Metabolic Engineering and Systems Biology Laboratory

Downloads

1. Network Component Analysis:
   • NCA toolbox v. 2.3 for Matlab 7 (released Feb. 19, 2007)
   • NCA proofs (Liao et al. PNAS 2003, 15522-15527 appendices.)
   • NCA Modules and Data files (Kao et al. PNAS 2004, 641-646.)
2. Software for Statistical Analysis of Microarray data: lcDNA.
   • Tseng et al. NAR 2001
   • Hyduke et al. OMICS 2003
3. Supplemental information for papers:
   • Huang et al. PNAS 2001, 11771-11776:
     • Competition Assay Protocol
     • Software for Competition Assay
   • Oh et al. JBC 2002, 277, 13175-13183: Microarray data file
   • Sabatti et al. NAR 2002, 2886-2893: E. coli Operon Map
4. A synthetic gene-matabolic oscillator
   • links to the paper: Fung et al. Nature, 435, 118-122.
   • Download Supplementary material
5. Brynildsen, M.P., Tran, L. M. and Liao, J.C. (2006) A Gibbs Sampler for the Identification of Gene Expression and Network Connectivity Consistency. Bioinformatics, 22, 3040-3046.
   • link to paper: Brynildsen et al. Bioinformatics, 22, 3040-3046
   • Software and Supplementary Information: download software uploaded 5/8/2007
   • Network visualization: Osprey - SIF uploaded 3/30/2007

6. Brynildsen, M.P.; Wu, T.Y.;  Jang, S.S. and Liao, J.C. (2007) Biological Network Mapping and Source Signal Deduction, Bioinformatics, 23: 1783-1791

   • link to Network Component Mapping  modules

7. Tran, L.M, Hydguke, D.R., and Liao, J.C. Trimming of Mammalian Transcriptional Networks using Network Component Analysis, submitted to Bioinformatics,  Download Matlab code here

8. Ensemble Modeling: Download Matlab Code and Examples.

9.  "Ensemble Modeling and the Mathematical Modeling of Metabolic Networks" by Rizk & Liao. Download example here.