73 Publications

Mark all

[73]
2019 | Journal Article | IST-REx-ID: 6419   OA
An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape
V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).
View | Files available | DOI
 
[72]
2019 | Journal Article | IST-REx-ID: 7181   OA
Large multiple sequence alignments with a root-to-leaf regressive method
E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 5780   OA
Genetically encodable bioluminescent system from fungi
A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.
View | Files available | DOI
 
[70]
2018 | Journal Article | IST-REx-ID: 5995   OA
Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation
D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279   OA
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).
View | Files available | DOI
 
[68]
2016 | Journal Article | IST-REx-ID: 853
Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions
E. Rivkina, L. Petrovskaya, T. Vishnivetskaya, K. Krivushin, L. Shmakova, M. Tutukina, A. Meyers, F. Kondrashov, Biogeosciences 13 (2016) 2207–2219.
View | DOI
 
[67]
2016 | Journal Article | IST-REx-ID: 896
Structure and evolutionary history of a large family of NLR proteins in the zebrafish
K. Howe, P. Schiffer, J. Zielinski, T. Wiehe, G. Laird, J. Marioni, O. Soylemez, F. Kondrashov, M. Leptin, Open Biology 6 (2016).
View | DOI
 
[66]
2016 | Journal Article | IST-REx-ID: 850
Local fitness landscape of the green fluorescent protein
K. Sarkisyan, D. Bolotin, M. Meer, D. Usmanova, A. Mishin, G. Sharonov, D. Ivankov, N. Bozhanova, M. Baranov, O. Soylemez, N. Bogatyreva, P. Vlasov, E. Egorov, M. Logacheva, A. Kondrashov, D. Chudakov, E. Putintseva, I. Mamedov, D. Tawfik, K. Lukyanov, F. Kondrashov, Nature 533 (2016) 397–401.
View | DOI
 
[65]
2016 | Journal Article | IST-REx-ID: 849
Saturation of recognition elements blocks evolution of new tRNA identities
A. Saint Léger, C. Bello, P. Dans, A. Torres, E. Novoa, N. Camacho, M. Orozco, F. Kondrashov, L. Ribas De Pouplana, Science Advances 2 (2016) e1501860–e1501860.
View | DOI
 
[64]
2015 | Journal Article | IST-REx-ID: 866
Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13
C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.
View | DOI
 
[63]
2015 | Journal Article | IST-REx-ID: 886
Topological features of rugged fitness landscapes in sequence space
D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.
View | DOI
 
[62]
2015 | Journal Article | IST-REx-ID: 906
Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer
O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 848
A model of substitution trajectories in sequence space and long-term protein evolution
D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 845
Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity
V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 852
Long-Term asymmetrical acceleration of protein evolution after gene duplication
O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
View | DOI
 
[58]
2014 | Journal Article | IST-REx-ID: 865
Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling
A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
View | DOI
 
[57]
2014 | Journal Article | IST-REx-ID: 892
A structural perspective of compensatory evolution
D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112.
View | DOI
 
[56]
2014 | Journal Article | IST-REx-ID: 856
Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network
K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014).
View | DOI
 
[55]
2014 | Journal Article | IST-REx-ID: 863
The ctenophore genome and the evolutionary origins of neural systems
L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
View | DOI
 
[54]
2013 | Journal Article | IST-REx-ID: 905   OA
Birds of Mys Shmidta, north Chukotka, Russia
V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.
View | Download (ext.)
 
[53]
2013 | Journal Article | IST-REx-ID: 894
Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R
R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).
View | DOI
 
[52]
2013 | Journal Article | IST-REx-ID: 899
Breen et al. reply
M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3.
View | DOI
 
[51]
2012 | Journal Article | IST-REx-ID: 846
Estimating the rate of irreversibility in protein evolution
O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.
View | DOI
 
[50]
2012 | Journal Article | IST-REx-ID: 858
Stop codons in bacteria are not selectively equivalent
I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).
View | DOI
 
[49]
2012 | Journal Article | IST-REx-ID: 900
Epistasis as the primary factor in molecular evolution
M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538.
View | DOI
 
[48]
2012 | Journal Article | IST-REx-ID: 887
Gene duplication as a mechanism of genomic adaptation to a changing environment
F. Kondrashov, Proceedings of the Royal Society of London Series B Biological Sciences 279 (2012) 5048–5057.
View | DOI
 
[47]
2011 | Journal Article | IST-REx-ID: 890
Acrocephalus orinus: A case of Mistaken identity
E. Koblik, Y. Red’Kin, M. Meer, R. Derelle, S. Golenkina, F. Kondrashov, V. Arkhipov, PLoS One 6 (2011).
View | DOI
 
[46]
2011 | Book Chapter | IST-REx-ID: 881
Gene Dosage and Duplication
F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.
View | DOI
 
[45]
2010 | Journal Article | IST-REx-ID: 857
Sequence space and the ongoing expansion of the protein universe
I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 872
Measurements of spontaneous rates of mutations in the recent past and the near future
F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 884
Rate of sequence divergence under constant selection
A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010).
View | DOI
 
[42]
2010 | Journal Article | IST-REx-ID: 891
The evolution of gene duplications: Classifying and distinguishing between models
H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.
View | DOI
 
[41]
2010 | Journal Article | IST-REx-ID: 901
Mitochondrial pathogenic mutations are population-specific
M. Breen, F. Kondrashov, Biology Direct 5 (2010).
View | DOI
 
[40]
2010 | Journal Article | IST-REx-ID: 862
Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282.
View | DOI
 
[39]
2009 | Journal Article | IST-REx-ID: 908
Translation termination in pyrrolysine-utilizing archaea
E. Alkalaeva, B. Eliseev, A. Ambrogelly, P. Vlasov, F. Kondrashov, S. Gundllapalli, L. Frolova, D. Söll, L. Kisselev, FEBS Letters 583 (2009) 3455–3460.
View | DOI
 
[38]
2008 | Journal Article | IST-REx-ID: 895
Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene
Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008).
View | DOI
 
[37]
2008 | Journal Article | IST-REx-ID: 844
Hypermutable non-synonymous sites are under stronger negative selection
S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008).
View | DOI
 
[36]
2008 | Journal Article | IST-REx-ID: 907
Nested genes and increasing organizational complexity of metazoan genomes
R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24 (2008) 475–478.
View | DOI
 
[35]
2007 | Journal Article | IST-REx-ID: 860
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
O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev, American Journal of Human Genetics 81 (2007) 32–43.
View | DOI
 
[34]
2007 | Journal Article | IST-REx-ID: 904
Extensive parallelism in protein evolution
G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, A. Kondrashov, Biology Direct 2 (2007).
View | DOI
 
[33]
2007 | Journal Article | IST-REx-ID: 861
A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures
K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).
View | DOI
 
[32]
2007 | Journal Article | IST-REx-ID: 879
Selection for functional uniformity of tuf duplicates in γ-proteobacteria
F. Kondrashov, T. Gurbich, P. Vlasov, Trends in Genetics 23 (2007) 215–218.
View | DOI
 
[31]
2006 | Journal Article | IST-REx-ID: 903
Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis
V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006).
View | DOI
 
[30]
2006 | Journal Article | IST-REx-ID: 869
Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites
F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology 240 (2006) 616–626.
View | DOI
 
[29]
2006 | Journal Article | IST-REx-ID: 854
Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius
E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov, A. Grigorenko, PLoS Biology 4 (2006) 0403–0410.
View | DOI
 
[28]
2006 | Journal Article | IST-REx-ID: 873
Role of selection in fixation of gene duplications
F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151.
View | DOI
 
[27]
2006 | Journal Article | IST-REx-ID: 868
Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation
F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology Direct 1 (2006).
View | DOI
 
 
[25]
2005 | Journal Article | IST-REx-ID: 878
In search of the limits of evolution
F. Kondrashov, Nature Genetics 37 (2005) 9–10.
View | DOI
 
 
[23]
2005 | Journal Article | IST-REx-ID: 893
A universal trend of amino acid gain and loss in protein evolution
I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 843
Distribution of the strength of selection against amino acid replacements in human proteins
L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201.
View | DOI
 
[21]
2005 | Journal Article | IST-REx-ID: 882
Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
Prediction of functional sites by analysis of sequence and structure conservation
A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 889
Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs
A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 898
Positive selection at sites of multiple amino acid replacements since rat-mouse divergence
G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 870
Bioinformatical assay of human gene morbidity
F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.
View | DOI
 
[16]
2004 | Journal Article | IST-REx-ID: 875 View | DOI
 
[15]
2004 | Journal Article | IST-REx-ID: 902
The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811.
View | DOI
 
[14]
2003 | Journal Article | IST-REx-ID: 876 View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 847
Impact of selection, mutation rate and genetic drift on human genetic variation
S. Sunyaev, F. Kondrashov, P. Bork, V. Ramensky, Human Molecular Genetics 12 (2003) 3325–3330.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 871
Selection in the evolution of gene duplications
F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002).
View | DOI
 
[11]
2002 | Journal Article | IST-REx-ID: 859
Evolution of the mouse polyubiquitin C gene
A. Perelygin, F. Kondrashov, I. Rogozin, M. Brinton, Journal of Molecular Evolution 55 (2002) 202–210.
View | DOI
 
[10]
2002 | Journal Article | IST-REx-ID: 885
Dobzhansky-Muller incompatibilities in protein evolution
A. Kondrashov, S. Sunyaev, F. Kondrashov, PNAS 99 (2002) 14878–14883.
View | DOI
 
[9]
2002 | Journal Article | IST-REx-ID: 897
Selection for short introns in highly expressed genes
C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, F. Kondrashov, Nature Genetics 31 (2002) 415–418.
View | DOI
 
[8]
2001 | Journal Article | IST-REx-ID: 888
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins
I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome Biology 2 (2001).
View | DOI
 
[7]
2001 | Journal Article | IST-REx-ID: 841
Footprints of primordial introns on the eukaryotic genome: still no clear traces
Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 17 (2001) 499–501.
View | DOI
 
[6]
2001 | Journal Article | IST-REx-ID: 874
Multidimensional epistasis and the disadvantage of sex
F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.
View | DOI
 
[5]
2001 | Journal Article | IST-REx-ID: 855
Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon
I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, L. Milanesi, Bioinformatics 17 (2001) 890–900.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 867
Origin of alternative splicing by tandem exon duplication
F. Kondrashov, E. Koonin, Human Molecular Genetics 10 (2001) 2661–2669.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 851
Use of mutation spectra analysis software
I. Rogozin, F. Kondrashov, G. Glazko, Human Mutation 17 (2001) 83–102.
View | DOI
 
[2]
2000 | Journal Article | IST-REx-ID: 842
No footprints of primordial introns in a eukaryotic genome
Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 16 (2000) 333–334.
View | DOI
 
[1]
1999 | Journal Article | IST-REx-ID: 883
Interactions among quantitative traits in the course of sympatric speciation
A. Kondrashov, F. Kondrashov, Nature 400 (1999) 351–354.
View | DOI
 

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73 Publications

Mark all

[73]
2019 | Journal Article | IST-REx-ID: 6419   OA
An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape
V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).
View | Files available | DOI
 
[72]
2019 | Journal Article | IST-REx-ID: 7181   OA
Large multiple sequence alignments with a root-to-leaf regressive method
E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 5780   OA
Genetically encodable bioluminescent system from fungi
A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.
View | Files available | DOI
 
[70]
2018 | Journal Article | IST-REx-ID: 5995   OA
Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation
D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279   OA
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).
View | Files available | DOI
 
[68]
2016 | Journal Article | IST-REx-ID: 853
Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions
E. Rivkina, L. Petrovskaya, T. Vishnivetskaya, K. Krivushin, L. Shmakova, M. Tutukina, A. Meyers, F. Kondrashov, Biogeosciences 13 (2016) 2207–2219.
View | DOI
 
[67]
2016 | Journal Article | IST-REx-ID: 896
Structure and evolutionary history of a large family of NLR proteins in the zebrafish
K. Howe, P. Schiffer, J. Zielinski, T. Wiehe, G. Laird, J. Marioni, O. Soylemez, F. Kondrashov, M. Leptin, Open Biology 6 (2016).
View | DOI
 
[66]
2016 | Journal Article | IST-REx-ID: 850
Local fitness landscape of the green fluorescent protein
K. Sarkisyan, D. Bolotin, M. Meer, D. Usmanova, A. Mishin, G. Sharonov, D. Ivankov, N. Bozhanova, M. Baranov, O. Soylemez, N. Bogatyreva, P. Vlasov, E. Egorov, M. Logacheva, A. Kondrashov, D. Chudakov, E. Putintseva, I. Mamedov, D. Tawfik, K. Lukyanov, F. Kondrashov, Nature 533 (2016) 397–401.
View | DOI
 
[65]
2016 | Journal Article | IST-REx-ID: 849
Saturation of recognition elements blocks evolution of new tRNA identities
A. Saint Léger, C. Bello, P. Dans, A. Torres, E. Novoa, N. Camacho, M. Orozco, F. Kondrashov, L. Ribas De Pouplana, Science Advances 2 (2016) e1501860–e1501860.
View | DOI
 
[64]
2015 | Journal Article | IST-REx-ID: 866
Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13
C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.
View | DOI
 
[63]
2015 | Journal Article | IST-REx-ID: 886
Topological features of rugged fitness landscapes in sequence space
D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.
View | DOI
 
[62]
2015 | Journal Article | IST-REx-ID: 906
Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer
O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 848
A model of substitution trajectories in sequence space and long-term protein evolution
D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 845
Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity
V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 852
Long-Term asymmetrical acceleration of protein evolution after gene duplication
O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
View | DOI
 
[58]
2014 | Journal Article | IST-REx-ID: 865
Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling
A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
View | DOI
 
[57]
2014 | Journal Article | IST-REx-ID: 892
A structural perspective of compensatory evolution
D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112.
View | DOI
 
[56]
2014 | Journal Article | IST-REx-ID: 856
Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network
K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014).
View | DOI
 
[55]
2014 | Journal Article | IST-REx-ID: 863
The ctenophore genome and the evolutionary origins of neural systems
L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
View | DOI
 
[54]
2013 | Journal Article | IST-REx-ID: 905   OA
Birds of Mys Shmidta, north Chukotka, Russia
V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.
View | Download (ext.)
 
[53]
2013 | Journal Article | IST-REx-ID: 894
Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R
R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).
View | DOI
 
[52]
2013 | Journal Article | IST-REx-ID: 899
Breen et al. reply
M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3.
View | DOI
 
[51]
2012 | Journal Article | IST-REx-ID: 846
Estimating the rate of irreversibility in protein evolution
O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.
View | DOI
 
[50]
2012 | Journal Article | IST-REx-ID: 858
Stop codons in bacteria are not selectively equivalent
I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).
View | DOI
 
[49]
2012 | Journal Article | IST-REx-ID: 900
Epistasis as the primary factor in molecular evolution
M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538.
View | DOI
 
[48]
2012 | Journal Article | IST-REx-ID: 887
Gene duplication as a mechanism of genomic adaptation to a changing environment
F. Kondrashov, Proceedings of the Royal Society of London Series B Biological Sciences 279 (2012) 5048–5057.
View | DOI
 
[47]
2011 | Journal Article | IST-REx-ID: 890
Acrocephalus orinus: A case of Mistaken identity
E. Koblik, Y. Red’Kin, M. Meer, R. Derelle, S. Golenkina, F. Kondrashov, V. Arkhipov, PLoS One 6 (2011).
View | DOI
 
[46]
2011 | Book Chapter | IST-REx-ID: 881
Gene Dosage and Duplication
F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76.
View | DOI
 
[45]
2010 | Journal Article | IST-REx-ID: 857
Sequence space and the ongoing expansion of the protein universe
I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 872
Measurements of spontaneous rates of mutations in the recent past and the near future
F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 884
Rate of sequence divergence under constant selection
A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010).
View | DOI
 
[42]
2010 | Journal Article | IST-REx-ID: 891
The evolution of gene duplications: Classifying and distinguishing between models
H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.
View | DOI
 
[41]
2010 | Journal Article | IST-REx-ID: 901
Mitochondrial pathogenic mutations are population-specific
M. Breen, F. Kondrashov, Biology Direct 5 (2010).
View | DOI
 
[40]
2010 | Journal Article | IST-REx-ID: 862
Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282.
View | DOI
 
[39]
2009 | Journal Article | IST-REx-ID: 908
Translation termination in pyrrolysine-utilizing archaea
E. Alkalaeva, B. Eliseev, A. Ambrogelly, P. Vlasov, F. Kondrashov, S. Gundllapalli, L. Frolova, D. Söll, L. Kisselev, FEBS Letters 583 (2009) 3455–3460.
View | DOI
 
[38]
2008 | Journal Article | IST-REx-ID: 895
Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene
Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008).
View | DOI
 
[37]
2008 | Journal Article | IST-REx-ID: 844
Hypermutable non-synonymous sites are under stronger negative selection
S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008).
View | DOI
 
[36]
2008 | Journal Article | IST-REx-ID: 907
Nested genes and increasing organizational complexity of metazoan genomes
R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24 (2008) 475–478.
View | DOI
 
[35]
2007 | Journal Article | IST-REx-ID: 860
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
O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev, American Journal of Human Genetics 81 (2007) 32–43.
View | DOI
 
[34]
2007 | Journal Article | IST-REx-ID: 904
Extensive parallelism in protein evolution
G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, A. Kondrashov, Biology Direct 2 (2007).
View | DOI
 
[33]
2007 | Journal Article | IST-REx-ID: 861
A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures
K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).
View | DOI
 
[32]
2007 | Journal Article | IST-REx-ID: 879
Selection for functional uniformity of tuf duplicates in γ-proteobacteria
F. Kondrashov, T. Gurbich, P. Vlasov, Trends in Genetics 23 (2007) 215–218.
View | DOI
 
[31]
2006 | Journal Article | IST-REx-ID: 903
Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis
V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006).
View | DOI
 
[30]
2006 | Journal Article | IST-REx-ID: 869
Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites
F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology 240 (2006) 616–626.
View | DOI
 
[29]
2006 | Journal Article | IST-REx-ID: 854
Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius
E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov, A. Grigorenko, PLoS Biology 4 (2006) 0403–0410.
View | DOI
 
[28]
2006 | Journal Article | IST-REx-ID: 873
Role of selection in fixation of gene duplications
F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151.
View | DOI
 
[27]
2006 | Journal Article | IST-REx-ID: 868
Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation
F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology Direct 1 (2006).
View | DOI
 
 
[25]
2005 | Journal Article | IST-REx-ID: 878
In search of the limits of evolution
F. Kondrashov, Nature Genetics 37 (2005) 9–10.
View | DOI
 
 
[23]
2005 | Journal Article | IST-REx-ID: 893
A universal trend of amino acid gain and loss in protein evolution
I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 843
Distribution of the strength of selection against amino acid replacements in human proteins
L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201.
View | DOI
 
[21]
2005 | Journal Article | IST-REx-ID: 882
Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
Prediction of functional sites by analysis of sequence and structure conservation
A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 889
Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs
A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 898
Positive selection at sites of multiple amino acid replacements since rat-mouse divergence
G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 870
Bioinformatical assay of human gene morbidity
F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.
View | DOI
 
[16]
2004 | Journal Article | IST-REx-ID: 875 View | DOI
 
[15]
2004 | Journal Article | IST-REx-ID: 902
The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811.
View | DOI
 
[14]
2003 | Journal Article | IST-REx-ID: 876 View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 847
Impact of selection, mutation rate and genetic drift on human genetic variation
S. Sunyaev, F. Kondrashov, P. Bork, V. Ramensky, Human Molecular Genetics 12 (2003) 3325–3330.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 871
Selection in the evolution of gene duplications
F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002).
View | DOI
 
[11]
2002 | Journal Article | IST-REx-ID: 859
Evolution of the mouse polyubiquitin C gene
A. Perelygin, F. Kondrashov, I. Rogozin, M. Brinton, Journal of Molecular Evolution 55 (2002) 202–210.
View | DOI
 
[10]
2002 | Journal Article | IST-REx-ID: 885
Dobzhansky-Muller incompatibilities in protein evolution
A. Kondrashov, S. Sunyaev, F. Kondrashov, PNAS 99 (2002) 14878–14883.
View | DOI
 
[9]
2002 | Journal Article | IST-REx-ID: 897
Selection for short introns in highly expressed genes
C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, F. Kondrashov, Nature Genetics 31 (2002) 415–418.
View | DOI
 
[8]
2001 | Journal Article | IST-REx-ID: 888
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins
I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome Biology 2 (2001).
View | DOI
 
[7]
2001 | Journal Article | IST-REx-ID: 841
Footprints of primordial introns on the eukaryotic genome: still no clear traces
Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 17 (2001) 499–501.
View | DOI
 
[6]
2001 | Journal Article | IST-REx-ID: 874
Multidimensional epistasis and the disadvantage of sex
F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.
View | DOI
 
[5]
2001 | Journal Article | IST-REx-ID: 855
Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon
I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, L. Milanesi, Bioinformatics 17 (2001) 890–900.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 867
Origin of alternative splicing by tandem exon duplication
F. Kondrashov, E. Koonin, Human Molecular Genetics 10 (2001) 2661–2669.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 851
Use of mutation spectra analysis software
I. Rogozin, F. Kondrashov, G. Glazko, Human Mutation 17 (2001) 83–102.
View | DOI
 
[2]
2000 | Journal Article | IST-REx-ID: 842
No footprints of primordial introns in a eukaryotic genome
Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 16 (2000) 333–334.
View | DOI
 
[1]
1999 | Journal Article | IST-REx-ID: 883
Interactions among quantitative traits in the course of sympatric speciation
A. Kondrashov, F. Kondrashov, Nature 400 (1999) 351–354.
View | DOI
 

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