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Topological features of rugged fitness landscapes in sequence space.
Kondrashov DA, Kondrashov FA. Kondrashov DA, et al. Trends Genet. 2015 Jan;31(1):24-33. doi: 10.1016/j.tig.2014.09.009. Epub 2014 Oct 15. Trends Genet. 2015. PMID: 25438718 Review.
Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M. Howe K, et al. Open Biol. 2016 Apr;6(4):160009. doi: 10.1098/rsob.160009. Epub 2016 Apr 27. Open Biol. 2016. PMID: 27248802 Free PMC article.
Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13.
Kretz CA, Dai M, Soylemez O, Yee A, Desch KC, Siemieniak D, Tomberg K, Kondrashov FA, Meng F, Ginsburg D. Kretz CA, et al. Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9328-33. doi: 10.1073/pnas.1511328112. Epub 2015 Jul 13. Proc Natl Acad Sci U S A. 2015. PMID: 26170332 Free PMC article.
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. Sarkisyan KS, et al. Nature. 2016 May 19;533(7603):397-401. doi: 10.1038/nature17995. Epub 2016 May 11. Nature. 2016. PMID: 27193686 Free PMC article.
Rate of sequence divergence under constant selection.
Kondrashov AS, Povolotskaya IS, Ivankov DN, Kondrashov FA. Kondrashov AS, et al. Biol Direct. 2010 Jan 21;5:5. doi: 10.1186/1745-6150-5-5. Biol Direct. 2010. PMID: 20092641 Free PMC article.
Estimating the rate of irreversibility in protein evolution.
Soylemez O, Kondrashov FA. Soylemez O, et al. Genome Biol Evol. 2012;4(12):1213-22. doi: 10.1093/gbe/evs096. Genome Biol Evol. 2012. PMID: 23132897 Free PMC article.
Epistasis as the primary factor in molecular evolution.
Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA. Breen MS, et al. Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14. Nature. 2012. PMID: 23064225
Gene duplication as a mechanism of genomic adaptation to a changing environment.
Kondrashov FA. Kondrashov FA. Proc Biol Sci. 2012 Dec 22;279(1749):5048-57. doi: 10.1098/rspb.2012.1108. Epub 2012 Sep 12. Proc Biol Sci. 2012. PMID: 22977152 Free PMC article. Review.
Stop codons in bacteria are not selectively equivalent.
Povolotskaya IS, Kondrashov FA, Ledda A, Vlasov PK. Povolotskaya IS, et al. Biol Direct. 2012 Sep 13;7:30. doi: 10.1186/1745-6150-7-30. Biol Direct. 2012. PMID: 22974057 Free PMC article.
Measurements of spontaneous rates of mutations in the recent past and the near future.
Kondrashov FA, Kondrashov AS. Kondrashov FA, et al. Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1169-76. doi: 10.1098/rstb.2009.0286. Philos Trans R Soc Lond B Biol Sci. 2010. PMID: 20308091 Free PMC article. Review.
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