Ben Compani
Institute for Genomics and Bioinformatics
Department of Information and Computer Science
University of California, Irvine

In March 2012 I completed a PhD in computer science with a concentration in Informatics for Biology and Medicine at the University of California, Irvine.

My advisor was Eric Mjolsness. The main webpage for Eric's research group is Computable Plant.

My research interests lie within the realms of the simulation of biochemical reaction networks, database design and enzymatic reaction mechanisms.

My PhD dissertation focused on the schematic representation and database population strategies for Sigmoid, a biochemical network modeling tool. I also created a program, SigMech, to construct models of enzyme mechanisms.

My dissertation is available here as a PDF.


[Compani et al. 2010] B. Compani, T. Su, I. Chang, J. Cheng, K. H. Shah, T. Whisenant, Y. Dou, A. Bergmann, R. Cheong, B. Wold, L. Bardwell, A. Levchenko, P. Baldi, and E. Mjolsness, A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology. Adv Exp Med Biol. 2010; 680: 523–534. 

[Podkolodny et al. 2006] Podkolodny NL, Podkolodnaya NN, Miginsky DS, Poplavsky AS, Likhoshvai VA, Compani B, Mjolsness E. An integration of the descriptions of gene networks and their models presented in Sigmoid (Cellerator) and GeneNet, 5th International Conference on the Bioinformatics of Genome Regulation and Function (BGRS-2006), Volume 3, pp. 86-90.

A technical report on Sigmoid is available here as a PDF.