Fyodor Kondrashov
Kondrashov Group
95 Publications
2024 | Journal Article | IST-REx-ID: 15179 |
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
2023 | Journal Article | IST-REx-ID: 12758 |
M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.
[Published Version]
View
| Files available
| DOI
| WoS
2023 | Journal Article | IST-REx-ID: 13164 |
K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” Nature Communications, vol. 14. Springer Nature, 2023.
[Published Version]
View
| Files available
| DOI
| WoS
2023 | Journal Article | IST-REx-ID: 13976 |
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
2023 | Conference Abstract | IST-REx-ID: 14862 |
S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2.
[Published Version]
View
| Files available
| DOI
2022 | Journal Article | IST-REx-ID: 11187 |
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
2022 | Journal Article | IST-REx-ID: 11344 |
N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific Reports, vol. 12. Springer Nature, 2022.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2022 | Journal Article | IST-REx-ID: 11448 |
L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications, 2022.
[Published Version]
View
| Files available
| DOI
| WoS
2022 | Journal Article | IST-REx-ID: 11447 |
R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
[Published Version]
View
| Files available
| DOI
| WoS
2022 | Journal Article | IST-REx-ID: 12116 |
K. Chhugani et al., “Remote opportunities for scholars in Ukraine,” Science, vol. 378, no. 6626. American Association for the Advancement of Science, pp. 1285–1286, 2022.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| WoS
2021 | Journal Article | IST-REx-ID: 9910 |
S. A. Slavskii et al., “The limits of normal approximation for adult height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2021 | Journal Article | IST-REx-ID: 9905 |
S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Report | IST-REx-ID: 8151
M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
View
| Files available
2020 | Journal Article | IST-REx-ID: 7931 |
L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020.
[Published Version]
View
| Files available
| DOI
| WoS
2020 | Journal Article | IST-REx-ID: 8645 |
L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Journal Article | IST-REx-ID: 7889 |
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
2019 | Journal Article | IST-REx-ID: 6419 |
V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
| WoS
2019 | Research Data Reference | IST-REx-ID: 9790
V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
2019 | Research Data Reference | IST-REx-ID: 9797
V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
2019 | Research Data Reference | IST-REx-ID: 9789
V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
2019 | Journal Article | IST-REx-ID: 7181 |
E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.
[Submitted Version]
View
| Files available
| DOI
| Download Submitted Version (ext.)
| WoS
| PubMed | Europe PMC
2018 | Research Data Reference | IST-REx-ID: 13059 |
E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.
[Published Version]
View
| Files available
| DOI
| Download Published Version (ext.)
2018 | Journal Article | IST-REx-ID: 5780 |
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
2018 | Journal Article | IST-REx-ID: 279 |
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.
[Published Version]
View
| Files available
| DOI
| WoS
2018 | Research Data Reference | IST-REx-ID: 9812 |
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.
[Published Version]
View
| Files available
| DOI
| Download Published Version (ext.)
2018 | Research Data Reference | IST-REx-ID: 9811 |
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2018 | Journal Article | IST-REx-ID: 5995 |
D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2016 | Journal Article | IST-REx-ID: 850
Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533, 397–401.
View
| DOI
2015 | Journal Article | IST-REx-ID: 848
D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.
View
| DOI
2014 | Journal Article | IST-REx-ID: 863
Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114.
View
| DOI
2013 | Journal Article | IST-REx-ID: 905 |
V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30, 2013.
View
| Download (ext.)
2010 | Journal Article | IST-REx-ID: 872
F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, The, pp. 1169–1176, 2010.
View
| DOI
2007 | Journal Article | IST-REx-ID: 860
O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” American Journal of Human Genetics, vol. 81, no. 1. Cell Press, pp. 32–43, 2007.
View
| DOI
2006 | Journal Article | IST-REx-ID: 869
F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” Journal of Theoretical Biology, vol. 240, no. 4. Elsevier, pp. 616–626, 2006.
View
| DOI
2005 | Journal Article | IST-REx-ID: 877
F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.
View
| Download None (ext.)
| PubMed | Europe PMC
2005 | Journal Article | IST-REx-ID: 880
F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.
View
| Download None (ext.)
| PubMed | Europe PMC
2004 | Journal Article | IST-REx-ID: 902
C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” Genome Research, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.
View
| DOI
2002 | Journal Article | IST-REx-ID: 885 |
A. Kondrashov, S. Sunyaev, and F. Kondrashov, “Dobzhansky-Muller incompatibilities in protein evolution,” PNAS, vol. 99, no. 23. National Academy of Sciences, pp. 14878–14883, 2002.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2002 | Journal Article | IST-REx-ID: 897
C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, and F. Kondrashov, “Selection for short introns in highly expressed genes,” Nature Genetics, vol. 31, no. 4. Nature Publishing Group, pp. 415–418, 2002.
View
| DOI
| PubMed | Europe PMC
2002 | Journal Article | IST-REx-ID: 871 |
F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution of gene duplications ,” Genome Biology, vol. 3, no. 2. BioMed Central, 2002.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2002 | Journal Article | IST-REx-ID: 859
A. Perelygin, F. Kondrashov, I. Rogozin, and M. Brinton, “Evolution of the mouse polyubiquitin C gene,” Journal of Molecular Evolution, vol. 55, no. 2. Springer, pp. 202–210, 2002.
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 888 |
I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin, “Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol. 2, no. 12. BioMed Central, 2001.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 855
I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10. Oxford University Press, pp. 890–900, 2001.
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 874 |
F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage of sex,” PNAS, vol. 98, no. 21. National Academy of Sciences, pp. 12089–12092, 2001.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 867
F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon duplication,” Human Molecular Genetics, vol. 10, no. 23. Oxford University Press, pp. 2661–2669, 2001.
[Published Version]
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 851
I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis software,” Human Mutation, vol. 17, no. 2. Wiley-Blackwell, pp. 83–102, 2001.
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 841
Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns on the eukaryotic genome: still no clear traces ,” Trends in Genetics, vol. 17, no. 9. Elsevier, pp. 499–501, 2001.
View
| DOI
| PubMed | Europe PMC
2000 | Journal Article | IST-REx-ID: 842
Y. Wolf, F. Kondrashov, and E. Koonin, “No footprints of primordial introns in a eukaryotic genome,” Trends in Genetics, vol. 16, no. 8. Elsevier, pp. 333–334, 2000.
View
| DOI
| PubMed | Europe PMC
1999 | Journal Article | IST-REx-ID: 883
A. Kondrashov and F. Kondrashov, “Interactions among quantitative traits in the course of sympatric speciation,” Nature, vol. 400, no. 6742. Nature Publishing Group, pp. 351–354, 1999.
View
| DOI
| PubMed | Europe PMC
95 Publications
2024 | Journal Article | IST-REx-ID: 15179 |
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
2023 | Journal Article | IST-REx-ID: 12758 |
M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.
[Published Version]
View
| Files available
| DOI
| WoS
2023 | Journal Article | IST-REx-ID: 13164 |
K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” Nature Communications, vol. 14. Springer Nature, 2023.
[Published Version]
View
| Files available
| DOI
| WoS
2023 | Journal Article | IST-REx-ID: 13976 |
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
2023 | Conference Abstract | IST-REx-ID: 14862 |
S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2.
[Published Version]
View
| Files available
| DOI
2022 | Journal Article | IST-REx-ID: 11187 |
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
2022 | Journal Article | IST-REx-ID: 11344 |
N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific Reports, vol. 12. Springer Nature, 2022.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2022 | Journal Article | IST-REx-ID: 11448 |
L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications, 2022.
[Published Version]
View
| Files available
| DOI
| WoS
2022 | Journal Article | IST-REx-ID: 11447 |
R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
[Published Version]
View
| Files available
| DOI
| WoS
2022 | Journal Article | IST-REx-ID: 12116 |
K. Chhugani et al., “Remote opportunities for scholars in Ukraine,” Science, vol. 378, no. 6626. American Association for the Advancement of Science, pp. 1285–1286, 2022.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| WoS
2021 | Journal Article | IST-REx-ID: 9910 |
S. A. Slavskii et al., “The limits of normal approximation for adult height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2021 | Journal Article | IST-REx-ID: 9905 |
S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Report | IST-REx-ID: 8151
M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
View
| Files available
2020 | Journal Article | IST-REx-ID: 7931 |
L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020.
[Published Version]
View
| Files available
| DOI
| WoS
2020 | Journal Article | IST-REx-ID: 8645 |
L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2020 | Journal Article | IST-REx-ID: 7889 |
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
2019 | Journal Article | IST-REx-ID: 6419 |
V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
| WoS
2019 | Research Data Reference | IST-REx-ID: 9790
V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
2019 | Research Data Reference | IST-REx-ID: 9797
V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
2019 | Research Data Reference | IST-REx-ID: 9789
V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019.
[Published Version]
View
| Files available
| DOI
2019 | Journal Article | IST-REx-ID: 7181 |
E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.
[Submitted Version]
View
| Files available
| DOI
| Download Submitted Version (ext.)
| WoS
| PubMed | Europe PMC
2018 | Research Data Reference | IST-REx-ID: 13059 |
E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.
[Published Version]
View
| Files available
| DOI
| Download Published Version (ext.)
2018 | Journal Article | IST-REx-ID: 5780 |
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
2018 | Journal Article | IST-REx-ID: 279 |
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.
[Published Version]
View
| Files available
| DOI
| WoS
2018 | Research Data Reference | IST-REx-ID: 9812 |
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.
[Published Version]
View
| Files available
| DOI
| Download Published Version (ext.)
2018 | Research Data Reference | IST-REx-ID: 9811 |
L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.
[Preprint]
View
| Files available
| DOI
| Download Preprint (ext.)
2018 | Journal Article | IST-REx-ID: 5995 |
D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.
[Published Version]
View
| Files available
| DOI
| WoS
| PubMed | Europe PMC
2016 | Journal Article | IST-REx-ID: 850
Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533, 397–401.
View
| DOI
2015 | Journal Article | IST-REx-ID: 848
D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.
View
| DOI
2014 | Journal Article | IST-REx-ID: 863
Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114.
View
| DOI
2013 | Journal Article | IST-REx-ID: 905 |
V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30, 2013.
View
| Download (ext.)
2010 | Journal Article | IST-REx-ID: 872
F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, The, pp. 1169–1176, 2010.
View
| DOI
2007 | Journal Article | IST-REx-ID: 860
O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” American Journal of Human Genetics, vol. 81, no. 1. Cell Press, pp. 32–43, 2007.
View
| DOI
2006 | Journal Article | IST-REx-ID: 869
F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” Journal of Theoretical Biology, vol. 240, no. 4. Elsevier, pp. 616–626, 2006.
View
| DOI
2005 | Journal Article | IST-REx-ID: 877
F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.
View
| Download None (ext.)
| PubMed | Europe PMC
2005 | Journal Article | IST-REx-ID: 880
F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.
View
| Download None (ext.)
| PubMed | Europe PMC
2004 | Journal Article | IST-REx-ID: 902
C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” Genome Research, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.
View
| DOI
2002 | Journal Article | IST-REx-ID: 885 |
A. Kondrashov, S. Sunyaev, and F. Kondrashov, “Dobzhansky-Muller incompatibilities in protein evolution,” PNAS, vol. 99, no. 23. National Academy of Sciences, pp. 14878–14883, 2002.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2002 | Journal Article | IST-REx-ID: 897
C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, and F. Kondrashov, “Selection for short introns in highly expressed genes,” Nature Genetics, vol. 31, no. 4. Nature Publishing Group, pp. 415–418, 2002.
View
| DOI
| PubMed | Europe PMC
2002 | Journal Article | IST-REx-ID: 871 |
F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution of gene duplications ,” Genome Biology, vol. 3, no. 2. BioMed Central, 2002.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2002 | Journal Article | IST-REx-ID: 859
A. Perelygin, F. Kondrashov, I. Rogozin, and M. Brinton, “Evolution of the mouse polyubiquitin C gene,” Journal of Molecular Evolution, vol. 55, no. 2. Springer, pp. 202–210, 2002.
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 888 |
I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin, “Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol. 2, no. 12. BioMed Central, 2001.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 855
I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10. Oxford University Press, pp. 890–900, 2001.
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 874 |
F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage of sex,” PNAS, vol. 98, no. 21. National Academy of Sciences, pp. 12089–12092, 2001.
[Published Version]
View
| DOI
| Download Published Version (ext.)
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 867
F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon duplication,” Human Molecular Genetics, vol. 10, no. 23. Oxford University Press, pp. 2661–2669, 2001.
[Published Version]
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 851
I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis software,” Human Mutation, vol. 17, no. 2. Wiley-Blackwell, pp. 83–102, 2001.
View
| DOI
| PubMed | Europe PMC
2001 | Journal Article | IST-REx-ID: 841
Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns on the eukaryotic genome: still no clear traces ,” Trends in Genetics, vol. 17, no. 9. Elsevier, pp. 499–501, 2001.
View
| DOI
| PubMed | Europe PMC
2000 | Journal Article | IST-REx-ID: 842
Y. Wolf, F. Kondrashov, and E. Koonin, “No footprints of primordial introns in a eukaryotic genome,” Trends in Genetics, vol. 16, no. 8. Elsevier, pp. 333–334, 2000.
View
| DOI
| PubMed | Europe PMC
1999 | Journal Article | IST-REx-ID: 883
A. Kondrashov and F. Kondrashov, “Interactions among quantitative traits in the course of sympatric speciation,” Nature, vol. 400, no. 6742. Nature Publishing Group, pp. 351–354, 1999.
View
| DOI
| PubMed | Europe PMC