• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4618902)   Today's Articles (5438)   Subscriber (49402)
For: Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biol Direct 2007;2:20. [PMID: 17705846 PMCID: PMC2020468 DOI: 10.1186/1745-6150-2-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 08/16/2007] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cacti-associated yeasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557833. [PMID: 37745407 PMCID: PMC10515907 DOI: 10.1101/2023.09.14.557833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
2
Pascarelli S, Laurino P. Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins. PLoS Comput Biol 2022;18:e1010016. [PMID: 35377869 PMCID: PMC9009777 DOI: 10.1371/journal.pcbi.1010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/14/2022] [Accepted: 03/12/2022] [Indexed: 11/25/2022]  Open
3
Cummings TFM, Gori K, Sanchez-Pulido L, Gavriilidis G, Moi D, Wilson AR, Murchison E, Dessimoz C, Ponting CP, Christophorou MA. Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria. Mol Biol Evol 2021;39:6420225. [PMID: 34730808 PMCID: PMC8826395 DOI: 10.1093/molbev/msab317] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
4
Kim J, Lal A, Kil EJ, Kwak HR, Yoon HS, Choi HS, Kim M, Ali M, Lee S. Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses. Microorganisms 2021;9:microorganisms9061111. [PMID: 34063757 PMCID: PMC8223792 DOI: 10.3390/microorganisms9061111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022]  Open
5
Burskaia V, Naumenko S, Schelkunov M, Bedulina D, Neretina T, Kondrashov A, Yampolsky L, Bazykin GA. Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock. Genome Biol Evol 2020;12:1493-1503. [PMID: 32653919 DOI: 10.1093/gbe/evaa138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 11/12/2022]  Open
6
Recurrent sequence evolution after independent gene duplication. BMC Evol Biol 2020;20:98. [PMID: 32770961 PMCID: PMC7414715 DOI: 10.1186/s12862-020-01660-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/17/2020] [Indexed: 11/10/2022]  Open
7
Mendes FK, Livera AP, Hahn MW. The perils of intralocus recombination for inferences of molecular convergence. Philos Trans R Soc Lond B Biol Sci 2019;374:20180244. [PMID: 31154973 DOI: 10.1098/rstb.2018.0244] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
8
Rey C, Guéguen L, Sémon M, Boussau B. Accurate Detection of Convergent Amino-Acid Evolution with PCOC. Mol Biol Evol 2018;35:2296-2306. [PMID: 29986048 PMCID: PMC6106957 DOI: 10.1093/molbev/msy114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
9
Sundaram L, Gao H, Padigepati SR, McRae JF, Li Y, Kosmicki JA, Fritzilas N, Hakenberg J, Dutta A, Shon J, Xu J, Batzoglou S, Li X, Farh KKH. Predicting the clinical impact of human mutation with deep neural networks. Nat Genet 2018;50:1161-1170. [PMID: 30038395 PMCID: PMC6237276 DOI: 10.1038/s41588-018-0167-z] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022]
10
Zou Z, Zhang J. Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution. Mol Biol Evol 2017;34:1682-1688. [PMID: 28379570 DOI: 10.1093/molbev/msx109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
11
Naumenko SA, Logacheva MD, Popova NV, Klepikova AV, Penin AA, Bazykin GA, Etingova AE, Mugue NS, Kondrashov AS, Yampolsky LY. Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Mol Ecol 2017;26:536-553. [DOI: 10.1111/mec.13927] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022]
12
Evolutionary switches between two serine codon sets are driven by selection. Proc Natl Acad Sci U S A 2016;113:13109-13113. [PMID: 27799560 DOI: 10.1073/pnas.1615832113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
13
Bazykin GA. Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins. Biol Lett 2016;11:rsbl.2015.0315. [PMID: 26445980 DOI: 10.1098/rsbl.2015.0315] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
14
Mendes FK, Hahn Y, Hahn MW. Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time. Mol Biol Evol 2016;33:3299-3307. [PMID: 27634870 DOI: 10.1093/molbev/msw197] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
15
Storz JF. Causes of molecular convergence and parallelism in protein evolution. Nat Rev Genet 2016;17:239-50. [PMID: 26972590 PMCID: PMC5482790 DOI: 10.1038/nrg.2016.11] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
16
Zou Z, Zhang J. Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations? Mol Biol Evol 2015;32:2085-96. [PMID: 25862140 DOI: 10.1093/molbev/msv091] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
17
Zou Z, Zhang J. No genome-wide protein sequence convergence for echolocation. Mol Biol Evol 2015;32:1237-41. [PMID: 25631925 DOI: 10.1093/molbev/msv014] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
18
Usmanova DR, Ferretti L, Povolotskaya IS, Vlasov PK, Kondrashov FA. A model of substitution trajectories in sequence space and long-term protein evolution. Mol Biol Evol 2014;32:542-54. [PMID: 25415964 DOI: 10.1093/molbev/msu318] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
19
Livnat A. Interaction-based evolution: how natural selection and nonrandom mutation work together. Biol Direct 2013;8:24. [PMID: 24139515 PMCID: PMC4231362 DOI: 10.1186/1745-6150-8-24] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/26/2013] [Indexed: 12/30/2022]  Open
20
Naumenko SA, Kondrashov AS, Bazykin GA. Fitness conferred by replaced amino acids declines with time. Biol Lett 2012;8:825-8. [PMID: 22628094 DOI: 10.1098/rsbl.2012.0356] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
21
Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Mol Biol Evol 2012;29:1943-55. [PMID: 22337862 DOI: 10.1093/molbev/mss071] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
22
Bazykin GA, Kondrashov AS. Detecting past positive selection through ongoing negative selection. Genome Biol Evol 2011;3:1006-13. [PMID: 21859804 PMCID: PMC3184776 DOI: 10.1093/gbe/evr086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
23
Hughes AL, Friedman R. More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene 2009;440:50-6. [PMID: 19332110 DOI: 10.1016/j.gene.2009.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 03/16/2009] [Accepted: 03/19/2009] [Indexed: 02/04/2023]
24
Kryazhimskiy S, Bazykin GA, Plotkin JB, Plotkin J, Dushoff J. Directionality in the evolution of influenza A haemagglutinin. Proc Biol Sci 2008;275:2455-64. [PMID: 18647721 PMCID: PMC2603193 DOI: 10.1098/rspb.2008.0521] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
25
Rokas A, Carroll SB. Frequent and widespread parallel evolution of protein sequences. Mol Biol Evol 2008;25:1943-53. [PMID: 18583353 DOI: 10.1093/molbev/msn143] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
26
Zhang WK, Zhang C, Zhang JJ, Liu SV. Occurrence of cancer at multiple sites: towards distinguishing multigenesis from metastasis. Biol Direct 2008;3:14. [PMID: 18405362 PMCID: PMC2373780 DOI: 10.1186/1745-6150-3-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 04/11/2008] [Indexed: 12/11/2022]  Open
27
Rogozin IB, Thomson K, Csürös M, Carmel L, Koonin EV. Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. Biol Direct 2008;3:7. [PMID: 18346278 PMCID: PMC2292158 DOI: 10.1186/1745-6150-3-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 03/17/2008] [Indexed: 11/10/2022]  Open
28
Pinel-Galzi A, Rakotomalala M, Sangu E, Sorho F, Kanyeka Z, Traoré O, Sérémé D, Poulicard N, Rabenantoandro Y, Séré Y, Konaté G, Ghesquière A, Hébrard E, Fargette D. Theme and variations in the evolutionary pathways to virulence of an RNA plant virus species. PLoS Pathog 2007;3:e180. [PMID: 18039030 PMCID: PMC2094307 DOI: 10.1371/journal.ppat.0030180] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 10/12/2007] [Indexed: 11/19/2022]  Open
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA