Fyodor Kondrashov

Kondrashov Group

95 Publications

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[95]
2024 | Journal Article | IST-REx-ID: 15179 | OA
A hybrid pathway for self-sustained luminescence
Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992.
[Published Version] View | Files available | DOI
 
[94]
2023 | Journal Article | IST-REx-ID: 12758 | OA
Using AlphaFold to predict the impact of single mutations on protein stability and function
M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
[Published Version] View | Files available | DOI | WoS
 
[93]
2023 | Journal Article | IST-REx-ID: 13164 | OA
Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries
K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).
[Published Version] View | Files available | DOI | WoS
 
[92]
2023 | Journal Article | IST-REx-ID: 13976 | OA
Scientists without borders: Lessons from Ukraine
Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[91]
2023 | Conference Abstract | IST-REx-ID: 14862 | OA
Complex vaccination strategies prevent the emergence of vaccine resistance
S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.
[Published Version] View | Files available | DOI
 
[90]
2022 | Journal Article | IST-REx-ID: 11187 | OA
Unlocking capacities of genomics for the COVID-19 response and future pandemics
Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[89]
2022 | Journal Article | IST-REx-ID: 11344 | OA
Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia
N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2022 | Journal Article | IST-REx-ID: 11448 | OA
Heterogeneity of the GFP fitness landscape and data-driven protein design
L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).
[Published Version] View | Files available | DOI | WoS
 
[87]
2022 | Journal Article | IST-REx-ID: 11447 | OA
Relation between the number of peaks and the number of reciprocal sign epistatic interactions
R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).
[Published Version] View | Files available | DOI | WoS
 
[86]
2022 | Journal Article | IST-REx-ID: 12116 | OA
Remote opportunities for scholars in Ukraine
K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone, W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz, F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science 378 (2022) 1285–1286.
[Published Version] View | DOI | Download Published Version (ext.) | WoS
 
[85]
2021 | Journal Article | IST-REx-ID: 9910 | OA
The limits of normal approximation for adult height
S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[84]
2021 | Journal Article | IST-REx-ID: 9905 | OA
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains
S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2020 | Report | IST-REx-ID: 8151
Core Project Proceedings
M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N. Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020.
View | Files available
 
[82]
2020 | Journal Article | IST-REx-ID: 7931 | OA
A method for identification of the methylation level of CpG islands from NGS data
L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).
[Published Version] View | Files available | DOI | WoS
 
[81]
2020 | Journal Article | IST-REx-ID: 8645 | OA
HypercubeME: Two hundred million combinatorially complete datasets from a single experiment
L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[80]
2020 | Journal Article | IST-REx-ID: 7889 | OA
Plants with genetically encoded autoluminescence
Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.
[Submitted Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[79]
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).
[Published Version] View | Files available | DOI | WoS
 
[78]
2019 | Research Data Reference | IST-REx-ID: 9790
A statistical summary of segment libraries and sequencing results
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, (2019).
[Published Version] View | Files available | DOI
 
[77]
2019 | Research Data Reference | IST-REx-ID: 9797
A statistical summary of segment libraries and sequencing results
V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
[Published Version] View | Files available | DOI
 
[76]
2019 | Research Data Reference | IST-REx-ID: 9789
Multiple alignment of His3 orthologues
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, (2019).
[Published Version] View | Files available | DOI
 
[75]
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.
[Submitted Version] View | Files available | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[74]
2018 | Research Data Reference | IST-REx-ID: 13059 | OA
Fast and accurate 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, (2018).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[73]
2018 | Journal Article | IST-REx-ID: 5780 | OA
Genetically encodable bioluminescent system from fungi
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.
[Published Version] View | Files available | DOI | WoS
 
[72]
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).
[Published Version] View | Files available | DOI | WoS
 
[71]
2018 | Research Data Reference | IST-REx-ID: 9812 | OA
Additional file 2: Of 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, (2018).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[70]
2018 | Research Data Reference | IST-REx-ID: 9811 | OA
Additional file 1: Of 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, (2018).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[69]
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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[68]
2016 | Journal Article | IST-REx-ID: 850
Local fitness landscape of the green fluorescent protein
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
 
[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: 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
 
[65]
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
 
[64]
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
 
[63]
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
 
[62]
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
 
[61]
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
 
[60]
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
 
[59]
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
 
[58]
2014 | Journal Article | IST-REx-ID: 863
The ctenophore genome and the evolutionary origins of neural systems
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
 
[57]
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
 
[56]
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
 
[55]
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
 
[54]
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
 
[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: 905 | OA
Birds of Mys Shmidta, north Chukotka, Russia
V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.
View | Download (ext.)
 
[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: 891
The evolution of gene duplications: Classifying and distinguishing between models
H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 901
Mitochondrial pathogenic mutations are population-specific
M. Breen, F. Kondrashov, Biology Direct 5 (2010).
View | DOI
 
[43]
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
 
[42]
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
 
[41]
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
 
[40]
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
 
[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: 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
 
[37]
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
 
[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: 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
 
[33]
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
 
[32]
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
 
[31]
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
 
[30]
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
 
[29]
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
 
[28]
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
 
[27]
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
 
[26]
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
 
[25]
2005 | Journal Article | IST-REx-ID: 877
The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution
F. Kondrashov, Biofizika 50 (2005) 389–395.
View | Download None (ext.) | PubMed | Europe PMC
 
[24]
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: 882
Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 880
The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus
F. Kondrashov, Biofizika 50 (2005) 396–403.
View | Download None (ext.) | PubMed | Europe PMC
 
[21]
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
 
[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: 870
Bioinformatical assay of human gene morbidity
F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 875
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications
F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.
View | DOI
 
[17]
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
 
[16]
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
 
[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: 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
 
[13]
2003 | Journal Article | IST-REx-ID: 876
Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences
F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 885 | OA
Dobzhansky-Muller incompatibilities in protein evolution
A. Kondrashov, S. Sunyaev, F. Kondrashov, PNAS 99 (2002) 14878–14883.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
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 | PubMed | Europe PMC
 
[10]
2002 | Journal Article | IST-REx-ID: 871 | OA
Selection in the evolution of gene duplications
F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
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 | PubMed | Europe PMC
 
[8]
2001 | Journal Article | IST-REx-ID: 888 | OA
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).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[7]
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 | PubMed | Europe PMC
 
[6]
2001 | Journal Article | IST-REx-ID: 874 | OA
Multidimensional epistasis and the disadvantage of sex
F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
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.
[Published Version] View | DOI | PubMed | Europe PMC
 
[4]
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 | PubMed | Europe PMC
 
[3]
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 | PubMed | Europe PMC
 
[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 | PubMed | Europe PMC
 
[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 | PubMed | Europe PMC
 
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[95]
2024 | Journal Article | IST-REx-ID: 15179 | OA
A hybrid pathway for self-sustained luminescence
Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992.
[Published Version] View | Files available | DOI
 
[94]
2023 | Journal Article | IST-REx-ID: 12758 | OA
Using AlphaFold to predict the impact of single mutations on protein stability and function
M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
[Published Version] View | Files available | DOI | WoS
 
[93]
2023 | Journal Article | IST-REx-ID: 13164 | OA
Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries
K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).
[Published Version] View | Files available | DOI | WoS
 
[92]
2023 | Journal Article | IST-REx-ID: 13976 | OA
Scientists without borders: Lessons from Ukraine
Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[91]
2023 | Conference Abstract | IST-REx-ID: 14862 | OA
Complex vaccination strategies prevent the emergence of vaccine resistance
S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.
[Published Version] View | Files available | DOI
 
[90]
2022 | Journal Article | IST-REx-ID: 11187 | OA
Unlocking capacities of genomics for the COVID-19 response and future pandemics
Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 
[89]
2022 | Journal Article | IST-REx-ID: 11344 | OA
Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia
N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2022 | Journal Article | IST-REx-ID: 11448 | OA
Heterogeneity of the GFP fitness landscape and data-driven protein design
L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).
[Published Version] View | Files available | DOI | WoS
 
[87]
2022 | Journal Article | IST-REx-ID: 11447 | OA
Relation between the number of peaks and the number of reciprocal sign epistatic interactions
R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).
[Published Version] View | Files available | DOI | WoS
 
[86]
2022 | Journal Article | IST-REx-ID: 12116 | OA
Remote opportunities for scholars in Ukraine
K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone, W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz, F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science 378 (2022) 1285–1286.
[Published Version] View | DOI | Download Published Version (ext.) | WoS
 
[85]
2021 | Journal Article | IST-REx-ID: 9910 | OA
The limits of normal approximation for adult height
S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[84]
2021 | Journal Article | IST-REx-ID: 9905 | OA
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains
S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2020 | Report | IST-REx-ID: 8151
Core Project Proceedings
M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N. Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020.
View | Files available
 
[82]
2020 | Journal Article | IST-REx-ID: 7931 | OA
A method for identification of the methylation level of CpG islands from NGS data
L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).
[Published Version] View | Files available | DOI | WoS
 
[81]
2020 | Journal Article | IST-REx-ID: 8645 | OA
HypercubeME: Two hundred million combinatorially complete datasets from a single experiment
L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[80]
2020 | Journal Article | IST-REx-ID: 7889 | OA
Plants with genetically encoded autoluminescence
Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.
[Submitted Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[79]
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).
[Published Version] View | Files available | DOI | WoS
 
[78]
2019 | Research Data Reference | IST-REx-ID: 9790
A statistical summary of segment libraries and sequencing results
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, (2019).
[Published Version] View | Files available | DOI
 
[77]
2019 | Research Data Reference | IST-REx-ID: 9797
A statistical summary of segment libraries and sequencing results
V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
[Published Version] View | Files available | DOI
 
[76]
2019 | Research Data Reference | IST-REx-ID: 9789
Multiple alignment of His3 orthologues
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, (2019).
[Published Version] View | Files available | DOI
 
[75]
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.
[Submitted Version] View | Files available | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[74]
2018 | Research Data Reference | IST-REx-ID: 13059 | OA
Fast and accurate 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, (2018).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[73]
2018 | Journal Article | IST-REx-ID: 5780 | OA
Genetically encodable bioluminescent system from fungi
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.
[Published Version] View | Files available | DOI | WoS
 
[72]
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).
[Published Version] View | Files available | DOI | WoS
 
[71]
2018 | Research Data Reference | IST-REx-ID: 9812 | OA
Additional file 2: Of 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, (2018).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[70]
2018 | Research Data Reference | IST-REx-ID: 9811 | OA
Additional file 1: Of 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, (2018).
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[69]
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.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[68]
2016 | Journal Article | IST-REx-ID: 850
Local fitness landscape of the green fluorescent protein
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
 
[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: 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
 
[65]
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
 
[64]
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
 
[63]
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
 
[62]
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
 
[61]
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
 
[60]
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
 
[59]
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
 
[58]
2014 | Journal Article | IST-REx-ID: 863
The ctenophore genome and the evolutionary origins of neural systems
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
 
[57]
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
 
[56]
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
 
[55]
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
 
[54]
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
 
[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: 905 | OA
Birds of Mys Shmidta, north Chukotka, Russia
V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.
View | Download (ext.)
 
[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: 891
The evolution of gene duplications: Classifying and distinguishing between models
H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.
View | DOI
 
[44]
2010 | Journal Article | IST-REx-ID: 901
Mitochondrial pathogenic mutations are population-specific
M. Breen, F. Kondrashov, Biology Direct 5 (2010).
View | DOI
 
[43]
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
 
[42]
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
 
[41]
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
 
[40]
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
 
[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: 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
 
[37]
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
 
[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: 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
 
[33]
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
 
[32]
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
 
[31]
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
 
[30]
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
 
[29]
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
 
[28]
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
 
[27]
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
 
[26]
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
 
[25]
2005 | Journal Article | IST-REx-ID: 877
The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution
F. Kondrashov, Biofizika 50 (2005) 389–395.
View | Download None (ext.) | PubMed | Europe PMC
 
[24]
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: 882
Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 880
The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus
F. Kondrashov, Biofizika 50 (2005) 396–403.
View | Download None (ext.) | PubMed | Europe PMC
 
[21]
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
 
[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: 870
Bioinformatical assay of human gene morbidity
F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 875
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications
F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.
View | DOI
 
[17]
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
 
[16]
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
 
[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: 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
 
[13]
2003 | Journal Article | IST-REx-ID: 876
Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences
F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 885 | OA
Dobzhansky-Muller incompatibilities in protein evolution
A. Kondrashov, S. Sunyaev, F. Kondrashov, PNAS 99 (2002) 14878–14883.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
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 | PubMed | Europe PMC
 
[10]
2002 | Journal Article | IST-REx-ID: 871 | OA
Selection in the evolution of gene duplications
F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
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 | PubMed | Europe PMC
 
[8]
2001 | Journal Article | IST-REx-ID: 888 | OA
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).
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[7]
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 | PubMed | Europe PMC
 
[6]
2001 | Journal Article | IST-REx-ID: 874 | OA
Multidimensional epistasis and the disadvantage of sex
F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
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.
[Published Version] View | DOI | PubMed | Europe PMC
 
[4]
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 | PubMed | Europe PMC
 
[3]
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 | PubMed | Europe PMC
 
[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 | PubMed | Europe PMC
 
[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 | PubMed | Europe PMC
 
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