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Items: 46

1.

Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations.

Seplyarskiy VB, Akkuratov EE, Akkuratova N, Andrianova MA, Nikolaev SI, Bazykin GA, Adameyko I, Sunyaev SR.

Nat Genet. 2019 Jan;51(1):36-41. doi: 10.1038/s41588-018-0285-7. Epub 2018 Dec 3.

PMID:
30510240
2.

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.

3.

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.

4.
5.

Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection.

Popadin K, Peischl S, Garieri M, Sailani MR, Letourneau A, Santoni F, Lukowski SW, Bazykin GA, Nikolaev S, Meyer D, Excoffier L, Reymond A, Antonarakis SE.

Genome Res. 2018 Jan;28(1):1-10. doi: 10.1101/gr.228411.117. Epub 2017 Dec 13.

6.

Parallel Evolution of Metazoan Mitochondrial Proteins.

Klink GV, Bazykin GA.

Genome Biol Evol. 2017 May 1;9(5):1341-1350. doi: 10.1093/gbe/evx025.

7.

Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand.

Andrianova MA, Bazykin GA, Nikolaev SI, Seplyarskiy VB.

Genome Res. 2017 Aug;27(8):1336-1343. doi: 10.1101/gr.219915.116. Epub 2017 May 16.

8.

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.

9.

Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus.

Safina KR, Mironov AA, Bazykin GA.

Genome Biol Evol. 2017 Feb 1;9(2):340-349. doi: 10.1093/gbe/evw295.

10.

Evolution of Local Mutation Rate and Its Determinants.

Terekhanova NV, Seplyarskiy VB, Soldatov RA, Bazykin GA.

Mol Biol Evol. 2017 May 1;34(5):1100-1109. doi: 10.1093/molbev/msx060.

11.

APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context.

Seplyarskiy VB, Andrianova MA, Bazykin GA.

Genome Res. 2017 Feb;27(2):175-184. doi: 10.1101/gr.210336.116. Epub 2016 Dec 9.

12.

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.

13.

Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data.

Kainov YA, Aushev VN, Naumenko SA, Tchevkina EM, Bazykin GA.

Genome Biol Evol. 2016 Jul 2;8(6):1971-9. doi: 10.1093/gbe/evw137.

14.

APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication.

Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI.

Genome Res. 2016 Feb;26(2):174-82. doi: 10.1101/gr.197046.115. Epub 2016 Jan 11.

15.

Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.

Bazykin GA.

Biol Lett. 2015 Oct;11(10). pii: 20150315. doi: 10.1098/rsbl.2015.0315. Review.

16.

Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures.

Seplyarskiy VB, Bazykin GA, Soldatov RA.

Mol Biol Evol. 2015 Dec;32(12):3158-72. doi: 10.1093/molbev/msv184. Epub 2015 Sep 15.

PMID:
26376651
17.

Coordinated Evolution of Influenza A Surface Proteins.

Neverov AD, Kryazhimskiy S, Plotkin JB, Bazykin GA.

PLoS Genet. 2015 Aug 6;11(8):e1005404. doi: 10.1371/journal.pgen.1005404. eCollection 2015 Aug.

18.

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.

19.

Fitness Consequences of Advanced Ancestral Age over Three Generations in Humans.

Hayward AD, Lummaa V, Bazykin GA.

PLoS One. 2015 Jun 1;10(6):e0128197. doi: 10.1371/journal.pone.0128197. eCollection 2015.

20.

Gene age predicts the strength of purifying selection acting on gene expression variation in humans.

Popadin KY, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, Nikolaev SI, Lukowski SW, Bazykin GA, Seplyarskiy VB, Ioannidis P, Zdobnov EM, Dermitzakis ET, Antonarakis SE.

Am J Hum Genet. 2014 Dec 4;95(6):660-74. doi: 10.1016/j.ajhg.2014.11.003.

21.

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.

22.

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.

23.

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.

24.

Short indels are subject to insertion-biased gene conversion.

Leushkin EV, Bazykin GA.

Evolution. 2013 Sep;67(9):2604-13. doi: 10.1111/evo.12129. Epub 2013 May 11.

PMID:
24033170
25.

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.

26.

Functional implications of splicing polymorphisms in the human genome.

Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS.

Hum Mol Genet. 2013 Sep 1;22(17):3449-59. doi: 10.1093/hmg/ddt200. Epub 2013 May 2.

PMID:
23640990
27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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
34.

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.

35.

Prevalence of epistasis in the evolution of influenza A surface proteins.

Kryazhimskiy S, Dushoff J, Bazykin GA, Plotkin JB.

PLoS Genet. 2011 Feb;7(2):e1001301. doi: 10.1371/journal.pgen.1001301. Epub 2011 Feb 17.

36.

Evolution of prokaryotic genes by shift of stop codons.

Vakhrusheva AA, Kazanov MD, Mironov AA, Bazykin GA.

J Mol Evol. 2011 Feb;72(2):138-46. doi: 10.1007/s00239-010-9408-1. Epub 2010 Nov 17.

PMID:
21082168
37.

Young proteins experience more variable selection pressures than old proteins.

Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB.

Genome Res. 2010 Nov;20(11):1574-81. doi: 10.1101/gr.109595.110. Epub 2010 Oct 4.

38.

Alternative translation start sites are conserved in eukaryotic genomes.

Bazykin GA, Kochetov AV.

Nucleic Acids Res. 2011 Jan;39(2):567-77. doi: 10.1093/nar/gkq806. Epub 2010 Sep 22.

39.

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.

40.

Directionality in the evolution of influenza A haemagglutinin.

Kryazhimskiy S, Bazykin GA, Plotkin JB, Dushoff J.

Proc Biol Sci. 2008 Nov 7;275(1650):2455-64. doi: 10.1098/rspb.2008.0521. Erratum in: Proc Biol Sci. 2209 Aug 22;276(1669):3035. Plotkin, Joshua [corrected to Plotkin Joshua B].

41.

Natural selection for nucleotide usage at synonymous and nonsynonymous sites in influenza A virus genes.

Kryazhimskiy S, Bazykin GA, Dushoff J.

J Virol. 2008 May;82(10):4938-45. doi: 10.1128/JVI.02415-07. Epub 2008 Mar 5.

42.

Extensive parallelism in protein evolution.

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

Biol Direct. 2007 Aug 16;2:20.

43.

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.

44.
45.

Rate of promoter class turn-over in yeast evolution.

Bazykin GA, Kondrashov AS.

BMC Evol Biol. 2006 Feb 10;6:14.

46.

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

Bazykin GA, Kondrashov FA, Ogurtsov AY, Sunyaev S, Kondrashov AS.

Nature. 2004 Jun 3;429(6991):558-62.

PMID:
15175752

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