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Alexey Kondrashov

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Publications

TOP 3
Nadezhda V Terekhanova; Georgii A Bazykin; Alexey S Kondrashov; Alexey Neverov; Vladimir B Seplyarskiy
Prevalence of multinucleotide replacements in evolution of primates and Drosophila.
Olga A Vakhrusheva; Georgii A Bazykin; Alexey S Kondrashov
Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation.
Evgeny V Leushkin; Georgii A Bazykin; Alexey S Kondrashov
Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection.

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All Publications

2013: Nadezhda V Terekhanova; Georgii A Bazykin; Alexey S Kondrashov; Alexey Neverov; Vladimir B Seplyarskiy
Prevalence of multinucleotide replacements in evolution of primates and Drosophila.
Molecular biology and evolution 2013;30(6):1315-25.
2013: Olga A Vakhrusheva; Georgii A Bazykin; Alexey S Kondrashov
Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation.
Genome biology and evolution 2013;5(3):532-41.
2013: Evgeny V Leushkin; Georgii A Bazykin; Alexey S Kondrashov
Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection.
Genome biology and evolution 2013;5(3):514-24.
2012: Sergey A Naumenko; Alexey S Kondrashov; Georgii A Bazykin
Fitness conferred by replaced amino acids declines with time.
Biology letters 2012;8(5):825-8.
2012: Georgii A Bazykin; Alexey S Kondrashov
Major role of positive selection in the evolution of conservative segments of Drosophila proteins.
Proceedings. Biological sciences / The Royal Society 2012;279(1742):3409-17.
2012: Evgeny V Leushkin; Georgii A Bazykin; Alexey S Kondrashov
Insertions and deletions trigger adaptive walks in Drosophila proteins.
Proceedings. Biological sciences / The Royal Society 2012;279(1740):3075-82.
2012: Vladimir B Seplyarskiy; Peter Kharchenko; Alexey S Kondrashov; Georgii A Bazykin
Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes.
Molecular biology and evolution 2012;29(8):1943-55.
2012: Raquel Assis; Alexey S Kondrashov
Nonallelic gene conversion is not GC-biased in Drosophila or primates.
Molecular biology and evolution 2012;29(5):1291-5.
2012: Raquel Assis; Alexey S Kondrashov
A strong deletion bias in nonallelic gene conversion.
PLoS genetics 2012;8(2):e1002508.
2012: Sergey A Naumenko; Alexey S Kondrashov
Rate and breadth of protein evolution are only weakly correlated.
Biology direct 2012;7():8.
2011: Georgii A Bazykin; Alexey S Kondrashov
Detecting past positive selection through ongoing negative selection.
Genome biology and evolution 2011;3():1006-13.
2011: Emmanuil E Shnol; Elena A Ermakova; Alexey S Kondrashov
On the relationship between the load and the variance of relative fitness.
Biology direct 2011;6():20.
2010: Alexey S Kondrashov; Raquel Assis
Bridges: a tool for identifying local similarities in long sequences.
Bioinformatics (Oxford, England) 2010;26(16):2055-6.
2010: Fyodor A Kondrashov; Alexey S Kondrashov
Measurements of spontaneous rates of mutations in the recent past and the near future.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2010;365(1544):1169-76.
2010: Ivan A Adzhubei; Steffen Schmidt; Leonid Peshkin; Vasily E Ramensky; Anna Gerasimova; Peer Bork; Alexey S Kondrashov; Shamil R Sunyaev
A method and server for predicting damaging missense mutations.
Nature methods 2010;7(4):248-9.
2010: Margarita V Meer; Alexey S Kondrashov; Yael Artzy-Randrup; Fyodor A Kondrashov
Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness.
Nature 2010;464(7286):279-82.
2010: Alexey S Kondrashov; Inna S Povolotskaya; Dmitry N Ivankov; Fyodor A Kondrashov
Rate of sequence divergence under constant selection.
Biology direct 2010;5():5.
2009: Raquel Assis; Alexey S Kondrashov
Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(17):7079-82.
2009: Nilgun Donmez; Georgii A Bazykin; Michael Brudno; Alexey S Kondrashov
Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi.
Genetics 2009;181(2):685-90.
2008: Steffen Schmidt; Anna Gerasimova; Fyodor A Kondrashov; Ivan A Adzhubei; Ivan A Adzuhbei; Alexey S Kondrashov; Shamil Sunyaev
Hypermutable non-synonymous sites are under stronger negative selection.
PLoS genetics 2008;4(11):e1000281.
2008: Raquel Assis; Alexey S Kondrashov; Eugene V Koonin; Fyodor A Kondrashov
Nested genes and increasing organizational complexity of metazoan genomes.
Trends in genetics : TIG 2008;24(10):475-8.
2008: Alexey S Kondrashov
Another step toward quantifying spontaneous mutation.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(27):9133-4.
2007: Simon Minovitsky; Philip Stegmaier; Alexander Kel; Alexey S Kondrashov; Inna Dubchak
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences.
BMC genomics 2007;8():378.
2007: Georgii A Bazykin; Fyodor A Kondrashov; Michael Brudno; Alexander Poliakov; Inna Dubchak; Alexey S Kondrashov
Extensive parallelism in protein evolution.
Biology direct 2007;2():20.
2006: Georgii A Bazykin; Jonathan Dushoff; Simon A Levin; Alexey S Kondrashov
Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(51):19396-401.
2006: Yael Artzy-Randrup; Alexey S Kondrashov
Sympatric speciation under incompatibility selection.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(31):11619-24.
2006: John A Bernat; Gregory E Crawford; Aleksey Y Ogurtsov; Francis S Collins; David Ginsburg; Alexey S Kondrashov
Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs.
Human molecular genetics 2006;15(13):2098-105.
2006: Fyodor A Kondrashov; Aleksey Y Ogurtsov; Alexey S Kondrashov
Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites.
Journal of theoretical biology 2006;240(4):616-26.
2006: Aleksey Y Ogurtsov; Svetlana A Shabalina; Alexey S Kondrashov; Mikhail A Roytberg
Analysis of internal loops within the RNA secondary structure in almost quadratic time.
Bioinformatics (Oxford, England) 2006;22(11):1317-24.
2006: Fyodor A Kondrashov; Alexey S Kondrashov
Role of selection in fixation of gene duplications.
Journal of theoretical biology 2006;239(2):141-51.
2006: Georgii A Bazykin; Alexey S Kondrashov
Rate of promoter class turn-over in yeast evolution.
BMC evolutionary biology 2006;6():14.
2005: Lev Y Yampolsky; Chenoa Allen; Svetlana A Shabalina; Alexey S Kondrashov
Persistence time of loss-of-function mutations at nonessential loci affecting eye color in Drosophila melanogaster.
Genetics 2005;171(4):2133-8.
2005: Lev Y Yampolsky; Fyodor A Kondrashov; Alexey S Kondrashov
Distribution of the strength of selection against amino acid replacements in human proteins.
Human molecular genetics 2005;14(21):3191-201.
2005: Alexey S Kondrashov
Evolutionary biology: fruitfly genome is not junk.
Nature 2005;437(7062):1106.
2005: I King Jordan; Fyodor A Kondrashov; Ivan A Adzhubei; Yuri I Wolf; Eugene V Koonin; Alexey S Kondrashov; Shamil Sunyaev
A universal trend of amino acid gain and loss in protein evolution.
Nature 2005;433(7026):633-8.
2004: Amy R McCune; David Houle; Kyle McMillan; Rebecca Annable; Alexey S Kondrashov
Two classes of deleterious recessive alleles in a natural population of zebrafish, Danio rerio.
Proceedings. Biological sciences / The Royal Society 2004;271(1552):2025-33.
2004: Aleksey Y Ogurtsov; Shamil Sunyaev; Alexey S Kondrashov
Indel-based evolutionary distance and mouse-human divergence.
Genome research 2004;14(8):1610-6.
2004: Georgii A Bazykin; Fyodor A Kondrashov; Aleksey Y Ogurtsov; Shamil Sunyaev; Alexey S Kondrashov
Positive selection at sites of multiple amino acid replacements since rat-mouse divergence.
Nature 2004;429(6991):558-62.
2004: Matthew E Arnegard; Alexey S Kondrashov
Sympatric speciation by sexual selection alone is unlikely.
Evolution; international journal of organic evolution 2004;58(2):222-37.
2004: Alexey S Kondrashov; Igor Rogozin
Context of deletions and insertions in human coding sequences.
Human mutation 2004;23(2):177-85.
2004: Fyodor A Kondrashov; Aleksey Y Ogurtsov; Alexey S Kondrashov
Bioinformatical assay of human gene morbidity.
Nucleic acids research 2004;32(5):1731-7.
2003: Svetlana A Shabalina; Aleksey Y Ogurtsov; David Lipman; Alexey S Kondrashov
Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.
Nucleic acids research 2003;31(18):5433-9.
2003: Hsiao-Pei Yang; Alexey S Kondrashov
Cyclical dynamics under constant selection against mutations in haploid and diploid populations with facultative selfing.
Genetical research 2003;81(1):1-6.
2003: Alexey S Kondrashov
Accumulation of Dobzhansky-Muller incompatibilities within a spatially structured population.
Evolution; international journal of organic evolution 2003;57(1):151-3.
2003: Alexey S Kondrashov
Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases.
Human mutation 2003;21(1):12-27.
2002: Aleksey Y Ogurtsov; Mikhail A Roytberg; Svetlana A Shabalina; Alexey S Kondrashov
OWEN: aligning long collinear regions of genomes.
Bioinformatics (Oxford, England) 2002;18(12):1703-4.
2002: Mikhail A Roytberg; Aleksey Y Ogurtsov; Svetlana A Shabalina; Alexey S Kondrashov
A hierarchical approach to aligning collinear regions of genomes.
Bioinformatics (Oxford, England) 2002;18(12):1673-80.
2002: Alexey S Kondrashov; Shamil Sunyaev; Fyodor A Kondrashov
Dobzhansky-Muller incompatibilities in protein evolution.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(23):14878-83.
2002: Joana Carneiro Da Silva; Alexey S Kondrashov
Patterns in spontaneous mutation revealed by human-baboon sequence comparison.
Trends in genetics : TIG 2002;18(11):544-7.
2002: Amy R McCune; Rebecca C Fuller; Allisan A Aquilina; Robert M Dawley; James M Fadool; David Houle; Joseph Travis; Alexey S Kondrashov
A low genomic number of recessive lethals in natural populations of bluefin killifish and zebrafish.
Science (New York, N.Y.) 2002;296(5577):2398-401.
2002: Alexey S Kondrashov; Svetlana A Shabalina
Classification of common conserved sequences in mammalian intergenic regions.
Human molecular genetics 2002;11(6):669-74.
2002: Colleen T Webb; Svetlana A Shabalina; Aleksey Y Ogurtsov; Alexey S Kondrashov
Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae.
Nucleic acids research 2002;30(5):1233-9.
2002: David Houle; Alexey S Kondrashov
Coevolution of costly mate choice and condition-dependent display of good genes.
Proceedings. Biological sciences / The Royal Society 2002;269(1486):97-104.
2001: Fyodor A Kondrashov; Alexey S Kondrashov
Multidimensional epistasis and the disadvantage of sex.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(21):12089-92.
2001: Svetlana A Shabalina; Aleksey Y Ogurtsov; V A Kondrashov; Alexey S Kondrashov
Selective constraint in intergenic regions of human and mouse genomes.
Trends in genetics : TIG 2001;17(7):373-6.
2001: Shamil Sunyaev; Vasily Ramensky; I Koch; warren lathe; Alexey S Kondrashov; Peer Bork
Prediction of deleterious human alleles.
Human molecular genetics 2001;10(6):591-7.
2001: Hsiao-Pei Yang; A Y Tanikawa; Alexey S Kondrashov
Molecular nature of 11 spontaneous de novo mutations in Drosophila melanogaster.
Genetics 2001;157(3):1285-92.
2001: Hsiao-Pei Yang; A Y Tanikawa; W A Van Voorhies; Joana Carneiro Da Silva; Alexey S Kondrashov
Whole-genome effects of ethyl methanesulfonate-induced mutation on nine quantitative traits in outbred Drosophila melanogaster.
Genetics 2001;157(3):1257-65.
2001: Yuri I Wolf; Igor Rogozin; Alexey S Kondrashov; Eugene V Koonin
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
Genome research 2001;11(3):356-72.
2001: Alexey S Kondrashov
Sex and U.
Trends in genetics : TIG 2001;17(2):75-7.
2000: Yuri I Wolf; Alexey S Kondrashov; Eugene V Koonin
Interkingdom gene fusions.
Genome biology 2000;1(6):RESEARCH0013.
1999: Svetlana A Shabalina; Alexey S Kondrashov
Pattern of selective constraint in C. elegans and C. briggsae genomes.
Genetical research 1999;74(1):23-30.
1999: Alexey S Kondrashov; Fyodor A Kondrashov
Interactions among quantitative traits in the course of sympatric speciation.
Nature 1999;400(6742):351-4.
1998: Alexey S Kondrashov; M Shpak
On the origin of species by means of assortative mating.
Proceedings. Biological sciences / The Royal Society 1998;265(1412):2273-8.
1998: Alexey S Kondrashov
Measuring spontaneous deleterious mutation process.
Genetica 1998;102-103(1-6):183-97.
1997: Svetlana A Shabalina; Alexey S Kondrashov
Rapid decline of fitness in panmictic populations of Drosophila melanogaster maintained under relaxed natural selection.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(24):13034-9.
1997: David Houle; Alexey S Kondrashov; Lev Y Yampolsky; S Caldwell; P L Steponkus
The effect of cryopreservation on the lethal mutation rate in Drosophila melanogaster.
Genetical research 1997;69(3):209-13.
1995: Alexey S Kondrashov
Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?
Journal of theoretical biology 1995;175(4):583-94.
1995: Nafisa Nazipova; Svetlana A Shabalina; Alexey S Kondrashov; M A Roytberg; G V Buryakov; S E Vernoslov
SAMSON: a software package for the biopolymer primary structure analysis.
Computer applications in the biosciences : CABIOS 1995;11(4):423-6.
1995: Alexey S Kondrashov
Dynamics of unconditionally deleterious mutations: Gaussian approximation and soft selection.
Genetical research 1995;65(2):113-21.
1994: Alexey S Kondrashov; David Houle
Genotype-environment interactions and the estimation of the genomic mutation rate in Drosophila melanogaster.
Proceedings. Biological sciences / The Royal Society 1994;258(1353):221-7.
1994: Alexey S Kondrashov
The asexual ploidy cycle and the origin of sex.
Nature 1994;370(6486):213-6.
1994: Alexey S Kondrashov
Mutation load under vegetative reproduction and cytoplasmic inheritance.
Genetics 1994;137(1):311-8.
1994: Alexey S Kondrashov
Muller's ratchet under epistatic selection.
Genetics 1994;136(4):1469-73.
1993: Alexey S Kondrashov
Classification of hypotheses on the advantage of amphimixis.
The Journal of heredity 1993;84(5):372-87.
1993: E E Shnol; Alexey S Kondrashov
The effect of selection on the phenotypic variance.
Genetics 1993;134(3):995-6.
1993: Alexey S Kondrashov; J F Crow
A molecular approach to estimating the human deleterious mutation rate.
Human mutation 1993;2(3):229-34.
1992: Alexey S Kondrashov; M Turelli
Deleterious mutations, apparent stabilizing selection and the maintenance of quantitative variation.
Genetics 1992;132(2):603-18.
1991: Alexey S Kondrashov; J F Crow
Haploidy or diploidy: which is better?
Nature 1991;351(6324):314-5.
1991: Svetlana A Shabalina; O V Yurieva; Alexey S Kondrashov
On the frequencies of nucleotides and nucleotide substitutions in conservative regulatory DNA sequences.
Journal of theoretical biology 1991;149(1):43-54.
1990: S E Vernoslov; Alexey S Kondrashov; M A Roĭtberg; Svetlana A Shabalina; O V Iur'eva; Nafisa Nazipova
[The computer program package "SAMSON" for analysis of primary structure of biopolymers].
Molekuliarnaia biologiia 1990;24(2):524-9.
1988: Alexey S Kondrashov; J F Crow
King's formula for the mutation load with epistasis.
Genetics 1988;120(3):853-6.