Adam Arkin

Professor, Bioengineering Faculty Scientist, Physical Biosciences Division, Lawrence Berkeley National Laboratory Director, The Virtual Institute of Microbial Stress and Survival, Lawrence Berkeley National Laboratory Core Member, UCB/UCSF Graduate Group in Bioengineering 309B Hildebrand mailcode: 3220 (510) 643-5678 fax: (510) 643-3721 This e-mail address is being protected from spambots. You need JavaScript enabled to view it http://genomics.lbl.gov Membership effective July 2000

Research Interests

The Arkin laboratory seeks to uncover the evolutionary design principles of cellular networks and populations and to exploit them for applications. To do so they are developing a framework to effectively combine comparative functional genomics, quantitative measurement of cellular dynamics, biophysical modeling of cellular networks, and cellular circuit design to ultimately facilitate applications in health, the environment, and bioenergy.

Research Summary

My laboratory works on systems biology, cellular biophysics, comparative functional genomics, and synthetic biology. We aim to elucidate the evolutionary design principles of cellular networks and exploit these for design new function and behaviors in cells using a combination of experiment, theory and computation. Projects range from understanding the role of stochastic gene expression and memory in the stress response of Bacillus subtilis, to studies on the evolution of signal transduction pathways in bacteria, to detailed experiments and modeling of the stochastic control of HIV-1 gene expression and its role in latency, to the design and implementation of a tumor killing bacteria. In support of these projects we also develop technology for the statistical analysis of biological data, comparative functional genomics and model-based design of experiments as well as physical theory of cellular processes.

Selected Publications

Samoilov, M.S. and Arkin, A.P. (2006) Deviant effects in molecular reaction pathways. Nat Biotechnol, 24, 1235-1240.
Arkin, A.P. and Fletcher, D.A. (2006) Fast, cheap and somewhat in control. Genome Biol, 7, 114.
Anderson, J.C., Clarke, E.J., Arkin, A.P. and Voigt, C.A. (2006) Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria. J Mol Biol, 355, 619-627.
Alm, E., Huang, K. and Arkin, A. (2006) The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation. PLoS Comput Biol, 2.
Wolf, D.M., Vazirani, V.V. and Arkin, A.P. (2005) Diversity in times of adversity: probabilistic strategies in microbial survival games. J Theor Biol, 234, 227-253.
Weinberger, L.S., Burnett, J.C., Toettcher, J.E., Arkin, A.P. and Schaffer, D.V. (2005) Stochastic Gene Expression in a Lentiviral Positive-Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity. Cell, 122, 169-182.
Voigt, C.A., Wolf, D.M. and Arkin, A.P. (2005) The Bacillus subtilis sin Operon: An Evolvable Network Motif. Genetics, 169, 1187-1202.
Wolf, D.M. and Arkin, A.P. (2003) Motifs, modules and games in bacteria. Curr Opin Microbiol, 6, 125-134.