & Bioinformatics 5 (2), 86-101 (2077)

Posted by hpshanahan to motif search time-series systems biology on Sun Jul 13 2008 at 19:40 UTC | info | related

Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization

Paul Spellman et al.

Molecular Biology of the Cell 9 (12), 3273-97 (01 Dec 1998)

Posted by hpshanahan and 5 others to Microarray systems biology on Sun Jul 13 2008 at 15:14 UTC | info | related

Using Bayesian Networks to Analyze Expression Data

Nir Friedman et al.

Journal of Computational Biology 7 (3-4), 601-20 (01 Aug 2000)

Posted by hpshanahan and 1 other to bayesian systems biology on Sun Jul 13 2008 at 15:09 UTC | info | related

Ensemble learning of genetic networks from time-series expression data

Dougu Nam, Sung Yoon, and Jihyun Kim

Bioinformatics 23 (23), 3225 (01 Dec 2007)

info:pmid/17977884 | info:doi/10.1093/bioinformatics/btm514

Posted by hpshanahan and 1 other to time-series systems biology on Wed Jul 09 2008 at 22:04 UTC | info | related

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