Mathematical Biology

Network modeling (in refereed journals or proceedings)

Clarke, B. and Mittenthal, J. (1992). "Modularity and Reliability in the Organization of Organisms." Bulletin of Mathematical Biology, 54, 1-20.

Mittenthal, J., Clarke, B. and Levinthal, M. (1993). "Designing Bacteria". In Thinking about Biology, W. Stein and F. Varela, Eds., Addison-Wesley, Redwood City, CA, 65-104.
Clarke, B., Mittenthal, J. and Senn, M. (1993) "A Model for the Evolution of Networks of Genes." Journal of Theoretical Biology, 165, 269-289.

Mittenthal, J., Yuan, A., Clarke, B., and Scheeline, A., (1998). "Designing Metabolism: Alternative Connectivities for the Pentose Phosphate Pathway." Bull. Math. Biol. 60, 815-856.

Mittenthal, J,. Clarke, B., Waddel, T., and Fawcett, G. (2001). " A New Method for Assembling Metabolic Networks, with Application to the Krebs Citric Acid Cycle. " J. Theoretical Biology 208-3, 361-382.

Mittenthal, J.E., Clarke, B. and Scheeline, A. (2003). “How Cells Avoid Errors in Metabolic and Signaling Networks”. Int. J. Physics B. Vol. 17, No. 10, 2005-2022

Clarke, B., Fawcett, G. and Mittenthal, J. (2004). " Netscan: A Procedure for Generating Reaction Networks by Size. . J. Theor. Biol. Vol. 230, No. 4, 591-602.

See also the Software page: The Netscan software is freely available and we wrote a manual on how to use it.

Network modeling (not refereed)

Clarke, B. and Mittenthal, J. Reliability of Networks of Genes. In: Principles of Organization of Organisms, Proceedings Volume 13, Santa Fe Institute Studies in the Sciences of Complexity, pp. 333-336. Addison-Wesly, Reading, Massachusetts, 1992.

Other

Clarke, B., Mittenthal, J. and Arcuri, P. (1988). "An Optimality Criterion for Epimorphic Regeneration." Bulletin of Mathematical Biology 50, 395-434.

Clarke, B., McKay, I., Grigliatti, T., Lloyd, V., and Yuan, A. (1996). " A Markov Model for the Assembly of Heterochromatic Regions in PEV." " J. Theoretical Biology, 181, 137-155.