Gene Tyson

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I am a post-doctoral researcher in the DeLong Lab working on the analysis of metagenomic and metatranscriptomic data from several location in the global ocean.

Gene W. Tyson

Post-Doctoral Associate, September, 2006 - Present

Massachusetts Institute of Technology

Room 48-336

15 Vassar Street Cambridge, MA 02139 USA


University of California, Berkeley (2001-2006)

Ph.D., Microbiology

Department of Environmental Science, Policy and Management (Ecosystem Sciences)

Dissertation: A community genomic investigation of a low complexity acid mine drainage biofilms (Prof. Jill F. Banfield, advisor)

University of Queensland, Australia (1998-1999)

B.Sc. (Hons), Microbiology (Class 1)

Department of Microbiology and Parasitology

Thesis: Quantification of polyphosphate accumulating organisms using slot blot hybridization (Prof. Linda Blackall and Dr. Philip Hugenholtz)

University of Queensland, Australia (1996-1998)

B.Sc., Microbiology

Research experience

Massachusetts Institute of Technology (2006 - present)

Postdoctoral Associate, Marine Microbial Metagenomics

Department of Civil and Environmental Engineering

Prof. Ed Delong

University of California, Berkeley,

Ecosystem Sciences (2001 - 2006)

Graduate Student (PhD), Community Genomics

Prof. Jillian F. Banfield, advisor

University of Queensland, Australia,

Department of Microbiology and Parasitology (1999 – 2001)

Research Assistant, Microbial Ecology

Drs. Linda Blackall and Philip Hugenholtz, advisors

University of Queensland, Australia,

Department of Microbiology and Parasitology (1998 – 1999)

Honors Student, Microbial Ecology

Drs. Linda Blackall and Philip Hugenholtz, advisors

University of Queensland, Australia,

Department of Microbiology and Parasitology (1997)

Undergraduate Researcher, Microbial Ecology

Dr. Philip Hugenholtz, advisor

University of Queensland, Australia,

Department of Microbiology and Parasitology (1996)

Undergraduate Summer Research Student, Microbial Ecology

Dr. Phil Bond, advisor

Honors and awards

University of California, Berkeley Chang-Lin Tien Scholarship, 2005-06.

University of California, Berkeley Continuing Graduate Student Funding Award, 2004-05.

University of California, Berkeley Prof. Earl Storie Memorial Scholarship, 2002.

CRC for Waste Management and Pollution Control, Australia Honors Research Scholarship, 1998.

University of Queensland, Australia Commendation for High Achievement, 1998.

Professional affiliations and activities

American Society for Microbiology (2001 - 2006)

Ad hoc reviewer for the following journals; Environmental Microbiology and Applied and Environmental Microbiology. Ad hoc reviewer of grant proposals for NSF.

Teaching experience

University of California, Berkeley ESPM2 - Graduate Student Instructor, Spring 2005 – 3 x 1 hr discussion section per week

Research publications

Frias-Lopez, J., Y. Shi, G.W. Tyson, M. Coleman, P. Chisholm, E. DeLong (2007). Microbial community gene expression in ocean surface waters. Proceeding of the National Academy Sciences (accepted).

Eppley, J.M., G.W. Tyson, W.M. Getz, J.F. Banfield (2007). Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinformatics.17;8:398.

Tyson, G.W., and J.F. Banfield (2007). Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology. Epub.

Tyson, G.W.*, J.M. Eppley*, W. Getz and J.F. Banfield. Genetic exchange across an archaeal species boundary. Genetics, 177:407-416.

Lo I., V.J. Denef, N.C. Verberkmoes, M.B. Shah, D. Goltsman, G. DiBartolo, G.W. Tyson, E.E Allen, R.J. Ram, J.C. Detter, P. Richardson, M.P. Thelen, R.L. Hettich, J.F. Banfield. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446:537-541

Allen E.E., G.W. Tyson, C. Detter, R. Whitaker, P. Richardson, J.F. Banfield. (2007) Genome evolution in a natural microbial strain population. Proceeding of the National Academy Sciences, 104:1883-1888.

Baker, B.J., G.W. Tyson, R.I. Webb, J. Flanagan, P. Hugenholtz, E.E. Allen and J.F. Banfield. (2006) Novel lineages of acidophilic, ultra-small Archaea revealed by community genome sequencing. Science, 314,1933-1935.

Banfield, J.F., G.W., Tyson, E.E. Allen, R.J. Whitaker (2005). The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles. Molecular Geomicrobiology Reviews in Mineralogy and Geochemistry 59, 1-7.

Tyson, G.W., and J.F. Banfield (2005). Culturing the unculturable: A community genomics prespective. Trends in Microbiology 13, 411-415.

Tyson, G.W., I. Lo, B.J. Baker, E.E. Allen, P. Hugenholtz, and J.F. Banfield (2005). Genome directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Applied and Environmental Microbiology 71, 6319-6324.

Ram, R.J., N.C.VerBerkmoes, M.P. Thelen, G.W. Tyson, B.J. Baker, R.C. Blake II, M. Shah, R.L. Hettich, and Jillian F. Banfield (2005). Community proteomics reveals key roles for “hypothetical” proteins in a natural microbial biofilm. Science 308, 1915-1920.

Tyson, G.W. and P. Hugenholtz (2005). Environmental shotgun sequence. In, Encyclopedia of genetics, genomics, proteomics and bioinformatics. John Wiley & Sons, Inc.

Tyson, G.W., J. Chapman, P. Hugenholtz, E.E. Allen, R.J. Ram, P.M. Richardson, V.V. Solovyev, E.M. Rubin, D.S. Rokhsar, and J.F. Banfield (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43.

Björnsson, L., P. Hugenholtz,G.W. Tyson and L.L. Blackall (2002). Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in activated sludges. Microbiology–SGM 148, 2309-2318.

Hugenholtz, P., G.W. Tyson, R.I. Webb, A.M. Wagner and L.L. Blackall (2001). Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Applied and Environmental Microbiology 67, 411-419.

Hugenholtz, P., G.W. Tyson and L.L. Blackall (2001). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation. In, Gene Probes: Principles and Protocols. pp. 29-42. Eds. M Aquino de Muro & R. Rapley. Methods in Molecular Biology Series no. 179. Humana Press Inc.

Tyson, G.W. (1999) Honours Thesis. Quantification of polyphosphate accumulating organisms using slot blot hybridization. University of Queensland, Brisbane, Australia.

Professional activities (selected)

2007 Invited Spealer - Metatranscriptomic analysis of microbial communities in the North Pacific Subtropical Gyre. Genomes, Medicine and the Environment (GME2007). Paradise Point Resort, San Diego, CA., October 8-10, 2007.

2007 Invited Speaker – Metagenomics informs central metabolism. 2nd ASM Conference on Integrating Metabolism and Genomics (IMAGE2). Montreal, Quebec, Canada April 30 – May 3, 2007.

2005 Invited Speaker – Community genomics-enabled investigation of ecology and evolution in a low complexity system. GRC Applied and Environmental Microbiology Conference. Connecticut College, New London, CT., July 24-29, 2005.

2004 Invited Speaker – Community genomics-enabled investigation of ecology and evolution in a low complexity system. 12th International Conference on Microbial Genomes. UCLA Conference Center, Lake Arrowhead, CA., September 8-12, 2004.

2004 Invited Speaker – Genome-direction isolation of the key nitrogen fixer in acid mine drainage. 10th International Symposium on Microbial Ecology. Cancun, Mexico, August 22-27, 2004.

2003 Invited Speaker – A culture-independent community genomics study of microorganisms associated with acid mine drainage generation. NASA Astrobiology Institute, Arizona State, February 10-12, 2003

2003 Invited Speaker – Genomics-based analysis of evolution and adaption in an acidic microbial ecosystem. 3rd ASM and TIGR Conference on Microbial Genomes, New Orleans, Louisiana, January 29 - February 1, 2003.