Howard Ochman

Professor, Ecology & Evolutionary Biology

Director, Microbial Diversity Institute

howard.ochman@yale.edu
West Campus Building 42A, Room 271A

My research attempts to elucidate the factors that influence the generation and maintenance of variation in bacterial genomes.

More on the Microbial Diversity Institute

Academic History

Ph.D., University of Rochester 1984
M.S., University of Rochester 1979
B.A., Vassar College 1975

Professional History

Professor, Depts. of Biochemistry & Molecular Biophysics, Ecology & Evolutionary Biology, University of Arizona 1998-2009
Assistant Professor to Full Professor, Department of Biology, University of Rochester 1992-1998
Research Assistant, Department of Genetics, Washington University School of Medicine 1987-1991
Postdoctoral, University of California, Berkeley 1984-1987

Awards and Honors

University of Arizona Regents' Professor, elected 2008
Fellow, American Association for the Advancement of Science, 2006
Fellow, American Academy of Microbiology, 2001
National Institutes of Health, Research Career Development Award
Lucille P. Markey Charitable Trust, Center Award for New Faculty, Washington University

Current Research Support

National Institutes of Health, R01GM-74738 "Elucidating the Origins and Functions of Unknown Genes" (Howard Ochman, PI)
National Institutes of Health, R01GM-56120 "Genome Erosion in Infectious Microorganisms"-funded through 2007 (Howard Ochman, PI)
National Institutes of Health, R01DK-066288 "Comparative Community Genomics of Gut Microbiota"-funded through 2007 (Collaborator; Pilar Francino, PI)

Scientific Activities

Editorial Board, Genome Research, 2005-2007
Editorial Board, Environmental Microbiology, 2005-2007
Associate Editor, Journal of Molecular Evolution, 2005-2007

Dissertations Directed

M. Pilar Francino (Ph.D. 1999)
Ulfar Bergthorsson (Ph.D. 1997)

Recent Publications (last three years)

Vaishampayan, P.A., J.V. Kuehl, J.L. Froula, J.L. Morgan, H. Ochman, M.P. Francino (2010) Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol. Evol. 2010:53-66. pdf

Engelbrektson, A., V. Kunin, K.C. Wrighton, N. Zvenigorodsky, F. Chen, H. Ochman, P. Hugenholtz (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. Jan 21. [Epub ahead of print] pdf

Jarvik, T., C. Smillie, E.A. Groisman, H. Ochman (2010) Short-term signatures of evolutionary change in the Salmonella enterica serovar Typhimurium 14028 genome. J. Bacteriol. 192:560-7. pdf

Stavrinides, J., A. No, H. Ochman (2010) A single genetic locus in the phytopathogen Pantoea stewartii enables gut colonization and pathogenicity in an insect host. Environ. Microbiol. 12:147-55. pdf

Ochman, H. and R. Raghavan. (2009) Excavating the functional landscape of bacterial cells (Perspective). Science 326:1200-1. pdf

Kuo, C.H., H. Ochman. (2009) Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol. Direct. 4:35. pdf

Ochman, H. (2009) Afterword: Genomics Update update. Environ. Microbiol. 11:2193. pdf

Kunin, V., A. Engelbrektson, H. Ochman, P. Hugenholtz (2009) Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ. Microbiol. 2009 Aug 27. [Epub ahead of print] pdf

Kuo, C.H., N.A. Moran, H. Ochman (2009) The consequences of genetic drift for bacterial genome complexity. Genome Res. 19:1450-4. pdf

Ochman, H. (2009) Radical views of the Tree of Life. Environ. Microbiol. 11:731-2. pdf

Stavrinides, J., J.K. McCloskey, H. Ochman (2009) The pea aphid as both host and vector for the phytopathogenic bacterium, Pseudomonas syringae. Appl. Environ. Microbiol. 75:2230-5. pdf

Kuo, C.H., H. Ochman (2009) Deletional bias across the three domains of life. Genome Biol. Evol. 1:145-152. pdf

Kuo C.H., H. Ochman (2009) The fate of new bacterial genes. FEMS Microbiol. Rev. 33:38-43. pdf

Narra, H.P., M.H. Cordes, H. Ochman (2008) Structural features and the persistence of acquired proteins. Proteomics. 8:4772-81. pdf

Marri, P.R., L.K. Harris, K. Houmiel, S.C. Slater, and H. Ochman (2008) The effect of chromosome geometry on genetic diversity. Genetics. 179:511-516. pdf

van Passel, M.W., P.R. Marri, and H. Ochman (2008) The emergence and fate of horizontally acquired genes in Escherichia coli. PLoS Comput. Biol. 4:e1000059. pdf