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Computational Biology

181. Thomas, R., Mehrotra, S., Papoutsakis, E.T., Hatzimanikatis., V., "A model-based optimization framework for the inference of gene regulatory networks from DNA array data", Bioinformatics. 20: 3221-3235 (2004). (Download PDF)

198. Thomas, R., Paredes, CJ, Mehrotra, S., Papoutsakis, E.T., Hatzimanikatis., V., "A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data", BMC Bioinformatics 8: 228 (2007). (Download PDF)

207. Senger, R. S. and E. T. Papoutsakis, Genome-Scale Model for Clostridium acetobutylicum. Part 1. Reverse engineering to resolve network gaps, pathway discovery, and extrapolation to other clostridia. Biotechnol. Bioeng. in revision (2008). 208. Senger, R. S. and E. T. Papoutsakis, Genome-Scale Model for Clostridium acetobutylicum. Part 1: Development of Specific Proton Flux States and Numerically-Determined Sub-Spaces. Biotechnol. Bioeng. in revision (2008).

209. Senger, R.S. and Papoutsakis, E.T. 2008. Genome-Scale Model for Clostridium acetobutylicum. Part 2: Development of Specific Proton Flux States and Numerically-Determined Sub-Spaces. Biotechnol. Bioeng. 101: 1053-71.

227. Chen, Y., Indurthi, I., Jones, S. W. and Papoutsakis, E. T. Non-coding RNAs on clostridial genomes: the more genomes in the genus the better, and the importance of the physiological niche. Submitted (2010).(Download PDF)