A. Kondrashov

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Selection against harmful mutations in large sexual and asexual populations.

A. Kondrashov, 1982, Genetical research.

A method and server for predicting damaging missense mutations

P. Bork, L. Peshkin, S. Schmidt, 2010, Nature Methods.

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

E. Koonin, Y. Wolf, A. Kondrashov, 2001, Genome research.

Paratrypanosoma Is a Novel Early-Branching Trypanosomatid

A. Kondrashov, P. Volf, J. Lukeš, 2013, Current Biology.

Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation

A. Kondrashov, O. Vakhrusheva, G. Bazykin, 2013, Genome biology and evolution.

Role of selection in fixation of gene duplications.

A. Kondrashov, F. Kondrashov, 2006, Journal of theoretical biology.

Dobzhansky–Muller incompatibilities in protein evolution

S. Sunyaev, A. Kondrashov, F. Kondrashov, 2002, Proceedings of the National Academy of Sciences of the United States of America.

The Impact of Comparative Genomics on Our Understanding of Evolution

E. Koonin, L. Aravind, A. Kondrashov, 2000, Cell.

Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?

A. Kondrashov, 1995, Journal of theoretical biology.

SYMPATRIC SPECIATION BY SEXUAL SELECTION ALONE IS UNLIKELY

M. Arnegard, A. Kondrashov, 2004, Evolution; international journal of organic evolution.

A universal trend of amino acid gain and loss in protein evolution

E. Koonin, Y. Wolf, I. Adzhubei, 2005, Nature.

Deleterious mutations and the evolution of sexual reproduction

A. Kondrashov, 1988, Nature.

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Corinne Da Silva, Manolis Kellis, J. Poulain, 2013, Nature.

Pattern of selective constraint in C. elegans and C. briggsae genomes.

S. Shabalina, A. Kondrashov, 1999, Genetical research.

Prevalence of Multinucleotide Replacements in Evolution of Primates and Drosophila

A. Kondrashov, G. Bazykin, V. Seplyarskiy, 2013, Molecular biology and evolution.

Indel-based evolutionary distance and mouse-human divergence.

Aleksey Y Ogurtsov, Shamil Sunyaev, Alexey S Kondrashov, 2004, Genome research.

Classification of hypotheses on the advantage of amphimixis.

A. Kondrashov, A S Kondrashov, Alexey S. Kondrashov, 1993, The Journal of heredity.

Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

A. Kondrashov, I. Arkhipova, M. Logacheva, 2020, Nature communications.

Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

S. A. Naumenko, A. Kondrashov, I. Arkhipova, 2018, Nature Communications.

Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases

Alexey S Kondrashov, A. Kondrashov, 2003, Human mutation.

On the origin of species by means of assortative mating

A. Kondrashov, M. Shpak, A S Kondrashov, 1998, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Interactions among quantitative traits in the course of sympatric speciation

Fyodor A. Kondrashov, Alexey S. Kondrashov, A. Kondrashov, 1999, Nature.

Three mechanisms of Red Queen dynamics

Alexander I Khibnik, Alexey S. Kondrashov, A. Kondrashov, 1997, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Alexey S Kondrashov, Colleen T Webb, C. Webb, 2002, Nucleic acids research.

Detecting Past Positive Selection through Ongoing Negative Selection

A. Kondrashov, G. Bazykin, 2011, Genome biology and evolution.

Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes.

Georgii A. Bazykin, Alexey S. Kondrashov, Peter Kharchenko, 2012, Molecular biology and evolution.

Sympatric speciation: when is it possible?

Alexey S. Kondrashov, Mikhail V. Mina, A. Kondrashov, 1986 .

Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes

Georgii A. Bazykin, Alexey S. Kondrashov, A. Kondrashov, 2014, PLoS genetics.

Patterns in spontaneous mutation revealed by human-baboon sequence comparison.

Alexey S Kondrashov, A. Kondrashov, J. C. Silva, 2002, Trends in genetics : TIG.

Cyclical dynamics under constant selection against mutations in haploid and diploid populations with facultative selfing.

A. Kondrashov, Hsiao-Pei Yang, 2003, Genetical research.

Context of deletions and insertions in human coding sequences

Alexey S Kondrashov, A. Kondrashov, I. Rogozin, 2004, Human mutation.

Fitness conferred by replaced amino acids declines with time

A. Kondrashov, G. Bazykin, S. Naumenko, 2012, Biology Letters.

Sex and deleterious mutation

A. Kondrashov, 1994, Nature.

Multilocus model of sympatric speciation. III. Computer simulations.

A. Kondrashov, 1986, Theoretical population biology.

Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection

S. Schmidt, S. Sunyaev, A. Kondrashov, 2008, PLoS genetics.

Rate of promoter class turn-over in yeast evolution

A. Kondrashov, G. Bazykin, 2006, BMC Evolutionary Biology.

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus

A. Kondrashov, M. Logacheva, A. Penin, 2014, PLoS genetics.

Two linked loci under mutation-selection balance and Muller’s ratchet

A. Kondrashov, T. Neretina, K. A. Khudyakova, 2018 .

Extraordinary Genetic Diversity in a Wood Decay Mushroom

Yana Safonova, A. Kondrashov, M. Logacheva, 2015, Molecular biology and evolution.

Nested genes and increasing organizational complexity of metazoan genomes.

E. Koonin, A. Kondrashov, F. Kondrashov, 2008, Trends in genetics : TIG.

The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences

E. Nabieva, A. Kondrashov, M. Logacheva, 2013, BMC Genomics.

Extended family with germline pathogenic variant in polymerase delta provides strong evidence for recessive effect of proofreading inactivation

A. Kondrashov, F. Kondrashov, L. Valle, 2022, bioRxiv.

National Center for Biotechnology Information National Library of Medicine National Institutes of Health an excess of genes of apparent archaeal origin

E. Koonin, L. Aravind, A. Kondrashov, 2000 .

Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.

D. Lipman, A. Ogurtsov, S. Shabalina, 2003, Nucleic acids research.

Genetics: The rate of human mutation

A. Kondrashov, Alexey S. Kondrashov, 2012, Nature.

Sympatric speciation under incompatibility selection.

A. Kondrashov, Yael A. Artzy‐Randrup, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Two regions of M13 phage genome hybridizing with human DNA are similar to several keratin genes.

A. Kondrashov, T. Beridze, N. B. Chiaureli, 1990, Biochimie.

Species and speciation

A. Kondrashov, 1992, Nature.

Report Paratrypanosoma Is a Novel Early-Branching Trypanosomatid

A. Kondrashov, P. Volf, J. Lukeš, 2013 .

Correction: Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection

S. Schmidt, I. Adzhubei, S. Sunyaev, 2008, PLoS genetics.

The effect of cryopreservation on the lethal mutation rate in Drosophila melanogaster.

A. Kondrashov, D. Houle, L. Yampolsky, 1997, Genetical research.

A molecular approach to estimating the human deleterious mutation rate

J. Crow, A. Kondrashov, 1993, Human mutation.

Bursts of amino acid replacements in protein evolution

A. Kondrashov, G. Bazykin, T. Neretina, 2019, Royal Society open science.

Deleterious mutations, apparent stabilizing selection and the maintenance of quantitative variation.

M. Turelli, A. Kondrashov, Alexey S. Kondrashov, 1992, Genetics.

Local fitness landscape of the green fluorescent protein

Dmitry Chudakov, Dmitry Bolotin, Alexander S. Mishin, 2016, Nature.

Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

A. Kondrashov, L. Yampolsky, M. Logacheva, 2017, Molecular ecology.

Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution

Raquel Assis, Alexey S Kondrashov, A. Kondrashov, 2009, Proceedings of the National Academy of Sciences.

Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages

A. Kondrashov, M. Logacheva, A. Penin, 2015, BMC Genomics.

Analysis of internal loops within the RNA secondary structure in almost quadratic time

Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Mikhail A. Roytberg, 2006, Bioinform..

Strong Mutational Bias Toward Deletions in the Drosophila melanogaster Genome Is Compensated by Selection

Georgii A. Bazykin, Alexey S. Kondrashov, A. Kondrashov, 2013, Genome biology and evolution.

Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites.

Aleksey Y Ogurtsov, Fyodor A Kondrashov, Alexey S Kondrashov, 2006, Journal of theoretical biology.

Distribution of the strength of selection against amino acid replacements in human proteins.

A. Kondrashov, F. Kondrashov, L. Yampolsky, 2005, Human molecular genetics.

Measurements of spontaneous rates of mutations in the recent past and the near future

Fyodor A Kondrashov, Alexey S Kondrashov, A. Kondrashov, 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

Rapid decline of fitness in panmictic populations of Drosophila melanogaster maintained under relaxed natural selection.

S. Shabalina, A. Kondrashov, L. Yampolsky, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Evolutionary biology: Fruitfly genome is not junk

A. Kondrashov, 2005, Nature.

Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs.

Aleksey Y Ogurtsov, Francis S Collins, Alexey S Kondrashov, 2006, Human molecular genetics.

Classification of common conserved sequences in mammalian intergenic regions.

Alexey S Kondrashov, S. Shabalina, A. Kondrashov, 2002, Human molecular genetics.

Negative selection in humans and fruit flies involves synergistic epistasis

P. D. de Bakker, S. Sunyaev, S. Pulit, 2016, Science.

High‐quality genome assembly of Capsella bursa‐pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution

A. Kondrashov, I. Kulakovskiy, M. Logacheva, 2017, The Plant journal : for cell and molecular biology.

Conserved proteins are fragile.

Raquel Assis, Alexey S Kondrashov, A. Kondrashov, 2014, Molecular biology and evolution.

Letter Conserved Proteins Are Fragile

A. Kondrashov, Raquel Assis, 2013 .

Bioinformatical assay of human gene morbidity.

Aleksey Y Ogurtsov, Fyodor A Kondrashov, Alexey S Kondrashov, 2004, Nucleic acids research.

THE THIRD PHASE OF WRIGHT'S SHIFTING‐BALANCE: A SIMPLE ANALYSIS OF THE EXTREME CASE

A. Kondrashov, 1992, Evolution; international journal of organic evolution.

Crossing-Over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity

A. Kondrashov, F. Kondrashov, M. Logacheva, 2014, Molecular biology and evolution.

Nonallelic gene conversion is not GC-biased in Drosophila or primates.

A. Kondrashov, Raquel Assis, 2012, Molecular biology and evolution.

Multidimensional epistasis and the disadvantage of sex

A. Kondrashov, F. Kondrashov, A S Kondrashov, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness

Fyodor A. Kondrashov, Alexey S. Kondrashov, Margarita V. Meer, 2010, Nature.

Protein evolution: Causes of trends in amino-acid gain and loss (Reply)

E. Koonin, Y. Wolf, I. Adzhubei, 2006, Nature.

Persistence Time of Loss-of-Function Mutations at Nonessential Loci Affecting Eye Color in Drosophila melanogaster

S. Shabalina, A. Kondrashov, L. Yampolsky, 2005, Genetics.

Two classes of deleterious recessive alleles in a natural population of zebrafish, Danio rerio

A. Kondrashov, D. Houle, A. McCune, 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Major role of positive selection in the evolution of conservative segments of Drosophila proteins

A. Kondrashov, G. Bazykin, 2012, Proceedings of the Royal Society B: Biological Sciences.

Selective constraint in intergenic regions of human and mouse genomes.

A. Ogurtsov, S. Shabalina, A. Kondrashov, 2001, Trends in genetics : TIG.

Comparative genomics and evolutionary biology.

A. Kondrashov, 1999, Current opinion in genetics & development.

Rate of sequence divergence under constant selection

A. Kondrashov, D. Ivankov, F. Kondrashov, 2010, Biology Direct.

Extensive parallelism in protein evolution

M. Brudno, I. Dubchak, Alexander Poliakov, 2007, Biology Direct.

OWEN: aligning long collinear regions of genomes

Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Mikhail A. Roytberg, 2002, Bioinform..

Weak Negative and Positive Selection and the Drift Load at Splice Sites

Alexander V. Favorov, M. Gelfand, A. Mironov, 2014, Genome biology and evolution.

Sex and U.

A. Kondrashov, 2001, Trends in genetics : TIG.

Interkingdom gene fusions

Eugene V Koonin, Yuri I Wolf, Alexey S Kondrashov, 2000, Genome Biology.

Another step toward quantifying spontaneous mutation

A. Kondrashov, 2008, Proceedings of the National Academy of Sciences.

Change in CpG Context is a Leading Cause of Correlation between the Rates of Non-Synonymous and Synonymous Substitutions in Rodents

A. Ogurtsov, A. Kondrashov, G. Bazykin, 2006 .

Positive selection at sites of multiple amino acid replacements since rat–mouse divergence

Georgii A. Bazykin, Aleksey Y. Ogurtsov, Fyodor A. Kondrashov, 2004, Nature.

Measuring spontaneous deleterious mutation process

A. Kondrashov, 2004, Genetica.

A Low Genomic Number of Recessive Lethals in Natural Populations of Bluefin Killifish and Zebrafish

A. Kondrashov, J. Travis, D. Houle, 2002, Science.

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences

Inna Dubchak, Philip Stegmaier, Simon Minovitsky, 2007, BMC Genomics.

The asexual ploidy cycle and the origin of sex

Alexey S. Kondrashov, A. Kondrashov, 1994, Nature.

NGS-based identification of druggable alterations and signaling pathways – hepatocellular carcinoma case report

E. Nabieva, A. Kondrashov, E. Kotelnikova, 2015 .

Haploidy or diploidy: which is better?

J. Crow, A. Kondrashov, 1991, Nature.

EVOLUTIONARY GENETICS OF LIFE CYCLES

Alexey S. Kondrashov, A. Kondrashov, 1997 .

Characteristics and possible mechanisms of formation of microinversions distinguishing human and chimpanzee genomes

S. Mirkin, A. Kondrashov, N. A. Potapova, 2022, Scientific reports.

Architecture of Parallel Adaptation in Ten Lacustrine Threespine Stickleback Populations from the White Sea Area

A. Kondrashov, G. Bazykin, A. Barmintseva, 2019, Genome biology and evolution.

Architecture of parallel adaptation to freshwater in multiple populations of threespine stickleback

A. Kondrashov, G. Bazykin, A. Barmintseva, 2018, bioRxiv.

Polymorphism Due to Multiple Amino Acid Substitutions at a Codon Site Within Ciona savignyi

M. Brudno, Nilgun Donmez, A. Kondrashov, 2009, Genetics.

Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites

Jonathan Dushoff, Alexey S Kondrashov, J. Dushoff, 2006, Proceedings of the National Academy of Sciences.

A Strong Deletion Bias in Nonallelic Gene Conversion

A. Kondrashov, Raquel Assis, 2012, PLoS genetics.

This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon.

Alexey S Kondrashov, A. Kondrashov, 2007 .

Coevolution of costly mate choice and condition-dependent display of good genes

A. Kondrashov, D. Houle, 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Deleterious mutations as an evolutionary factor. III. Mating preference and some general remarks.

A. Kondrashov, 1988, Journal of theoretical biology.

Bursts of amino acid replacements in protein evolution

A. Kondrashov, G. Bazykin, T. Neretina, 2017, bioRxiv.

Excessive parallelism in protein evolution of Lake Baikal amphipod species flock.

A. Kondrashov, L. Yampolsky, G. Bazykin, 2020, Genome biology and evolution.

Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation

A. Kondrashov, M. Logacheva, A. Penin, 2018, bioRxiv.

Through Sex, Nature Is Telling Us Something Important.

A. Kondrashov, 2018, Trends in genetics : TIG.

Rapid Accumulation of Mutations in Growing Mycelia of a Hypervariable Fungus Schizophyllum commune

A. Kondrashov, A. Penin, A. Kasianov, 2019, bioRxiv.

ACCUMULATION OF DOBZHANSKY‐MULLER INCOMPATIBILITIES WITHIN A SPATIALLY STRUCTURED POPULATION

A. Kondrashov, 2003, Evolution; international journal of organic evolution.

Deleterious mutations as an evolutionary factor. II. Facultative apomixis and selfing.

A. Kondrashov, 1985, Genetics.

Multilocus model of sympatric speciation. I: One character

A. Kondrashov, 1983 .

Muller's ratchet under epistatic selection.

A. Kondrashov, A S Kondrashov, 1994, Genetics.

Deleterious mutations as an evolutionary factor. 1. The advantage of recombination.

A. Kondrashov, 1984, Genetical research.

Whole-genome effects of ethyl methanesulfonate-induced mutation on nine quantitative traits in outbred Drosophila melanogaster.

A. Kondrashov, W. V. Van Voorhies, A. Tanikawa, 2001, Genetics.

MODIFIERS OF MUTATION-SELECTION BALANCE - GENERAL-APPROACH AND THE EVOLUTION OF MUTATION-RATES

A. Kondrashov, 1995 .

Genotype—environment interactions and the estimation of the genomic mutation rate in Drosophila melanogaster

A. Kondrashov, D. Houle, A S Kondrashov, 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Dynamics of unconditionally deleterious mutations: Gaussian approximation and soft selection.

A. Kondrashov, 1995, Genetical research.

Study program: Gerontology

A. Kondrashov, 2010 .

Molecular nature of 11 spontaneous de novo mutations in Drosophila melanogaster.

A. Kondrashov, A. Tanikawa, H. P. Yang, 2001, Genetics.

Bacterial homologs of the small subunit of eukaryotic DNA primase.

E. Koonin, L. Aravind, Y. I. Wolf, 2000, Journal of Molecular Microbiology and Biotechnology.

Efficient capture of unique sequences from eukaryotic genomes

Alexey S. Kondrashov, A. Kondrashov, J. C. Silva, 2002 .

Mutation load under vegetative reproduction and cytoplasmic inheritance.

A. Kondrashov, A S Kondrashov, Alexey S. Kondrashov, 1994, Genetics.

Rapid accumulation of a vertically transmitted parasite triggered by relaxation of natural selection among hosts

C. Webb, S. Shabalina, A. Kondrashov, 1999 .

Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge

Alexander S. Mikheyev, Jennifer H. Wisecaver, A. Kondrashov, 2014, Nature Communications.

Artificial Selection for Reduced Fitness in Panmictic Populations of Drosophila melanogaster

A. Kondrashov, T. Neretina, A. Stupnikova, 2019, Russian Journal of Genetics.

HIGH GENETIC VARIABILITY UNDER THE BALANCE BETWEEN SYMMETRIC MUTATION AND FLUCTUATING STABILIZING SELECTION

A. Kondrashov, L. Yampolsky, 1996 .

Extended family with an inherited pathogenic variant in polymerase delta provides strong evidence for recessive effect of proofreading deficiency in human cells

A. Kondrashov, F. Kondrashov, L. Valle, 2023, bioRxiv.

Crumbling Genome: The Impact of Deleterious Mutations on Humans

A. Kondrashov, 2017 .

The comparative and genetic methods for East European Unionidae taxonomy

A. Kondrashov, T. Neretina, A. Anisimova, 2018, bioRxiv.

Games of life — Explorations in ecology, evolution & behaviour: by Karl Sigmund Oxford University Press, 1993. £9.95 pbk, £30.00 hbk (vi + 244 pages) ISBN 0 19 854665 3

A. Kondrashov, A. Kondrashov, 1994 .

Prediction of deleterious human alleles.

Warren C. Lathe, P. Bork, S. Sunyaev, 2001, Human molecular genetics.

Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes.

David G. Harris, J. Spouge, S. Shabalina, 2003, Genetical research.

Are Nonsense Alleles of Drosophila melanogaster Genes under Any Selection?

A. Kondrashov, G. Bazykin, M. Andrianova, 2017, bioRxiv.

Rate and breadth of protein evolution are only weakly correlated

A. Kondrashov, S. Naumenko, 2012, Biology Direct.

A. N. Spiridonov, S. Shabalina, A. Kondrashov, 2000 .

Negative selection in humans and fruit flies involves synergistic epistasis

P. D. de Bakker, S. Sunyaev, S. Pulit, 2016, Science.

A hierarchical approach to aligning collinear regions of genomes

Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Mikhail A. Roytberg, 2002, Bioinform..

Insertions and deletions trigger adaptive walks in Drosophila proteins

A. Kondrashov, G. Bazykin, Evgeny Leushkin, 2012, Proceedings of the Royal Society B: Biological Sciences.

Speciation: Darwin revisited

A. Kondrashov, 2001 .

The effect of selection on the phenotypic variance.

A. Kondrashov, E. Shnol, 1993, Genetics.