Alexey S. Kondrashov CV

EDUCATION:

1978 - 1984 Candidate of Biology (PhD) (Evolutionary Genetics) from Research Computing Center, Pushchino

1973 - 1978 Diploma of Higher Education (MSc) (Zoology and Genetics) from Lomonosov Moscow Federal University

RESEARCH EXPERIENCE:

2006 - Andrei R. Skovoroda Collegiate Professor, Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan

1999 - 2006 Senior Investigator, National Center for Biotechnology Information, NIH

1993 - 1999 Assistant and Associate (1996) Professor, Section of Ecology and Systematics, Cornell University

1990 - 1992 Associate Visiting Scientist, Lab. of Genetics, U. of Wisconsin, Madison; Research Associate, Department of Ecology and Evolution, U. of Chicago; Research Associate, Department of Biology, U. of Oregon, Eugene

1978 - 1990 Junior Researcher and Researcher (1986), Research Computing Center, Pushchino, USSR

TEACHING EXPERIENCE:

2006 – present University of Michigan. Evolution (a junior-level required course and an introductory graduate course), Population and Quantitative Genetics (senior-level elective course).

1993 - 1999 Cornell University. Evolution (two sophomore-level courses: for biology majors and for non-majors); Population and Evolutionary Ecology (advanced undergraduate course, with D. Winkler); Population Genetics (advanced undergraduate course); Theoretical Population Genetics (introductory graduate course); Mathematical Ecology (introductory graduate course, with C. Castillo-Chavez); Evolutionary Genetics of Reproduction (graduate course); Genetics of Structured Populations (graduate course, with R. Durret and C. Green); Speciation (advanced graduate course).

1991 University of Chicago. Evolution of Reproduction (with B. and D. Charlesworth and S. Pruett-Jones)

1984 - 1990 Moscow State University. Population Genetics; Mathematical and Computer Methods in Biology, Moscow State University (a team course)

1981 - 1989 Pushchino High School. Advanced Biology (with S. I.Rozanov)

GRANTS:

1995 - 1998 PI to NSF grant "Evolutionary Genetics of Deleterious Mutations"

1996 - 1998 PI to NSF grant "The Effect of Relaxed Selection on Population Fitness"

1999 - 2002 co-PI (later, consultant) to NSF grant "Recessive Lethals in Wild Fish Populations"

2010 - 2012 PI to Russian Government grant № 11.G34.31.0008

GEOGRAPHY OF INVITED PRESENTATIONS:

Baku (Azerbajan); Montreal, Toronto (Canada); Beijing (China); San Jose (Costa Rica); Cologne, Heidelberg, Seewiesen (Germany); Debrecen (Hungary); Sde Boker, Eilat, Haifa, Tel Aviv, Rehovot (Israel); Riga (Latvia); Ignalina, Vilnius (Lithuania); Cisinau (Moldova); Chernogolovka, Dubna, Moskva, Novosibirsk, Primorskiij, Pushchino, Sankt-Piterburg (Russia); El Escorial (Spain); Stockholm (Sweden); Bath, Brighton, Cambridge, Edinburgh, London, Liverpool, Oxford, Warwick (UK); Ann Arbor, Asilomar, Baltimore, Bethesda, Blacksburg, Boston, Boulder, Cold Spring Harbor, Atlanta, Davis, DeKalb, Madison, New Haven, Raleigh, Rochester, Salt Lake City, Santa Barbara, Santa Cruz, Snowbird, St. Paul, Stony Brook (USA); Samarkand (Uzbekistan).

PUBLICATIONS DURING THE LAST 5 YEARS:

1. Kondrashov A. S. (2008). Another step toward quantifying spontaneous mutation. Proc. Natl. Acad. Sci. USA 105, 9133-9134.

2. Assis R., Kondrashov A. S., Koonin E. V. and Kondrashov F. A. (2008). Nested genes and increasing organizational complexity of metazoan genomes. Trends Genet. 24, 475-478.

   1. Schmidt S., Gerasimova A., Kondrashov F. A., Adzhubei I. A., Kondrashov A. S. and Sunyaev S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genet. 4(11):e1000281.

3. Donmez N., Bazykin G. A., Brudno M. and Kondrashov A. S. (2009). Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi. Genetics 181, 685-690.

4. Assis R. and Kondrashov A. S. (2009). Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution. Proceedings of the National Academy of Sciences USA 106, 7079-7082.

   1. Kondrashov A. S., Povolotskaya I. S., Ivankov D. N. and Kondrashov F. A. (2010). Rate of sequence divergence under constant selection. Biology Direct 5:5.

5. Meer M. V., Kondrashov A. S., Artzy-Randrup Y. and Kondrashov F. A. (2010). Compensatory evolution in mt-tRNAs navigates valleys of low fitness. Nature 464, 279-282.

6. Kondrashov F. A. and Kondrashov A. S. (2010). Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London B 365, 1169-1176.

7. Adzhubei I. A., Schmidt S., Peshkin L., Ramensky V. E., Gerasimova A. V., Bork P., Kondrashov A. S. and Sunyaev S. R. (2010). A method and server for predicting damaging missense mutations. Nature Methods 7, 248-249.

8. Kondrashov A. S. and Assis R. (2010). Bridges: a tool for identifying local similarities in long sequences. Bioinformatics. 26(16) 2055-56

9. Bazykin GA, Kondrashov AS. Detecting Past Positive Selection through Ongoing Negative Selection. Genome Biol Evol. 2011;3:1006-13

10. Assis R, Kondrashov AS. A strong deletion bias in nonallelic gene conversion. PLoS Genet. 2012 Feb;8(2):e1002508.

11. Leushkin EV, Bazykin GA, Kondrashov AS. Insertions and deletions trigger adaptive walks in Drosophila proteins.Proc Biol Sci. 2012 Aug 7;279(1740):3075-82.

12. Assis R, Kondrashov AS.Nonallelic gene conversion is not GC-biased in Drosophila or primates.Mol Biol Evol. 2012 May;29(5):1291-5.

13. Naumenko SA, Kondrashov AS. Rate and breadth of protein evolution are only weakly correlated. Biol Direct. 2012 Feb 15;7:8.

14. Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the Transition/Transversion Ratio in Drosophila and Hominidae Genomes. Mol Biol Evol. 2012. 29(8): 1943 - 1955.

15. Kondrashov AS (2012). Genetics: the rate of human mutation. Nature (news and views) 488, 467–468

16. Bazykin GA, Kondrashov AS. Major role of positive selection in the evolution of conservative segments of Drosophila proteins. Proc Biol Sci. 2012. 279(1742):3409-17

17. Naumenko SA, Kondrashov AS, Bazykin GA. Fitness conferred by replaced amino acids declines with time. Biol Lett. 2012 Oct 23;8(5):825-8. Epub 2012 May 23.

TEN MOST SIGNIFICANT EARLIER PUBLICATIONS:

1. Kondrashov A. S. (1988). Deleterious mutations and the evolution of sexual reproduction. Nature 336, 435-440.

2. Kondrashov A. S. and Crow J. F. (1991). Haploidy or diploidy: which is better? Nature 351, 314-315.

3. Kondrashov A. S. (1994). The asexual ploidy cycle and the origin of sex. Nature 370, 213-216.

4. Shabalina S. A., Yampolsky L. Y. and Kondrashov A. S. (1997). Rapid decline of fitness in panmictic populations of Drosophila under relaxed selection. Proceedings of the National Academy of Sciences USA 94, 13034-13039.

5. Kondrashov A. S. and Kondrashov F. A. (1999). Interactions among quantitative traits in the course of sympatric speciation. Nature 400, 351- 354.

6. Shabalina S. A., Ogurtsov A. Y., Kondrashov V. A. and Kondrashov A. S. (2001). Selective constraint in intergenic regions of human and mouse genomes. Trends in Genetics 17, 373-376.

7. McCune A. R., Fuller R. C., Aquilina A. A., Dawley R. M., Fadool J. M., Houle D., Travis J. and Kondrashov A. S. (2002). A low genomic number of recessive lethals in natural populations of bluefin killifish and zebrafish. Science 296, 2398-2401.

8. Kondrashov A. S., Sunyaev S. and Kondrashov F. A. (2002). Dobzhansky-Muller incompatibilities in protein evolution. Proceedings of the National Academy of Sciences USA 99, 14878-14883.

9. Kondrashov F. A., Ogurtsov A. Y. and Kondrashov A. S. (2004). Bioinformatical assay of human gene morbidity. Nucleic Acids Research 32, 1731-1737.

10. Bazykin G. A., Kondrashov F. A., Sunyaev S., Ogurtsov A. Y. and Kondrashov A. S. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature 429, 558-562.