Fyodor Kondrashov

Kondrashov Group

95 Publications

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[95]
2024 | Journal Article | IST-REx-ID: 15179 | OA
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
Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
[Published Version] View | Files available | DOI | WoS
 
[93]
2023 | Journal Article | IST-REx-ID: 13164 | OA
Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications, vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4.
[Published Version] View | Files available | DOI | WoS
 
[92]
2023 | Journal Article | IST-REx-ID: 13976 | OA
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
Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.
[Published Version] View | Files available | DOI
 
[90]
2022 | Journal Article | IST-REx-ID: 11187 | OA
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.
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[89]
2022 | Journal Article | IST-REx-ID: 11344 | OA
Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer Nature, 2022, doi:10.1038/s41598-022-10827-3.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2022 | Journal Article | IST-REx-ID: 11448 | OA
Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences Publications, 2022, doi:10.7554/elife.75842.
[Published Version] View | Files available | DOI | WoS
 
[87]
2022 | Journal Article | IST-REx-ID: 11447 | OA
Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
[Published Version] View | Files available | DOI | WoS
 
[86]
2022 | Journal Article | IST-REx-ID: 12116 | OA
Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.” Science, vol. 378, no. 6626, American Association for the Advancement of Science, 2022, pp. 1285–86, doi:10.1126/science.adg0797.
[Published Version] View | DOI | Download Published Version (ext.) | WoS
 
[85]
2021 | Journal Article | IST-REx-ID: 9910 | OA
Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:10.1038/s41431-021-00836-7.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[84]
2021 | Journal Article | IST-REx-ID: 9905 | OA
Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2020 | Report | IST-REx-ID: 8151
Maslov, Mikhail, et al. Core Project Proceedings. IST Austria, 2020.
View | Files available
 
[82]
2020 | Journal Article | IST-REx-ID: 7931 | OA
Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.
[Published Version] View | Files available | DOI | WoS
 
[81]
2020 | Journal Article | IST-REx-ID: 8645 | OA
Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[80]
2020 | Journal Article | IST-REx-ID: 7889 | OA
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
Pokusaeva, Victoria, 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, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.
[Published Version] View | Files available | DOI | WoS
 
[78]
2019 | Research Data Reference | IST-REx-ID: 9790
Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
[Published Version] View | Files available | DOI
 
[77]
2019 | Research Data Reference | IST-REx-ID: 9797
Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
[Published Version] View | Files available | DOI
 
[76]
2019 | Research Data Reference | IST-REx-ID: 9789
Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.
[Published Version] View | Files available | DOI
 
[75]
2019 | Journal Article | IST-REx-ID: 7181 | OA
Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.
[Submitted Version] View | Files available | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[74]
2018 | Research Data Reference | IST-REx-ID: 13059 | OA
Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[73]
2018 | Journal Article | IST-REx-ID: 5780 | OA
Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Journal Article | IST-REx-ID: 279 | OA
Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.
[Published Version] View | Files available | DOI | WoS
 
[71]
2018 | Research Data Reference | IST-REx-ID: 9812 | OA
Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[70]
2018 | Research Data Reference | IST-REx-ID: 9811 | OA
Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[69]
2018 | Journal Article | IST-REx-ID: 5995 | OA
Usmanova, Dinara R., 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 , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[68]
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
 
[67]
2016 | Journal Article | IST-REx-ID: 896
Howe, Kerstin, et al. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology, vol. 6, no. 4, Royal Society, The, 2016, doi:10.1098/rsob.160009.
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[66]
2016 | Journal Article | IST-REx-ID: 849
Saint Léger, Adélaïde, et al. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances, vol. 2, no. 4, American Association for the Advancement of Science, 2016, pp. e1501860–e1501860, doi:10.1126/sciadv.1501860.
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[65]
2016 | Journal Article | IST-REx-ID: 853
Rivkina, Elizaveta, et al. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences, vol. 13, no. 7, European Geosciences Union, 2016, pp. 2207–19, doi:10.5194/bg-13-2207-2016.
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[64]
2015 | Journal Article | IST-REx-ID: 848
Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.
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[63]
2015 | Journal Article | IST-REx-ID: 906
Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.
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[62]
2015 | Journal Article | IST-REx-ID: 866
Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 886
Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 852
Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 856
Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications, vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
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[58]
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
 
[57]
2014 | Journal Article | IST-REx-ID: 865
Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
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[56]
2014 | Journal Article | IST-REx-ID: 845
Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.
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[55]
2014 | Journal Article | IST-REx-ID: 892
Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014, pp. 104–12, doi:10.1016/j.sbi.2014.05.004.
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[54]
2013 | Journal Article | IST-REx-ID: 899
Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.
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[53]
2013 | Journal Article | IST-REx-ID: 894
Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central, 2013, doi:10.1186/1756-0500-6-310.
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[52]
2013 | Journal Article | IST-REx-ID: 905 | OA
Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30.
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[51]
2012 | Journal Article | IST-REx-ID: 846
Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.
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[50]
2012 | Journal Article | IST-REx-ID: 858
Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30.
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[49]
2012 | Journal Article | IST-REx-ID: 900
Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510.
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[48]
2012 | Journal Article | IST-REx-ID: 887
Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57, doi:10.1098/rspb.2012.1108.
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[47]
2011 | Journal Article | IST-REx-ID: 890
Koblik, Evgeniy, et al. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One, vol. 6, no. 4, Public Library of Science, 2011, doi:10.1371/journal.pone.0017716.
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[46]
2011 | Book Chapter | IST-REx-ID: 881
Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4.
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[45]
2010 | Journal Article | IST-REx-ID: 891
Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” Nature Reviews Genetics, vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:10.1038/nrg2689.
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[44]
2010 | Journal Article | IST-REx-ID: 901
Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-68.
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[43]
2010 | Journal Article | IST-REx-ID: 857
Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature, vol. 465, no. 7300, Nature Publishing Group, 2010, pp. 922–26, doi:10.1038/nature09105.
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[42]
2010 | Journal Article | IST-REx-ID: 862
Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” Nature, vol. 464, no. 7286, Nature Publishing Group, 2010, pp. 279–82, doi:10.1038/nature08691.
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[41]
2010 | Journal Article | IST-REx-ID: 872
Kondrashov, Fyodor, and Alexey 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, 2010, pp. 1169–76, doi:10.1098/rstb.2009.0286.
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[40]
2010 | Journal Article | IST-REx-ID: 884
Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.” Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-5.
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[39]
2009 | Journal Article | IST-REx-ID: 908
Alkalaeva, Elena, et al. “Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters, vol. 583, no. 21, Elsevier, 2009, pp. 3455–60, doi:10.1016/j.febslet.2009.09.044.
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[38]
2008 | Journal Article | IST-REx-ID: 844
Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science, 2008, doi:10.1371/journal.pgen.1000281.
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[37]
2008 | Journal Article | IST-REx-ID: 895
Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180.
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[36]
2008 | Journal Article | IST-REx-ID: 907
Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics, vol. 24, no. 10, Elsevier, 2008, pp. 475–78, doi:10.1016/j.tig.2008.08.003.
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[35]
2007 | Journal Article | IST-REx-ID: 860
Plotnikova, Olga, et al. “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, 2007, pp. 32–43, doi:10.1086/518616.
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[34]
2007 | Journal Article | IST-REx-ID: 879
Kondrashov, Fyodor, et al. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics, vol. 23, no. 5, Elsevier, 2007, pp. 215–18, doi:10.1016/j.tig.2007.03.002.
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[33]
2007 | Journal Article | IST-REx-ID: 904
Bazykin, Georgii, et al. “Extensive Parallelism in Protein Evolution.” Biology Direct, vol. 2, BioMed Central, 2007, doi:10.1186/1745-6150-2-20.
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[32]
2007 | Journal Article | IST-REx-ID: 861
Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics, vol. 8, BioMed Central, 2007, doi:10.1186/1471-2105-8-441.
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[31]
2006 | Journal Article | IST-REx-ID: 854
Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073.
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[30]
2006 | Journal Article | IST-REx-ID: 868
Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct, vol. 1, BioMed Central, 2006, doi:10.1186/1745-6150-1-31.
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[29]
2006 | Journal Article | IST-REx-ID: 873
Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology, vol. 239, no. 2, Elsevier, 2006, pp. 141–51, doi:10.1016/j.jtbi.2005.08.033.
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[28]
2006 | Journal Article | IST-REx-ID: 869
Kondrashov, Fyodor, et al. “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, 2006, pp. 616–26, doi:10.1016/j.jtbi.2005.10.020.
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[27]
2006 | Journal Article | IST-REx-ID: 903
Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer, vol. 6, BioMed Central, 2006, doi:10.1186/1471-2407-6-36.
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[26]
2005 | Journal Article | IST-REx-ID: 843
Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350.
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[25]
2005 | Journal Article | IST-REx-ID: 877
Kondrashov, Fyodor. “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, 2005, pp. 389–95.
View | Download None (ext.) | PubMed | Europe PMC
 
[24]
2005 | Journal Article | IST-REx-ID: 878
Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9.
View | DOI
 
[23]
2005 | Journal Article | IST-REx-ID: 882
Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 880
Kondrashov, Fyodor. “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, 2005, pp. 396–403.
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[21]
2005 | Journal Article | IST-REx-ID: 893
Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:10.1038/nature03306.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:10.1110/ps.03465504.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 870
Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:10.1093/nar/gkh330.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 875
Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 889
Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451.
View | DOI
 
[16]
2004 | Journal Article | IST-REx-ID: 898
Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:10.1038/nature02601.
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[15]
2004 | Journal Article | IST-REx-ID: 902
Castillo Davis, Cristian, et al. “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, 2004, pp. 802–11, doi:10.1101/gr.2195604.
View | DOI
 
[14]
2003 | Journal Article | IST-REx-ID: 847
Sunyaev, Shamil, et al. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics, vol. 12, no. 24, Oxford University Press, 2003, pp. 3325–30, doi:10.1093/hmg/ddg359.
View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 876
Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” Trends in Genetics, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:10.1016/S0168-9525(02)00029-X.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 885 | OA
Kondrashov, Alexey, et al. “Dobzhansky-Muller Incompatibilities in Protein Evolution.” PNAS, vol. 99, no. 23, National Academy of Sciences, 2002, pp. 14878–83, doi:10.1073/pnas.232565499.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
2002 | Journal Article | IST-REx-ID: 897
Castillo Davis, Cristian, et al. “Selection for Short Introns in Highly Expressed Genes.” Nature Genetics, vol. 31, no. 4, Nature Publishing Group, 2002, pp. 415–18, doi:10.1038/ng940.
View | DOI | PubMed | Europe PMC
 
[10]
2002 | Journal Article | IST-REx-ID: 871 | OA
Kondrashov, Fyodor, et al. “Selection in the Evolution of Gene Duplications .” Genome Biology, vol. 3, no. 2, BioMed Central, 2002, doi:10.1186/gb-2002-3-2-research0008.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
2002 | Journal Article | IST-REx-ID: 859
Perelygin, Andrey, et al. “Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution, vol. 55, no. 2, Springer, 2002, pp. 202–10, doi:10.1007/s00239-002-2318-0.
View | DOI | PubMed | Europe PMC
 
[8]
2001 | Journal Article | IST-REx-ID: 888 | OA
Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001, doi:10.1186/gb-2001-2-12-research0053.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[7]
2001 | Journal Article | IST-REx-ID: 855
Rogozin, Igor, et al. “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, 2001, pp. 890–900, doi:10.1093/bioinformatics/17.10.890.
View | DOI | PubMed | Europe PMC
 
[6]
2001 | Journal Article | IST-REx-ID: 874 | OA
Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS, vol. 98, no. 21, National Academy of Sciences, 2001, pp. 12089–92, doi:10.1073/pnas.211214298.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
2001 | Journal Article | IST-REx-ID: 867
Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics, vol. 10, no. 23, Oxford University Press, 2001, pp. 2661–69, doi:10.1093/hmg/10.23.2661.
[Published Version] View | DOI | PubMed | Europe PMC
 
[4]
2001 | Journal Article | IST-REx-ID: 851
Rogozin, Igor, et al. “Use of Mutation Spectra Analysis Software.” Human Mutation, vol. 17, no. 2, Wiley-Blackwell, 2001, pp. 83–102, doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
View | DOI | PubMed | Europe PMC
 
[3]
2001 | Journal Article | IST-REx-ID: 841
Wolf, Yuri, et al. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics, vol. 17, no. 9, Elsevier, 2001, pp. 499–501, doi:10.1016/S0168-9525(01)02376-9.
View | DOI | PubMed | Europe PMC
 
[2]
2000 | Journal Article | IST-REx-ID: 842
Wolf, Yuri, et al. “No Footprints of Primordial Introns in a Eukaryotic Genome.” Trends in Genetics, vol. 16, no. 8, Elsevier, 2000, pp. 333–34, doi:10.1016/S0168-9525(00)02059-X.
View | DOI | PubMed | Europe PMC
 
[1]
1999 | Journal Article | IST-REx-ID: 883
Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative Traits in the Course of Sympatric Speciation.” Nature, vol. 400, no. 6742, Nature Publishing Group, 1999, pp. 351–54, doi:10.1038/22514.
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[95]
2024 | Journal Article | IST-REx-ID: 15179 | OA
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
Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
[Published Version] View | Files available | DOI | WoS
 
[93]
2023 | Journal Article | IST-REx-ID: 13164 | OA
Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications, vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4.
[Published Version] View | Files available | DOI | WoS
 
[92]
2023 | Journal Article | IST-REx-ID: 13976 | OA
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
Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.
[Published Version] View | Files available | DOI
 
[90]
2022 | Journal Article | IST-REx-ID: 11187 | OA
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.
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[89]
2022 | Journal Article | IST-REx-ID: 11344 | OA
Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer Nature, 2022, doi:10.1038/s41598-022-10827-3.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[88]
2022 | Journal Article | IST-REx-ID: 11448 | OA
Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences Publications, 2022, doi:10.7554/elife.75842.
[Published Version] View | Files available | DOI | WoS
 
[87]
2022 | Journal Article | IST-REx-ID: 11447 | OA
Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
[Published Version] View | Files available | DOI | WoS
 
[86]
2022 | Journal Article | IST-REx-ID: 12116 | OA
Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.” Science, vol. 378, no. 6626, American Association for the Advancement of Science, 2022, pp. 1285–86, doi:10.1126/science.adg0797.
[Published Version] View | DOI | Download Published Version (ext.) | WoS
 
[85]
2021 | Journal Article | IST-REx-ID: 9910 | OA
Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:10.1038/s41431-021-00836-7.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[84]
2021 | Journal Article | IST-REx-ID: 9905 | OA
Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[83]
2020 | Report | IST-REx-ID: 8151
Maslov, Mikhail, et al. Core Project Proceedings. IST Austria, 2020.
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[82]
2020 | Journal Article | IST-REx-ID: 7931 | OA
Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.
[Published Version] View | Files available | DOI | WoS
 
[81]
2020 | Journal Article | IST-REx-ID: 8645 | OA
Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[80]
2020 | Journal Article | IST-REx-ID: 7889 | OA
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
Pokusaeva, Victoria, 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, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.
[Published Version] View | Files available | DOI | WoS
 
[78]
2019 | Research Data Reference | IST-REx-ID: 9790
Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
[Published Version] View | Files available | DOI
 
[77]
2019 | Research Data Reference | IST-REx-ID: 9797
Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
[Published Version] View | Files available | DOI
 
[76]
2019 | Research Data Reference | IST-REx-ID: 9789
Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.
[Published Version] View | Files available | DOI
 
[75]
2019 | Journal Article | IST-REx-ID: 7181 | OA
Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.
[Submitted Version] View | Files available | DOI | Download Submitted Version (ext.) | WoS | PubMed | Europe PMC
 
[74]
2018 | Research Data Reference | IST-REx-ID: 13059 | OA
Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[73]
2018 | Journal Article | IST-REx-ID: 5780 | OA
Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.
[Published Version] View | Files available | DOI | WoS
 
[72]
2018 | Journal Article | IST-REx-ID: 279 | OA
Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.
[Published Version] View | Files available | DOI | WoS
 
[71]
2018 | Research Data Reference | IST-REx-ID: 9812 | OA
Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[70]
2018 | Research Data Reference | IST-REx-ID: 9811 | OA
Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.
[Preprint] View | Files available | DOI | Download Preprint (ext.)
 
[69]
2018 | Journal Article | IST-REx-ID: 5995 | OA
Usmanova, Dinara R., 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 , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[68]
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.
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[67]
2016 | Journal Article | IST-REx-ID: 896
Howe, Kerstin, et al. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology, vol. 6, no. 4, Royal Society, The, 2016, doi:10.1098/rsob.160009.
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[66]
2016 | Journal Article | IST-REx-ID: 849
Saint Léger, Adélaïde, et al. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances, vol. 2, no. 4, American Association for the Advancement of Science, 2016, pp. e1501860–e1501860, doi:10.1126/sciadv.1501860.
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[65]
2016 | Journal Article | IST-REx-ID: 853
Rivkina, Elizaveta, et al. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences, vol. 13, no. 7, European Geosciences Union, 2016, pp. 2207–19, doi:10.5194/bg-13-2207-2016.
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[64]
2015 | Journal Article | IST-REx-ID: 848
Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.
View | DOI
 
[63]
2015 | Journal Article | IST-REx-ID: 906
Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.
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[62]
2015 | Journal Article | IST-REx-ID: 866
Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 886
Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.
View | DOI
 
[60]
2014 | Journal Article | IST-REx-ID: 852
Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
View | DOI
 
[59]
2014 | Journal Article | IST-REx-ID: 856
Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications, vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
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[58]
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.
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[57]
2014 | Journal Article | IST-REx-ID: 865
Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
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[56]
2014 | Journal Article | IST-REx-ID: 845
Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.
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[55]
2014 | Journal Article | IST-REx-ID: 892
Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014, pp. 104–12, doi:10.1016/j.sbi.2014.05.004.
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[54]
2013 | Journal Article | IST-REx-ID: 899
Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.
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[53]
2013 | Journal Article | IST-REx-ID: 894
Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central, 2013, doi:10.1186/1756-0500-6-310.
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[52]
2013 | Journal Article | IST-REx-ID: 905 | OA
Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30.
View | Download (ext.)
 
[51]
2012 | Journal Article | IST-REx-ID: 846
Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.
View | DOI
 
[50]
2012 | Journal Article | IST-REx-ID: 858
Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30.
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[49]
2012 | Journal Article | IST-REx-ID: 900
Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510.
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[48]
2012 | Journal Article | IST-REx-ID: 887
Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57, doi:10.1098/rspb.2012.1108.
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[47]
2011 | Journal Article | IST-REx-ID: 890
Koblik, Evgeniy, et al. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One, vol. 6, no. 4, Public Library of Science, 2011, doi:10.1371/journal.pone.0017716.
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[46]
2011 | Book Chapter | IST-REx-ID: 881
Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4.
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[45]
2010 | Journal Article | IST-REx-ID: 891
Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” Nature Reviews Genetics, vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:10.1038/nrg2689.
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[44]
2010 | Journal Article | IST-REx-ID: 901
Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-68.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 857
Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature, vol. 465, no. 7300, Nature Publishing Group, 2010, pp. 922–26, doi:10.1038/nature09105.
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[42]
2010 | Journal Article | IST-REx-ID: 862
Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” Nature, vol. 464, no. 7286, Nature Publishing Group, 2010, pp. 279–82, doi:10.1038/nature08691.
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[41]
2010 | Journal Article | IST-REx-ID: 872
Kondrashov, Fyodor, and Alexey 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, 2010, pp. 1169–76, doi:10.1098/rstb.2009.0286.
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[40]
2010 | Journal Article | IST-REx-ID: 884
Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.” Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-5.
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[39]
2009 | Journal Article | IST-REx-ID: 908
Alkalaeva, Elena, et al. “Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters, vol. 583, no. 21, Elsevier, 2009, pp. 3455–60, doi:10.1016/j.febslet.2009.09.044.
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[38]
2008 | Journal Article | IST-REx-ID: 844
Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science, 2008, doi:10.1371/journal.pgen.1000281.
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[37]
2008 | Journal Article | IST-REx-ID: 895
Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180.
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[36]
2008 | Journal Article | IST-REx-ID: 907
Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics, vol. 24, no. 10, Elsevier, 2008, pp. 475–78, doi:10.1016/j.tig.2008.08.003.
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[35]
2007 | Journal Article | IST-REx-ID: 860
Plotnikova, Olga, et al. “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, 2007, pp. 32–43, doi:10.1086/518616.
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[34]
2007 | Journal Article | IST-REx-ID: 879
Kondrashov, Fyodor, et al. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics, vol. 23, no. 5, Elsevier, 2007, pp. 215–18, doi:10.1016/j.tig.2007.03.002.
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[33]
2007 | Journal Article | IST-REx-ID: 904
Bazykin, Georgii, et al. “Extensive Parallelism in Protein Evolution.” Biology Direct, vol. 2, BioMed Central, 2007, doi:10.1186/1745-6150-2-20.
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[32]
2007 | Journal Article | IST-REx-ID: 861
Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics, vol. 8, BioMed Central, 2007, doi:10.1186/1471-2105-8-441.
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[31]
2006 | Journal Article | IST-REx-ID: 854
Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073.
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[30]
2006 | Journal Article | IST-REx-ID: 868
Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct, vol. 1, BioMed Central, 2006, doi:10.1186/1745-6150-1-31.
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[29]
2006 | Journal Article | IST-REx-ID: 873
Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology, vol. 239, no. 2, Elsevier, 2006, pp. 141–51, doi:10.1016/j.jtbi.2005.08.033.
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[28]
2006 | Journal Article | IST-REx-ID: 869
Kondrashov, Fyodor, et al. “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, 2006, pp. 616–26, doi:10.1016/j.jtbi.2005.10.020.
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[27]
2006 | Journal Article | IST-REx-ID: 903
Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer, vol. 6, BioMed Central, 2006, doi:10.1186/1471-2407-6-36.
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[26]
2005 | Journal Article | IST-REx-ID: 843
Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350.
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[25]
2005 | Journal Article | IST-REx-ID: 877
Kondrashov, Fyodor. “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, 2005, pp. 389–95.
View | Download None (ext.) | PubMed | Europe PMC
 
[24]
2005 | Journal Article | IST-REx-ID: 878
Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9.
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[23]
2005 | Journal Article | IST-REx-ID: 882
Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243.
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[22]
2005 | Journal Article | IST-REx-ID: 880
Kondrashov, Fyodor. “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, 2005, pp. 396–403.
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[21]
2005 | Journal Article | IST-REx-ID: 893
Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:10.1038/nature03306.
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[20]
2004 | Journal Article | IST-REx-ID: 864
Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:10.1110/ps.03465504.
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[19]
2004 | Journal Article | IST-REx-ID: 870
Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:10.1093/nar/gkh330.
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[18]
2004 | Journal Article | IST-REx-ID: 875
Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001.
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[17]
2004 | Journal Article | IST-REx-ID: 889
Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451.
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[16]
2004 | Journal Article | IST-REx-ID: 898
Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:10.1038/nature02601.
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[15]
2004 | Journal Article | IST-REx-ID: 902
Castillo Davis, Cristian, et al. “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, 2004, pp. 802–11, doi:10.1101/gr.2195604.
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[14]
2003 | Journal Article | IST-REx-ID: 847
Sunyaev, Shamil, et al. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics, vol. 12, no. 24, Oxford University Press, 2003, pp. 3325–30, doi:10.1093/hmg/ddg359.
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[13]
2003 | Journal Article | IST-REx-ID: 876
Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” Trends in Genetics, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:10.1016/S0168-9525(02)00029-X.
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[12]
2002 | Journal Article | IST-REx-ID: 885 | OA
Kondrashov, Alexey, et al. “Dobzhansky-Muller Incompatibilities in Protein Evolution.” PNAS, vol. 99, no. 23, National Academy of Sciences, 2002, pp. 14878–83, doi:10.1073/pnas.232565499.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
2002 | Journal Article | IST-REx-ID: 897
Castillo Davis, Cristian, et al. “Selection for Short Introns in Highly Expressed Genes.” Nature Genetics, vol. 31, no. 4, Nature Publishing Group, 2002, pp. 415–18, doi:10.1038/ng940.
View | DOI | PubMed | Europe PMC
 
[10]
2002 | Journal Article | IST-REx-ID: 871 | OA
Kondrashov, Fyodor, et al. “Selection in the Evolution of Gene Duplications .” Genome Biology, vol. 3, no. 2, BioMed Central, 2002, doi:10.1186/gb-2002-3-2-research0008.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
2002 | Journal Article | IST-REx-ID: 859
Perelygin, Andrey, et al. “Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution, vol. 55, no. 2, Springer, 2002, pp. 202–10, doi:10.1007/s00239-002-2318-0.
View | DOI | PubMed | Europe PMC
 
[8]
2001 | Journal Article | IST-REx-ID: 888 | OA
Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001, doi:10.1186/gb-2001-2-12-research0053.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[7]
2001 | Journal Article | IST-REx-ID: 855
Rogozin, Igor, et al. “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, 2001, pp. 890–900, doi:10.1093/bioinformatics/17.10.890.
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[6]
2001 | Journal Article | IST-REx-ID: 874 | OA
Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS, vol. 98, no. 21, National Academy of Sciences, 2001, pp. 12089–92, doi:10.1073/pnas.211214298.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
2001 | Journal Article | IST-REx-ID: 867
Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics, vol. 10, no. 23, Oxford University Press, 2001, pp. 2661–69, doi:10.1093/hmg/10.23.2661.
[Published Version] View | DOI | PubMed | Europe PMC
 
[4]
2001 | Journal Article | IST-REx-ID: 851
Rogozin, Igor, et al. “Use of Mutation Spectra Analysis Software.” Human Mutation, vol. 17, no. 2, Wiley-Blackwell, 2001, pp. 83–102, doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
View | DOI | PubMed | Europe PMC
 
[3]
2001 | Journal Article | IST-REx-ID: 841
Wolf, Yuri, et al. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics, vol. 17, no. 9, Elsevier, 2001, pp. 499–501, doi:10.1016/S0168-9525(01)02376-9.
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[2]
2000 | Journal Article | IST-REx-ID: 842
Wolf, Yuri, et al. “No Footprints of Primordial Introns in a Eukaryotic Genome.” Trends in Genetics, vol. 16, no. 8, Elsevier, 2000, pp. 333–34, doi:10.1016/S0168-9525(00)02059-X.
View | DOI | PubMed | Europe PMC
 
[1]
1999 | Journal Article | IST-REx-ID: 883
Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative Traits in the Course of Sympatric Speciation.” Nature, vol. 400, no. 6742, Nature Publishing Group, 1999, pp. 351–54, doi:10.1038/22514.
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