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Items: 1 to 50 of 119

1.

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

Kudryavtseva OA, Safina KR, Vakhrusheva OA, Logacheva MD, Penin AA, Neretina TV, Moskalenko VN, Glagoleva ES, Bazykin GA, Kondrashov AS.

Genome Biol Evol. 2019 Oct 1;11(10):2807-2817. doi: 10.1093/gbe/evz194.

2.

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

Terekhanova NV, Barmintseva AE, Kondrashov AS, Bazykin GA, Mugue NS.

Genome Biol Evol. 2019 Sep 1;11(9):2605-2618. doi: 10.1093/gbe/evz175.

3.

Bursts of amino acid replacements in protein evolution.

Stolyarova AV, Bazykin GA, Neretina TV, Kondrashov AS.

R Soc Open Sci. 2019 Mar 27;6(3):181095. doi: 10.1098/rsos.181095. eCollection 2019 Mar.

4.

Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans.

Bezmenova AV, Bazykin GA, Kondrashov AS.

Biol Direct. 2018 Mar 2;13(1):4. doi: 10.1186/s13062-018-0206-9.

5.

Are Nonsense Alleles of Drosophila melanogaster Genes under Any Selection?

Potapova NA, Andrianova MA, Bazykin GA, Kondrashov AS.

Genome Biol Evol. 2018 Apr 1;10(4):1012-1018. doi: 10.1093/gbe/evy032.

6.

Through Sex, Nature Is Telling Us Something Important.

Kondrashov AS.

Trends Genet. 2018 May;34(5):352-361. doi: 10.1016/j.tig.2018.01.003. Epub 2018 Feb 4. Review.

PMID:
29409661
7.

Negative selection in humans and fruit flies involves synergistic epistasis.

Sohail M, Vakhrusheva OA, Sul JH, Pulit SL, Francioli LC; Genome of the Netherlands Consortium; Alzheimer’s Disease Neuroimaging Initiative, van den Berg LH, Veldink JH, de Bakker PIW, Bazykin GA, Kondrashov AS, Sunyaev SR.

Science. 2017 May 5;356(6337):539-542. doi: 10.1126/science.aah5238.

8.

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

Kasianov AS, Klepikova AV, Kulakovskiy IV, Gerasimov ES, Fedotova AV, Besedina EG, Kondrashov AS, Logacheva MD, Penin AA.

Plant J. 2017 Jul;91(2):278-291. doi: 10.1111/tpj.13563. Epub 2017 Jun 12.

9.

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

Naumenko SA, Logacheva MD, Popova NV, Klepikova AV, Penin AA, Bazykin GA, Etingova AE, Mugue NS, Kondrashov AS, Yampolsky LY.

Mol Ecol. 2017 Jan;26(2):536-553. doi: 10.1111/mec.13927. Epub 2017 Jan 2.

10.

Local fitness landscape of the green fluorescent protein.

Sarkisyan KS, Bolotin DA, Meer MV, Usmanova DR, Mishin AS, Sharonov GV, Ivankov DN, Bozhanova NG, Baranov MS, Soylemez O, Bogatyreva NS, Vlasov PK, Egorov ES, Logacheva MD, Kondrashov AS, Chudakov DM, Putintseva EV, Mamedov IZ, Tawfik DS, Lukyanov KA, Kondrashov FA.

Nature. 2016 May 19;533(7603):397-401. doi: 10.1038/nature17995. Epub 2016 May 11.

11.

Extraordinary Genetic Diversity in a Wood Decay Mushroom.

Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova YY, Naumenko SA, Klepikova AV, Gerasimov ES, Bazykin GA, James TY, Kondrashov AS.

Mol Biol Evol. 2015 Oct;32(10):2775-83. doi: 10.1093/molbev/msv153. Epub 2015 Jul 10.

12.

Dynasty Foundation: Russian science loses to politics.

Kondrashov FA, Kondrashov AS, Gelfand MS.

Nature. 2015 Jun 25;522(7557):419. doi: 10.1038/522419a. No abstract available.

PMID:
26108844
13.

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

Leushkin EV, Logacheva MD, Penin AA, Sutormin RA, Gerasimov ES, Kochkina GA, Ivanushkina NE, Vasilenko OV, Kondrashov AS, Ozerskaya SM.

BMC Genomics. 2015 May 21;16:400. doi: 10.1186/s12864-015-1570-9.

14.

Fast evolution from precast bricks: genomics of young freshwater populations of threespine stickleback Gasterosteus aculeatus.

Terekhanova NV, Logacheva MD, Penin AA, Neretina TV, Barmintseva AE, Bazykin GA, Kondrashov AS, Mugue NS.

PLoS Genet. 2014 Oct 9;10(10):e1004696. doi: 10.1371/journal.pgen.1004696. eCollection 2014 Oct.

15.

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

Gusev O, Suetsugu Y, Cornette R, Kawashima T, Logacheva MD, Kondrashov AS, Penin AA, Hatanaka R, Kikuta S, Shimura S, Kanamori H, Katayose Y, Matsumoto T, Shagimardanova E, Alexeev D, Govorun V, Wisecaver J, Mikheyev A, Koyanagi R, Fujie M, Nishiyama T, Shigenobu S, Shibata TF, Golygina V, Hasebe M, Okuda T, Satoh N, Kikawada T.

Nat Commun. 2014 Sep 12;5:4784. doi: 10.1038/ncomms5784.

16.

Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity.

Seplyarskiy VB, Logacheva MD, Penin AA, Baranova MA, Leushkin EV, Demidenko NV, Klepikova AV, Kondrashov FA, Kondrashov AS, James TY.

Mol Biol Evol. 2014 Nov;31(11):3016-25. doi: 10.1093/molbev/msu242. Epub 2014 Aug 18.

17.

Weak negative and positive selection and the drift load at splice sites.

Denisov SV, Bazykin GA, Sutormin R, Favorov AV, Mironov AA, Gelfand MS, Kondrashov AS.

Genome Biol Evol. 2014 May 14;6(6):1437-47. doi: 10.1093/gbe/evu100.

18.

Intrasubtype reassortments cause adaptive amino acid replacements in H3N2 influenza genes.

Neverov AD, Lezhnina KV, Kondrashov AS, Bazykin GA.

PLoS Genet. 2014 Jan;10(1):e1004037. doi: 10.1371/journal.pgen.1004037. Epub 2014 Jan 9.

19.

Conserved proteins are fragile.

Assis R, Kondrashov AS.

Mol Biol Evol. 2014 Feb;31(2):419-24. doi: 10.1093/molbev/mst217. Epub 2013 Nov 7.

20.

Paratrypanosoma is a novel early-branching trypanosomatid.

Flegontov P, Votýpka J, Skalický T, Logacheva MD, Penin AA, Tanifuji G, Onodera NT, Kondrashov AS, Volf P, Archibald JM, Lukeš J.

Curr Biol. 2013 Sep 23;23(18):1787-93. doi: 10.1016/j.cub.2013.07.045. Epub 2013 Sep 5.

21.

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.

Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K.

Nature. 2013 Aug 22;500(7463):453-7. doi: 10.1038/nature12326. Epub 2013 Jul 21.

22.

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

Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD.

BMC Genomics. 2013 Jul 15;14:476. doi: 10.1186/1471-2164-14-476.

23.

Prevalence of multinucleotide replacements in evolution of primates and Drosophila.

Terekhanova NV, Bazykin GA, Neverov A, Kondrashov AS, Seplyarskiy VB.

Mol Biol Evol. 2013 Jun;30(6):1315-25. doi: 10.1093/molbev/mst036. Epub 2013 Feb 27.

24.

Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation.

Vakhrusheva OA, Bazykin GA, Kondrashov AS.

Genome Biol Evol. 2013;5(3):532-41. doi: 10.1093/gbe/evt023.

25.

Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection.

Leushkin EV, Bazykin GA, Kondrashov AS.

Genome Biol Evol. 2013;5(3):514-24. doi: 10.1093/gbe/evt021.

26.

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

Bazykin GA, Kondrashov AS.

Proc Biol Sci. 2012 Sep 7;279(1742):3409-17. doi: 10.1098/rspb.2012.0776. Epub 2012 Jun 6.

27.

Fitness conferred by replaced amino acids declines with time.

Naumenko SA, Kondrashov AS, Bazykin GA.

Biol Lett. 2012 Oct 23;8(5):825-8. doi: 10.1098/rsbl.2012.0356. Epub 2012 May 23.

28.

Insertions and deletions trigger adaptive walks in Drosophila proteins.

Leushkin EV, Bazykin GA, Kondrashov AS.

Proc Biol Sci. 2012 Aug 7;279(1740):3075-82. doi: 10.1098/rspb.2011.2571. Epub 2012 Mar 28.

29.

A strong deletion bias in nonallelic gene conversion.

Assis R, Kondrashov AS.

PLoS Genet. 2012;8(2):e1002508. doi: 10.1371/journal.pgen.1002508. Epub 2012 Feb 16.

30.

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

Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA.

Mol Biol Evol. 2012 Aug;29(8):1943-55. doi: 10.1093/molbev/mss071. Epub 2012 Feb 15.

PMID:
22337862
31.

Rate and breadth of protein evolution are only weakly correlated.

Naumenko SA, Kondrashov AS.

Biol Direct. 2012 Feb 15;7:8. doi: 10.1186/1745-6150-7-8.

32.

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

Assis R, Kondrashov AS.

Mol Biol Evol. 2012 May;29(5):1291-5. doi: 10.1093/molbev/msr304. Epub 2011 Dec 8.

PMID:
22160767
33.

Detecting past positive selection through ongoing negative selection.

Bazykin GA, Kondrashov AS.

Genome Biol Evol. 2011;3:1006-13. doi: 10.1093/gbe/evr086. Epub 2011 Aug 22.

34.

On the relationship between the load and the variance of relative fitness.

Shnol EE, Ermakova EA, Kondrashov AS.

Biol Direct. 2011 Apr 14;6:20. doi: 10.1186/1745-6150-6-20.

35.

Bridges: a tool for identifying local similarities in long sequences.

Kondrashov AS, Assis R.

Bioinformatics. 2010 Aug 15;26(16):2055-6. doi: 10.1093/bioinformatics/btq320. Epub 2010 Jun 20.

PMID:
20562450
36.

A method and server for predicting damaging missense mutations.

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR.

Nat Methods. 2010 Apr;7(4):248-9. doi: 10.1038/nmeth0410-248. No abstract available.

37.

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

Kondrashov FA, Kondrashov AS.

Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1169-76. doi: 10.1098/rstb.2009.0286. Review.

38.

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness.

Meer MV, Kondrashov AS, Artzy-Randrup Y, Kondrashov FA.

Nature. 2010 Mar 11;464(7286):279-82. doi: 10.1038/nature08691. Epub 2010 Feb 24.

PMID:
20182427
39.

Rate of sequence divergence under constant selection.

Kondrashov AS, Povolotskaya IS, Ivankov DN, Kondrashov FA.

Biol Direct. 2010 Jan 21;5:5. doi: 10.1186/1745-6150-5-5.

40.

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

Assis R, Kondrashov AS.

Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):7079-82. doi: 10.1073/pnas.0900523106. Epub 2009 Apr 8.

41.

Erratum.

Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS, Sunyaev S.

PLoS Genet. 2008 Dec;4(12). doi: 10.1371/annotation/a81b1fab-890c-447b-a308-5bc8ca3eb21d. Epub 2008 Dec 10.

42.

Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi.

Donmez N, Bazykin GA, Brudno M, Kondrashov AS.

Genetics. 2009 Feb;181(2):685-90. doi: 10.1534/genetics.108.097535. Epub 2008 Dec 15.

43.

Hypermutable non-synonymous sites are under stronger negative selection.

Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Adzuhbei IA, Kondrashov AS, Sunyaev S.

PLoS Genet. 2008 Nov;4(11):e1000281. doi: 10.1371/journal.pgen.1000281. Epub 2008 Nov 28. Erratum in: PLoS Genet. 2008 Dec;4(12):null.

44.

Nested genes and increasing organizational complexity of metazoan genomes.

Assis R, Kondrashov AS, Koonin EV, Kondrashov FA.

Trends Genet. 2008 Oct;24(10):475-8. doi: 10.1016/j.tig.2008.08.003. Epub 2008 Sep 5.

45.

Another step toward quantifying spontaneous mutation.

Kondrashov AS.

Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9133-4. doi: 10.1073/pnas.0804749105. Epub 2008 Jul 1. No abstract available.

46.

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

Minovitsky S, Stegmaier P, Kel A, Kondrashov AS, Dubchak I.

BMC Genomics. 2007 Oct 18;8:378.

47.

Extensive parallelism in protein evolution.

Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS.

Biol Direct. 2007 Aug 16;2:20.

48.

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

Bazykin GA, Dushoff J, Levin SA, Kondrashov AS.

Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19396-401. Epub 2006 Dec 12.

49.

Sympatric speciation under incompatibility selection.

Artzy-Randrup Y, Kondrashov AS.

Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11619-24. Epub 2006 Jul 24.

50.

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

Bernat JA, Crawford GE, Ogurtsov AY, Collins FS, Ginsburg D, Kondrashov AS.

Hum Mol Genet. 2006 Jul 1;15(13):2098-105. Epub 2006 May 24.

PMID:
16723375

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