People

Education

• B.S., 1995, University of Illinois, Urbana
• M.S., 1997, University of California, Riverside
• Ph.D., 2001, University of Washington, Seattle
• Postdoc, 2005, University of California, Berkeley/Lawrence Berkeley National Laboratory

Research Interests

Research in my group includes both computational/theoretical and experimental approaches to understanding the evolution of microorganisms, emphasizing a ‘systems-level’ perspective. Some areas of special interest include:

• Tools for detecting natural selection in microbes
• The evolutionary origin of gene families
• Mining metagenomic sequence data
• Experimental evolution of microbes
• Modeling bacterial ecology
• Gene regulatory networks in bacteria
• Protein structure and design

Teaching Interests

I have enjoyed teaching a variety of classes at MIT, spanning my own diverse interests in microbiology, computer algorithms, and thermodynamics of biomolecules. I am currently looking forward to teaching a new class on microbial evolution and genetics.

Selected Publications

1. Shapiro B.J. and Alm E.J. Comparing Patterns of Natural Selection Across Species Using Selective Signatures. PloS Genetics. In press.
2. Price, M.N., Arkin, A.P. and Alm, E.J.(*) (2006) The life-cycle of operons. PLoS Genetics, 2, e96
3. 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, e143.
4. Alm, E. and Arkin, A.P. (2003) Biological networks. Curr Opin Struct Biol, 13, 193-202.
5. Alm, E. and Baker, D. (1999) Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci U S A, 96, 11305-11310.