72 Publications

Mark all

[72]
2019 | Journal Article | IST-REx-ID: 6419   OA
Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.
View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 5780   OA
Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.
View | Files available | DOI
 
[70]
2018 | Journal Article | IST-REx-ID: 5995   OA
Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279   OA
Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19.
View | Files available | DOI
 
[68]
2016 | Journal Article | IST-REx-ID: 896
Howe K, Schiffer P, Zielinski J, Wiehe T, Laird G, Marioni J, Soylemez O, Kondrashov F, Leptin M. 2016. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. 6(4).
View | DOI
 
[67]
2016 | Journal Article | IST-REx-ID: 853
Rivkina E, Petrovskaya L, Vishnivetskaya T, Krivushin K, Shmakova L, Tutukina M, Meyers A, Kondrashov F. 2016. Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. 13(7), 2207–2219.
View | DOI
 
[66]
2016 | Journal Article | IST-REx-ID: 850
Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533, 397–401.
View | DOI
 
[65]
2016 | Journal Article | IST-REx-ID: 849
Saint Léger A, Bello C, Dans P, Torres A, Novoa E, Camacho N, Orozco M, Kondrashov F, Ribas De Pouplana L. 2016. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances. 2(4), e1501860–e1501860.
View | DOI
 
[64]
2015 | Journal Article | IST-REx-ID: 866
Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.
View | DOI
 
[63]
2015 | Journal Article | IST-REx-ID: 886
Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.
View | DOI
 
[62]
2015 | Journal Article | IST-REx-ID: 906
Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 848
Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 845
Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 852
Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
View | DOI
 
[58]
2014 | Journal Article | IST-REx-ID: 865
Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578.
View | DOI
 
[57]
2014 | Journal Article | IST-REx-ID: 892
Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.
View | DOI
 
[56]
2014 | Journal Article | IST-REx-ID: 856
Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5.
View | DOI
 
[55]
2014 | Journal Article | IST-REx-ID: 863
Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114.
View | DOI
 
[54]
2013 | Journal Article | IST-REx-ID: 905   OA
Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30.
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[53]
2013 | Journal Article | IST-REx-ID: 894
Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).
View | DOI
 
[52]
2013 | Journal Article | IST-REx-ID: 899
Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3.
View | DOI
 
[51]
2012 | Journal Article | IST-REx-ID: 846
Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.
View | DOI
 
[50]
2012 | Journal Article | IST-REx-ID: 858
Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7.
View | DOI
 
[49]
2012 | Journal Article | IST-REx-ID: 900
Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538.
View | DOI
 
[48]
2012 | Journal Article | IST-REx-ID: 887
Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 279(1749), 5048–5057.
View | DOI
 
[47]
2011 | Journal Article | IST-REx-ID: 890
Koblik E, Red’Kin Y, Meer M, Derelle R, Golenkina S, Kondrashov F, Arkhipov V. 2011. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 6(4).
View | DOI
 
[46]
2011 | Book Chapter | IST-REx-ID: 881
Kondrashov F. 2011. Gene Dosage and Duplication. Evolution after Gene Duplication. 57–76.
View | DOI
 
[45]
2010 | Journal Article | IST-REx-ID: 857
Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion of the protein universe. Nature. 465(7300), 922–926.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 872
Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 884
Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.
View | DOI
 
[42]
2010 | Journal Article | IST-REx-ID: 891
Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.
View | DOI
 
[41]
2010 | Journal Article | IST-REx-ID: 901
Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5.
View | DOI
 
[40]
2010 | Journal Article | IST-REx-ID: 862
Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.
View | DOI
 
[39]
2009 | Journal Article | IST-REx-ID: 908
Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli S, Frolova L, Söll D, Kisselev L. 2009. Translation termination in pyrrolysine-utilizing archaea. FEBS Letters. 583(21), 3455–3460.
View | DOI
 
[38]
2008 | Journal Article | IST-REx-ID: 895
Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).
View | DOI
 
[37]
2008 | Journal Article | IST-REx-ID: 907
Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478.
View | DOI
 
[36]
2008 | Journal Article | IST-REx-ID: 844
Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11).
View | DOI
 
[35]
2007 | Journal Article | IST-REx-ID: 904
Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. 2007. Extensive parallelism in protein evolution. Biology Direct. 2.
View | DOI
 
[34]
2007 | Journal Article | IST-REx-ID: 860
Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. 81(1), 32–43.
View | DOI
 
[33]
2007 | Journal Article | IST-REx-ID: 861
Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 8.
View | DOI
 
[32]
2007 | Journal Article | IST-REx-ID: 879
Kondrashov F, Gurbich T, Vlasov P. 2007. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. 23(5), 215–218.
View | DOI
 
[31]
2006 | Journal Article | IST-REx-ID: 903
Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. 6.
View | DOI
 
[30]
2006 | Journal Article | IST-REx-ID: 869
Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 240(4), 616–626.
View | DOI
 
[29]
2006 | Journal Article | IST-REx-ID: 854
Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 4(3), 0403–0410.
View | DOI
 
[28]
2006 | Journal Article | IST-REx-ID: 873
Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 239(2), 141–151.
View | DOI
 
[27]
2006 | Journal Article | IST-REx-ID: 868
Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. 1.
View | DOI
 
[26]
2005 | Journal Article | IST-REx-ID: 877
Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395.
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[25]
2005 | Journal Article | IST-REx-ID: 878
Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10.
View | DOI
 
[24]
2005 | Journal Article | IST-REx-ID: 880
Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403.
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[23]
2005 | Journal Article | IST-REx-ID: 893
Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 843
Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201.
View | DOI
 
[21]
2005 | Journal Article | IST-REx-ID: 882
Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 889
Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 898
Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 429(6991), 558–562.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 870
Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.
View | DOI
 
[16]
2004 | Journal Article | IST-REx-ID: 875
Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291.
View | DOI
 
[15]
2004 | Journal Article | IST-REx-ID: 902
Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 14(5), 802–811.
View | DOI
 
[14]
2003 | Journal Article | IST-REx-ID: 876
Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. 19(3), 115–119.
View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 847
Sunyaev S, Kondrashov F, Bork P, Ramensky V. 2003. Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. 12(24), 3325–3330.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 871
Kondrashov F, Rogozin I, Wolf Y, Koonin E. 2002. Selection in the evolution of gene duplications . Genome Biology. 3(2).
View | DOI
 
[11]
2002 | Journal Article | IST-REx-ID: 859
Perelygin A, Kondrashov F, Rogozin I, Brinton M. 2002. Evolution of the mouse polyubiquitin C gene. Journal of Molecular Evolution. 55(2), 202–210.
View | DOI
 
[10]
2002 | Journal Article | IST-REx-ID: 885
Kondrashov A, Sunyaev S, Kondrashov F. 2002. Dobzhansky-Muller incompatibilities in protein evolution. PNAS. 99(23), 14878–14883.
View | DOI
 
[9]
2002 | Journal Article | IST-REx-ID: 897
Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. 2002. Selection for short introns in highly expressed genes. Nature Genetics. 31(4), 415–418.
View | DOI
 
[8]
2001 | Journal Article | IST-REx-ID: 888
Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. 2001. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2(12).
View | DOI
 
[7]
2001 | Journal Article | IST-REx-ID: 841
Wolf Y, Kondrashov F, Koonin E. 2001. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 17(9), 499–501.
View | DOI
 
[6]
2001 | Journal Article | IST-REx-ID: 874
Kondrashov F, Kondrashov A. 2001. Multidimensional epistasis and the disadvantage of sex. PNAS. 98(21), 12089–12092.
View | DOI
 
[5]
2001 | Journal Article | IST-REx-ID: 855
Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. 2001. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. 17(10), 890–900.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 867
Kondrashov F, Koonin E. 2001. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 10(23), 2661–2669.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 851
Rogozin I, Kondrashov F, Glazko G. 2001. Use of mutation spectra analysis software. Human Mutation. 17(2), 83–102.
View | DOI
 
[2]
2000 | Journal Article | IST-REx-ID: 842
Wolf Y, Kondrashov F, Koonin E. 2000. No footprints of primordial introns in a eukaryotic genome. Trends in Genetics. 16(8), 333–334.
View | DOI
 
[1]
1999 | Journal Article | IST-REx-ID: 883
Kondrashov A, Kondrashov F. 1999. Interactions among quantitative traits in the course of sympatric speciation. Nature. 400(6742), 351–354.
View | DOI
 

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72 Publications

Mark all

[72]
2019 | Journal Article | IST-REx-ID: 6419   OA
Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.
View | Files available | DOI
 
[71]
2018 | Journal Article | IST-REx-ID: 5780   OA
Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.
View | Files available | DOI
 
[70]
2018 | Journal Article | IST-REx-ID: 5995   OA
Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279   OA
Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19.
View | Files available | DOI
 
[68]
2016 | Journal Article | IST-REx-ID: 896
Howe K, Schiffer P, Zielinski J, Wiehe T, Laird G, Marioni J, Soylemez O, Kondrashov F, Leptin M. 2016. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. 6(4).
View | DOI
 
[67]
2016 | Journal Article | IST-REx-ID: 853
Rivkina E, Petrovskaya L, Vishnivetskaya T, Krivushin K, Shmakova L, Tutukina M, Meyers A, Kondrashov F. 2016. Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. 13(7), 2207–2219.
View | DOI
 
[66]
2016 | Journal Article | IST-REx-ID: 850
Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533, 397–401.
View | DOI
 
[65]
2016 | Journal Article | IST-REx-ID: 849
Saint Léger A, Bello C, Dans P, Torres A, Novoa E, Camacho N, Orozco M, Kondrashov F, Ribas De Pouplana L. 2016. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances. 2(4), e1501860–e1501860.
View | DOI
 
[64]
2015 | Journal Article | IST-REx-ID: 866
Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.
View | DOI
 
[63]
2015 | Journal Article | IST-REx-ID: 886
Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.
View | DOI
 
[62]
2015 | Journal Article | IST-REx-ID: 906
Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 848
Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 845
Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 852
Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
View | DOI
 
[58]
2014 | Journal Article | IST-REx-ID: 865
Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578.
View | DOI
 
[57]
2014 | Journal Article | IST-REx-ID: 892
Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.
View | DOI
 
[56]
2014 | Journal Article | IST-REx-ID: 856
Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5.
View | DOI
 
[55]
2014 | Journal Article | IST-REx-ID: 863
Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114.
View | DOI
 
[54]
2013 | Journal Article | IST-REx-ID: 905   OA
Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30.
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[53]
2013 | Journal Article | IST-REx-ID: 894
Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).
View | DOI
 
[52]
2013 | Journal Article | IST-REx-ID: 899
Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3.
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[51]
2012 | Journal Article | IST-REx-ID: 846
Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.
View | DOI
 
[50]
2012 | Journal Article | IST-REx-ID: 858
Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7.
View | DOI
 
[49]
2012 | Journal Article | IST-REx-ID: 900
Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538.
View | DOI
 
[48]
2012 | Journal Article | IST-REx-ID: 887
Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 279(1749), 5048–5057.
View | DOI
 
[47]
2011 | Journal Article | IST-REx-ID: 890
Koblik E, Red’Kin Y, Meer M, Derelle R, Golenkina S, Kondrashov F, Arkhipov V. 2011. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 6(4).
View | DOI
 
[46]
2011 | Book Chapter | IST-REx-ID: 881
Kondrashov F. 2011. Gene Dosage and Duplication. Evolution after Gene Duplication. 57–76.
View | DOI
 
[45]
2010 | Journal Article | IST-REx-ID: 857
Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion of the protein universe. Nature. 465(7300), 922–926.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 872
Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 884
Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.
View | DOI
 
[42]
2010 | Journal Article | IST-REx-ID: 891
Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.
View | DOI
 
[41]
2010 | Journal Article | IST-REx-ID: 901
Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5.
View | DOI
 
[40]
2010 | Journal Article | IST-REx-ID: 862
Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.
View | DOI
 
[39]
2009 | Journal Article | IST-REx-ID: 908
Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli S, Frolova L, Söll D, Kisselev L. 2009. Translation termination in pyrrolysine-utilizing archaea. FEBS Letters. 583(21), 3455–3460.
View | DOI
 
[38]
2008 | Journal Article | IST-REx-ID: 895
Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).
View | DOI
 
[37]
2008 | Journal Article | IST-REx-ID: 907
Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478.
View | DOI
 
[36]
2008 | Journal Article | IST-REx-ID: 844
Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11).
View | DOI
 
[35]
2007 | Journal Article | IST-REx-ID: 904
Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. 2007. Extensive parallelism in protein evolution. Biology Direct. 2.
View | DOI
 
[34]
2007 | Journal Article | IST-REx-ID: 860
Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. 81(1), 32–43.
View | DOI
 
[33]
2007 | Journal Article | IST-REx-ID: 861
Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 8.
View | DOI
 
[32]
2007 | Journal Article | IST-REx-ID: 879
Kondrashov F, Gurbich T, Vlasov P. 2007. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. 23(5), 215–218.
View | DOI
 
[31]
2006 | Journal Article | IST-REx-ID: 903
Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. 6.
View | DOI
 
[30]
2006 | Journal Article | IST-REx-ID: 869
Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 240(4), 616–626.
View | DOI
 
[29]
2006 | Journal Article | IST-REx-ID: 854
Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 4(3), 0403–0410.
View | DOI
 
[28]
2006 | Journal Article | IST-REx-ID: 873
Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 239(2), 141–151.
View | DOI
 
[27]
2006 | Journal Article | IST-REx-ID: 868
Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. 1.
View | DOI
 
[26]
2005 | Journal Article | IST-REx-ID: 877
Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395.
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[25]
2005 | Journal Article | IST-REx-ID: 878
Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10.
View | DOI
 
[24]
2005 | Journal Article | IST-REx-ID: 880
Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403.
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[23]
2005 | Journal Article | IST-REx-ID: 893
Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 843
Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201.
View | DOI
 
[21]
2005 | Journal Article | IST-REx-ID: 882
Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 889
Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 898
Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 429(6991), 558–562.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 870
Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.
View | DOI
 
[16]
2004 | Journal Article | IST-REx-ID: 875
Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291.
View | DOI
 
[15]
2004 | Journal Article | IST-REx-ID: 902
Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 14(5), 802–811.
View | DOI
 
[14]
2003 | Journal Article | IST-REx-ID: 876
Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. 19(3), 115–119.
View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 847
Sunyaev S, Kondrashov F, Bork P, Ramensky V. 2003. Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. 12(24), 3325–3330.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 871
Kondrashov F, Rogozin I, Wolf Y, Koonin E. 2002. Selection in the evolution of gene duplications . Genome Biology. 3(2).
View | DOI
 
[11]
2002 | Journal Article | IST-REx-ID: 859
Perelygin A, Kondrashov F, Rogozin I, Brinton M. 2002. Evolution of the mouse polyubiquitin C gene. Journal of Molecular Evolution. 55(2), 202–210.
View | DOI
 
[10]
2002 | Journal Article | IST-REx-ID: 885
Kondrashov A, Sunyaev S, Kondrashov F. 2002. Dobzhansky-Muller incompatibilities in protein evolution. PNAS. 99(23), 14878–14883.
View | DOI
 
[9]
2002 | Journal Article | IST-REx-ID: 897
Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. 2002. Selection for short introns in highly expressed genes. Nature Genetics. 31(4), 415–418.
View | DOI
 
[8]
2001 | Journal Article | IST-REx-ID: 888
Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. 2001. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2(12).
View | DOI
 
[7]
2001 | Journal Article | IST-REx-ID: 841
Wolf Y, Kondrashov F, Koonin E. 2001. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 17(9), 499–501.
View | DOI
 
[6]
2001 | Journal Article | IST-REx-ID: 874
Kondrashov F, Kondrashov A. 2001. Multidimensional epistasis and the disadvantage of sex. PNAS. 98(21), 12089–12092.
View | DOI
 
[5]
2001 | Journal Article | IST-REx-ID: 855
Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. 2001. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. 17(10), 890–900.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 867
Kondrashov F, Koonin E. 2001. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 10(23), 2661–2669.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 851
Rogozin I, Kondrashov F, Glazko G. 2001. Use of mutation spectra analysis software. Human Mutation. 17(2), 83–102.
View | DOI
 
[2]
2000 | Journal Article | IST-REx-ID: 842
Wolf Y, Kondrashov F, Koonin E. 2000. No footprints of primordial introns in a eukaryotic genome. Trends in Genetics. 16(8), 333–334.
View | DOI
 
[1]
1999 | Journal Article | IST-REx-ID: 883
Kondrashov A, Kondrashov F. 1999. Interactions among quantitative traits in the course of sympatric speciation. Nature. 400(6742), 351–354.
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