EUGENE V KOONIN, PhD
CURRICULUM VITAE AND BIBLIOGRAPHY
Senior Investigator
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38A, 8600 Rockville Pike,
Bethesda, MD 20894; Fax (301)480-9241; Telephone (301)435-5913
email koonin@ncbi.nlm.nih.gov
url: http://www.ncbi.nlm.nih.gov/CBBresearch/Koonin/
Home address: 5427 Whitley Park Terrace, Bethesda, MD 20814
Telephone (301)564-1546
PRINCIPAL RESEARCH DIRECTIONS
- Evolutionary systems biology: emergence and evolution of genomic and organizational complexity in biological systems.
Comparative analysis of sequenced genomes and automatic methods for genome-scale annotation of gene functions. - Application of comparative genomics for phylogenetic analysis, reconstruction of ancestral life forms and building large-scale evolutionary scenarios.
- Mathematical modeling of genome evolution.
- Comparative-genomic study of the major transitions in the evolution of life, such as the origin of eukaryotes.
- Origin of cells and viruses.
- Origin and evolution of viruses infecting eukaryotes.
- Evolution of eukaryotic signaling and developmental pathways from the comparative-genomic perspective.
- Testing fundamental predictions of evolutionary theory, in particular, the relationship between neutral evolution and various modes of selection, using genome-wide sequence comparison.
- Developing a general theory of evolution using principles and models of statistical physics.
EDUCATION AND TRAINING
1973-1978 Virology department, School of Biology, Moscow State University
Biology diploma /equiv.of M.Sc./, 1978
Summa cum laude
Supervisor: Professor V. I. Agol
"A comparative study on the UV resistance of single-stranded and double-stranded RNA of encephalomyocarditis virus: Evaluation of the possible contribution of host-mediated repair".
PhD - Department of Biology, Moscow State University, 1983
Supervisor: Professor V. I. Agol
"Multienzyme organization of encephalomyocarditis virus replication complexes"
PROFESSIONAL EXPERIENCE:
1996-present Senior Investigator, National Center for Biotechnology Information, National Library of Medicine, N.I.H., Bethesda, MD
2002-2008 Adjunct Professor, Department of Biology, Georgia Institute of Technology, Atlanta, GA
2002-present Adjunct Professor of Bioinformatics, Program in Bioinformatics, Boston University, Boston, MA
11/15/1991-1996 Visiting Scientist, National Center for Biotechnology Information, National Library of Medicine, N.I.H., Bethesda, MD
02/1991-05/1991 Visiting Scientist, Biology Department, Texas A&M University, College Station, TX
1990-1991 Chief, Laboratory of Gene Systematics and Bacterial Evolution, Institute of Microbiology, USSR Academy of Sciences
1989-1990 Senior Research Scientist, Laboratory of Bacterial Genetics, Institute of Microbiology, USSR Academy of Sciences
1986-1988 Senior Research Scientist, Laboratory of Virus Biochemistry, Institute of Poliomyelitis, USSR Academy of Medical Sciences
1983-1985 Research Scientist, Laboratory of Virus Biochemistry, Institute of Poliomyelitis, USSR Academy of Medical Sciences
Teaching experience and supervision of other scientists:
April 2005 - Lecture course on "Computational Genomics", Boston University
November 2003 - Lecture course on "Computational Approaches in Comparative Genomics", Georgia Institute of Technology, Atlanta, GA
November 2002 - Lecture course on "Computational Approaches in Comparative Genomics", Georgia Institute of Technology, Atlanta, GA
December 1998 - Lecture course on "Computational Biology and Genome Analysis", Moscow State University, Moscow, Russia
1997 - present - supervision of a group including 5 Staff Scientists, 4-10 Postdoctoral Fellows and 5-15 bioinformatics analysts at the National Center for Biotechnology Information (NIH)
1993 - 1996 - supervision of 2-3 Postdoctoral Fellows at the National Center for Biotechnology Information (NIH)
1990-1991 - supervision of a laboratory staff of 7 scientists at the Institute of Microbiology, USSR Academy of Sciences
Honors, awards, chairmanships
2009 - Fellow, Institute of Biology, UK
2008, Co-Organizer, Aspen Workshop in Physics "From Atoms to Organisms"
2007 Chair, Gordon Research Conference on "Structural, Functional and Evolutionary Genomics" (Hinxton, Cambridge, UK)
2005 Vice-Chair, Gordon Research Conference on "Structural, Functional and Evolutionary Genomics" (Bates College, Maine)
2005 Co-organizer, International Workshop on Complex biomolecular networks: structure, evolution, and function (Montauk, NJ)
2001- Fellow of the American College of Medical Informatics
1999 National Library of Medicine Board of Regents' Award
- 1999 Guest Editor, Current Opinions in Genetics and Development - "Genomes and Evolution"
1999 Co-organizer, Cold Spring Harbor Laboratory Workshop on Computational Biology "Bridging the Gap Between Sequence and Function" , Cold Spring Harbor, Sept 7-9
1997, 1999, 2001, 2003, 2005 Co-Chair, Conference on "In Silico Biology", Atlanta, GA.
1995 - Georgia Institute of Technology Phi-Beta-Kappa Award for the best research paper of the year
1993 - 1999. Member of the Executive Committee, International Committee for Taxonomy of Viruses
1992. Guest Editor, Seminars in Virology - "Evolution of Viral Genomes"
Editorship, editorial boards and peer review
2005- present Editor-in-Chief, Biology Direct (a new Current Science Group journal with open peer review)
2009-present Associate Editor, Genome Biology and Evolution
2005- present Editorial Advisor, Gene
1998-2008 Editor of the "Genome Analysis" section, Trends in Genetics
2001- present Associate Editor, Archaea
1997-2004 Associate Editor, In silico Biology
2008-present Editorial Board, Journal of Biology
2002- present Editorial Board, Cell Cycle
2003 - presentEditorial Board, RNA Biology
2000 - present Editorial Board, Nucleic Acids Research
2000- presentEditorial Board, Genome Biology
1999 - 2001 Editorial Board, Bioinformatics
2001-2003Editorial Board, Molecular and Cellular Proteomics
Ad hoc Guest Editor - PNAS, PLOS Biol
Peer review of manuscripts for Nature, Nature Genetics, Science, Cell, PNAS, Trends Biochem. Sci., J. Mol. Biol., Nucleic Acids Res., Proteins etc.
Professional Affiliations
American Society for Microbiology (1992); American Society for Virology (1992); American Association for the Advancement of Science (1992); New York Academy of Sciences (1993).
Invited lectures (a small selection from major meetings in 2004-2008)
June 2008 American Society of Microbiology General Meeting, Toronto, Canada
Colloquium lecture "Big Bangs of viral evolution"
May 2008, Rockefeller University, New York, Evolution Symposium. Lecture "The Origin of Eukaryotes".
June 2007, Society for Molecular Biology and Evolution General meeting, Halifax, Canada, Symposium lecture "Evolution of eukaryotic introns"
September 2006, Fondation Les Treilles Meeting on The Last Universal Cellular Ancestor, Tourtour, France; lecture: "The viral scenario of the origin of cellular life"
June 2006 American Society of Microbiology General Meeting, Toronto, Canada
Symposium lectures "Minimal gene sets of prokaryotes" and "Evolutionary genomics of lactobacilli"
May 2006, Society for Molecular Biology and Evolution General meeting, Tempe, Arizona, Symposium lecture "Evolutionary systems biology"
June 2005, 14th Albany Conversation (Albany, NY)
Plenary lecture "Universal and lineage-specific trends in protein evolution"
February 2005, Gordon Research Conference on DNA Repair (Ventura, CA)
Keynote lecture "Evolution of eukaryotic DNA repair"
July 2004, Fondation Les Treilles Meeting on Origin and Evolution of the Eukaryotic Nucleus, Tourtour, France
Lectures: "Ancestral eukaryotic gene duplications" and "Evolution of the nuclear pore complex"
June 2004, Society for Molecular Biology and Evolution General meeting, Pennsylvania State University, Symposium lecture "Universal Trends in Protein Evolution"
