73 Publications

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[73]
2019 | Journal Article | IST-REx-ID: 6419   OA
Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics 15, no. 4 (2019). https://doi.org/10.1371/journal.pgen.1008079.
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[72]
2019 | Journal Article | IST-REx-ID: 7181   OA
Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology 37, no. 12 (2019): 1466–70. https://doi.org/10.1038/s41587-019-0333-6.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 5780   OA
Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America 115, no. 50 (2018): 12728–32. https://doi.org/10.1073/pnas.1803615115.
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[70]
2018 | Journal Article | IST-REx-ID: 5995   OA
Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics 34, no. 21 (2018): 3653–58. https://doi.org/10.1093/bioinformatics/bty340.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279   OA
Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology 19 (2018). https://doi.org/10.1186/s13059-018-1434-0.
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[68]
2016 | Journal Article | IST-REx-ID: 853
Rivkina, Elizaveta, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin, Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences 13, no. 7 (2016): 2207–19. https://doi.org/10.5194/bg-13-2207-2016.
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[67]
2016 | Journal Article | IST-REx-ID: 896
Howe, Kerstin, Philipp Schiffer, Julia Zielinski, Thomas Wiehe, Gavin Laird, John Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology 6, no. 4 (2016). https://doi.org/10.1098/rsob.160009.
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[66]
2016 | Journal Article | IST-REx-ID: 850
Sarkisyan, Karen, Dmitry Bolotin, Margarita Meer, Dinara Usmanova, Alexander Mishin, George Sharonov, Dmitry Ivankov, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” Nature 533 (2016): 397–401. https://doi.org/10.1038/nature17995.
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[65]
2016 | Journal Article | IST-REx-ID: 849
Saint Léger, Adélaïde, Carla Bello, Pablo Dans, Adrian Torres, Eva Novoa, Noelia Camacho, Modesto Orozco, Fyodor Kondrashov, and Lluís Ribas De Pouplana. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances 2, no. 4 (2016): e1501860–e1501860. https://doi.org/10.1126/sciadv.1501860.
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[64]
2015 | Journal Article | IST-REx-ID: 866
Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS 112, no. 30 (2015): 9328–33. https://doi.org/10.1073/pnas.1511328112.
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[63]
2015 | Journal Article | IST-REx-ID: 886
Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics 31, no. 1 (2015): 24–33. https://doi.org/10.1016/j.tig.2014.09.009.
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[62]
2015 | Journal Article | IST-REx-ID: 906
Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One 10, no. 5 (2015). https://doi.org/10.1371/journal.pone.0125888.
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[61]
2015 | Journal Article | IST-REx-ID: 848
Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution 32, no. 2 (2015): 542–54. https://doi.org/10.1093/molbev/msu318.
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[60]
2014 | Journal Article | IST-REx-ID: 845
Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution 31, no. 11 (2014): 3016–25. https://doi.org/10.1093/molbev/msu242.
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[59]
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 6, no. 8 (2014): 1949–55. https://doi.org/10.1093/gbe/evu159.
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[58]
2014 | Journal Article | IST-REx-ID: 865
Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology 87, no. 4 (2014): 571–78. https://doi.org/10.1016/j.bcp.2013.12.007.
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[57]
2014 | Journal Article | IST-REx-ID: 892
Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology 26, no. 1 (2014): 104–12. https://doi.org/10.1016/j.sbi.2014.05.004.
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[56]
2014 | Journal Article | IST-REx-ID: 856
Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications 5 (2014). https://doi.org/10.1038/ncomms5868.
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[55]
2014 | Journal Article | IST-REx-ID: 863
Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature 510, no. 7503 (2014): 109–14. https://doi.org/10.1038/nature13400.
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[54]
2013 | Journal Article | IST-REx-ID: 905   OA
Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29 (2013): 25–30.
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[53]
2013 | Journal Article | IST-REx-ID: 894
Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes 6, no. 1 (2013). https://doi.org/10.1186/1756-0500-6-310.
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[52]
2013 | Journal Article | IST-REx-ID: 899
Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” Nature 497, no. 7451 (2013): E2–3. https://doi.org/10.1038/nature12220.
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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 4, no. 12 (2012): 1213–22. https://doi.org/10.1093/gbe/evs096.
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[50]
2012 | Journal Article | IST-REx-ID: 858
Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct 7 (2012). https://doi.org/10.1186/1745-6150-7-30.
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[49]
2012 | Journal Article | IST-REx-ID: 900
Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature 490, no. 7421 (2012): 535–38. https://doi.org/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 279, no. 1749 (2012): 5048–57. https://doi.org/10.1098/rspb.2012.1108.
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[47]
2011 | Journal Article | IST-REx-ID: 890
Koblik, Evgeniy, Yaroslav Red’Kin, Margarita Meer, Romain Derelle, Sofia Golenkina, Fyodor Kondrashov, and Vladimir Arkhipov. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One 6, no. 4 (2011). https://doi.org/10.1371/journal.pone.0017716.
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[46]
2011 | Book Chapter | IST-REx-ID: 881
Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4.
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[45]
2010 | Journal Article | IST-REx-ID: 857
Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature 465, no. 7300 (2010): 922–26. https://doi.org/10.1038/nature09105.
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[44]
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 365, no. 1544 (2010): 1169–76. https://doi.org/10.1098/rstb.2009.0286.
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[43]
2010 | Journal Article | IST-REx-ID: 884
Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov. “Rate of Sequence Divergence under Constant Selection.” Biology Direct 5 (2010). https://doi.org/10.1186/1745-6150-5-5.
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[42]
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 11, no. 2 (2010): 97–108. https://doi.org/10.1038/nrg2689.
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[41]
2010 | Journal Article | IST-REx-ID: 901
Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” Biology Direct 5 (2010). https://doi.org/10.1186/1745-6150-5-68.
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[40]
2010 | Journal Article | IST-REx-ID: 862
Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” Nature 464, no. 7286 (2010): 279–82. https://doi.org/10.1038/nature08691.
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[39]
2009 | Journal Article | IST-REx-ID: 908
Alkalaeva, Elena, Boris Eliseev, Alexandre Ambrogelly, Peter Vlasov, Fyodor Kondrashov, Sarath Gundllapalli, Ludmila Frolova, Dieter Söll, and Lev Kisselev. “Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters 583, no. 21 (2009): 3455–60. https://doi.org/10.1016/j.febslet.2009.09.044.
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[38]
2008 | Journal Article | IST-REx-ID: 895
Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology 8, no. 1 (2008). https://doi.org/10.1186/1471-2148-8-180.
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[37]
2008 | Journal Article | IST-REx-ID: 844
Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics 4, no. 11 (2008). https://doi.org/10.1371/journal.pgen.1000281.
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[36]
2008 | Journal Article | IST-REx-ID: 907
Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics 24, no. 10 (2008): 475–78. https://doi.org/10.1016/j.tig.2008.08.003.
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[35]
2007 | Journal Article | IST-REx-ID: 860
Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko, Evgeny Ginter, and Evgeny 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 81, no. 1 (2007): 32–43. https://doi.org/10.1086/518616.
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[34]
2007 | Journal Article | IST-REx-ID: 904
Bazykin, Georgii, Fyodor Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, and Alexey Kondrashov. “Extensive Parallelism in Protein Evolution.” Biology Direct 2 (2007). https://doi.org/10.1186/1745-6150-2-20.
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[33]
2007 | Journal Article | IST-REx-ID: 861
Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics 8 (2007). https://doi.org/10.1186/1471-2105-8-441.
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[32]
2007 | Journal Article | IST-REx-ID: 879
Kondrashov, Fyodor, Tatiana Gurbich, and Peter Vlasov. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics 23, no. 5 (2007): 215–18. https://doi.org/10.1016/j.tig.2007.03.002.
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[31]
2006 | Journal Article | IST-REx-ID: 903
Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer 6 (2006). https://doi.org/10.1186/1471-2407-6-36.
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[30]
2006 | Journal Article | IST-REx-ID: 869
Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal of Theoretical Biology 240, no. 4 (2006): 616–26. https://doi.org/10.1016/j.jtbi.2005.10.020.
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[29]
2006 | Journal Article | IST-REx-ID: 854
Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology 4, no. 3 (2006): 0403–10. https://doi.org/10.1371/journal.pbio.0040073.
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[28]
2006 | Journal Article | IST-REx-ID: 873
Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology 239, no. 2 (2006): 141–51. https://doi.org/10.1016/j.jtbi.2005.08.033.
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[27]
2006 | Journal Article | IST-REx-ID: 868
Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct 1 (2006). https://doi.org/10.1186/1745-6150-1-31.
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[26]
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 50, no. 3 (2005): 389–95.
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[25]
2005 | Journal Article | IST-REx-ID: 878
Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics 37, no. 1 (2005): 9–10. https://doi.org/10.1038/ng0105-9.
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[24]
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 50, no. 3 (2005): 396–403.
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[23]
2005 | Journal Article | IST-REx-ID: 893
Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature 433, no. 7026 (2005): 633–38. https://doi.org/10.1038/nature03306.
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[22]
2005 | Journal Article | IST-REx-ID: 843
Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics 14, no. 21 (2005): 3191–3201. https://doi.org/10.1093/hmg/ddi350.
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[21]
2005 | Journal Article | IST-REx-ID: 882
Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics 14, no. 16 (2005): 2415–19. https://doi.org/10.1093/hmg/ddi243.
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[20]
2004 | Journal Article | IST-REx-ID: 864
Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science 13, no. 4 (2004): 884–92. https://doi.org/10.1110/ps.03465504.
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[19]
2004 | Journal Article | IST-REx-ID: 889
Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics 36, no. 11 (2004): 1207–12. https://doi.org/10.1038/ng1451.
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[18]
2004 | Journal Article | IST-REx-ID: 898
Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature 429, no. 6991 (2004): 558–62. https://doi.org/10.1038/nature02601.
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[17]
2004 | Journal Article | IST-REx-ID: 870
Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research 32, no. 5 (2004): 1731–37. https://doi.org/10.1093/nar/gkh330.
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[16]
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 20, no. 7 (2004): 287–91. https://doi.org/10.1016/j.tig.2004.05.001.
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[15]
2004 | Journal Article | IST-REx-ID: 902
Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research 14, no. 5 (2004): 802–11. https://doi.org/10.1101/gr.2195604.
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[14]
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 19, no. 3 (2003): 115–19. https://doi.org/10.1016/S0168-9525(02)00029-X.
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[13]
2003 | Journal Article | IST-REx-ID: 847
Sunyaev, Shamil, Fyodor Kondrashov, Peer Bork, and Vasily Ramensky. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics 12, no. 24 (2003): 3325–30. https://doi.org/10.1093/hmg/ddg359.
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[12]
2002 | Journal Article | IST-REx-ID: 871
Kondrashov, Fyodor, Igor Rogozin, Yuri Wolf, and Eugene Koonin. “Selection in the Evolution of Gene Duplications .” Genome Biology 3, no. 2 (2002). https://doi.org/10.1186/gb-2002-3-2-research0008.
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[11]
2002 | Journal Article | IST-REx-ID: 859
Perelygin, Andrey, Fyodor Kondrashov, Igor Rogozin, and Margo Brinton. “Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution 55, no. 2 (2002): 202–10. https://doi.org/10.1007/s00239-002-2318-0.
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[10]
2002 | Journal Article | IST-REx-ID: 885
Kondrashov, Alexey, Shamil Sunyaev, and Fyodor Kondrashov. “Dobzhansky-Muller Incompatibilities in Protein Evolution.” PNAS 99, no. 23 (2002): 14878–83. https://doi.org/10.1073/pnas.232565499.
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[9]
2002 | Journal Article | IST-REx-ID: 897
Castillo Davis, Cristian, Sergei Mekhedov, Daniel Hartl, Eugene Koonin, and Fyodor Kondrashov. “Selection for Short Introns in Highly Expressed Genes.” Nature Genetics 31, no. 4 (2002): 415–18. https://doi.org/10.1038/ng940.
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[8]
2001 | Journal Article | IST-REx-ID: 888
Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf, and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology 2, no. 12 (2001). https://doi.org/10.1186/gb-2001-2-12-research0053.
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[7]
2001 | Journal Article | IST-REx-ID: 841
Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics 17, no. 9 (2001): 499–501. https://doi.org/10.1016/S0168-9525(01)02376-9.
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[6]
2001 | Journal Article | IST-REx-ID: 874
Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS 98, no. 21 (2001): 12089–92. https://doi.org/10.1073/pnas.211214298.
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[5]
2001 | Journal Article | IST-REx-ID: 855
Rogozin, Igor, Alex Kochetov, Fyodor Kondrashov, Eugene Koonin, and Luciano Milanesi. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics 17, no. 10 (2001): 890–900. https://doi.org/10.1093/bioinformatics/17.10.890.
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[4]
2001 | Journal Article | IST-REx-ID: 867
Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics 10, no. 23 (2001): 2661–69. https://doi.org/10.1093/hmg/10.23.2661.
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[3]
2001 | Journal Article | IST-REx-ID: 851
Rogozin, Igor, Fyodor Kondrashov, and Galina Glazko. “Use of Mutation Spectra Analysis Software.” Human Mutation 17, no. 2 (2001): 83–102. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
View | DOI
 
[2]
2000 | Journal Article | IST-REx-ID: 842
Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “No Footprints of Primordial Introns in a Eukaryotic Genome.” Trends in Genetics 16, no. 8 (2000): 333–34. https://doi.org/10.1016/S0168-9525(00)02059-X.
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[1]
1999 | Journal Article | IST-REx-ID: 883
Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative Traits in the Course of Sympatric Speciation.” Nature 400, no. 6742 (1999): 351–54. https://doi.org/10.1038/22514.
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[73]
2019 | Journal Article | IST-REx-ID: 6419   OA
Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics 15, no. 4 (2019). https://doi.org/10.1371/journal.pgen.1008079.
View | Files available | DOI
 
[72]
2019 | Journal Article | IST-REx-ID: 7181   OA
Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology 37, no. 12 (2019): 1466–70. https://doi.org/10.1038/s41587-019-0333-6.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 5780   OA
Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America 115, no. 50 (2018): 12728–32. https://doi.org/10.1073/pnas.1803615115.
View | Files available | DOI
 
[70]
2018 | Journal Article | IST-REx-ID: 5995   OA
Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics 34, no. 21 (2018): 3653–58. https://doi.org/10.1093/bioinformatics/bty340.
View | Files available | DOI | PubMed | Europe PMC
 
[69]
2018 | Journal Article | IST-REx-ID: 279   OA
Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology 19 (2018). https://doi.org/10.1186/s13059-018-1434-0.
View | Files available | DOI
 
[68]
2016 | Journal Article | IST-REx-ID: 853
Rivkina, Elizaveta, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin, Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences 13, no. 7 (2016): 2207–19. https://doi.org/10.5194/bg-13-2207-2016.
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[67]
2016 | Journal Article | IST-REx-ID: 896
Howe, Kerstin, Philipp Schiffer, Julia Zielinski, Thomas Wiehe, Gavin Laird, John Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology 6, no. 4 (2016). https://doi.org/10.1098/rsob.160009.
View | DOI
 
[66]
2016 | Journal Article | IST-REx-ID: 850
Sarkisyan, Karen, Dmitry Bolotin, Margarita Meer, Dinara Usmanova, Alexander Mishin, George Sharonov, Dmitry Ivankov, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” Nature 533 (2016): 397–401. https://doi.org/10.1038/nature17995.
View | DOI
 
[65]
2016 | Journal Article | IST-REx-ID: 849
Saint Léger, Adélaïde, Carla Bello, Pablo Dans, Adrian Torres, Eva Novoa, Noelia Camacho, Modesto Orozco, Fyodor Kondrashov, and Lluís Ribas De Pouplana. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances 2, no. 4 (2016): e1501860–e1501860. https://doi.org/10.1126/sciadv.1501860.
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[64]
2015 | Journal Article | IST-REx-ID: 866
Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS 112, no. 30 (2015): 9328–33. https://doi.org/10.1073/pnas.1511328112.
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[63]
2015 | Journal Article | IST-REx-ID: 886
Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics 31, no. 1 (2015): 24–33. https://doi.org/10.1016/j.tig.2014.09.009.
View | DOI
 
[62]
2015 | Journal Article | IST-REx-ID: 906
Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One 10, no. 5 (2015). https://doi.org/10.1371/journal.pone.0125888.
View | DOI
 
[61]
2015 | Journal Article | IST-REx-ID: 848
Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution 32, no. 2 (2015): 542–54. https://doi.org/10.1093/molbev/msu318.
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[60]
2014 | Journal Article | IST-REx-ID: 845
Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution 31, no. 11 (2014): 3016–25. https://doi.org/10.1093/molbev/msu242.
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[59]
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 6, no. 8 (2014): 1949–55. https://doi.org/10.1093/gbe/evu159.
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[58]
2014 | Journal Article | IST-REx-ID: 865
Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology 87, no. 4 (2014): 571–78. https://doi.org/10.1016/j.bcp.2013.12.007.
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[57]
2014 | Journal Article | IST-REx-ID: 892
Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology 26, no. 1 (2014): 104–12. https://doi.org/10.1016/j.sbi.2014.05.004.
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[56]
2014 | Journal Article | IST-REx-ID: 856
Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications 5 (2014). https://doi.org/10.1038/ncomms5868.
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[55]
2014 | Journal Article | IST-REx-ID: 863
Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature 510, no. 7503 (2014): 109–14. https://doi.org/10.1038/nature13400.
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[54]
2013 | Journal Article | IST-REx-ID: 905   OA
Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29 (2013): 25–30.
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[53]
2013 | Journal Article | IST-REx-ID: 894
Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes 6, no. 1 (2013). https://doi.org/10.1186/1756-0500-6-310.
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[52]
2013 | Journal Article | IST-REx-ID: 899
Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” Nature 497, no. 7451 (2013): E2–3. https://doi.org/10.1038/nature12220.
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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 4, no. 12 (2012): 1213–22. https://doi.org/10.1093/gbe/evs096.
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[50]
2012 | Journal Article | IST-REx-ID: 858
Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct 7 (2012). https://doi.org/10.1186/1745-6150-7-30.
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[49]
2012 | Journal Article | IST-REx-ID: 900
Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature 490, no. 7421 (2012): 535–38. https://doi.org/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 279, no. 1749 (2012): 5048–57. https://doi.org/10.1098/rspb.2012.1108.
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[47]
2011 | Journal Article | IST-REx-ID: 890
Koblik, Evgeniy, Yaroslav Red’Kin, Margarita Meer, Romain Derelle, Sofia Golenkina, Fyodor Kondrashov, and Vladimir Arkhipov. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One 6, no. 4 (2011). https://doi.org/10.1371/journal.pone.0017716.
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[46]
2011 | Book Chapter | IST-REx-ID: 881
Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4.
View | DOI
 
[45]
2010 | Journal Article | IST-REx-ID: 857
Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature 465, no. 7300 (2010): 922–26. https://doi.org/10.1038/nature09105.
View | DOI
 
[44]
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 365, no. 1544 (2010): 1169–76. https://doi.org/10.1098/rstb.2009.0286.
View | DOI
 
[43]
2010 | Journal Article | IST-REx-ID: 884
Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov. “Rate of Sequence Divergence under Constant Selection.” Biology Direct 5 (2010). https://doi.org/10.1186/1745-6150-5-5.
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[42]
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 11, no. 2 (2010): 97–108. https://doi.org/10.1038/nrg2689.
View | DOI
 
[41]
2010 | Journal Article | IST-REx-ID: 901
Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” Biology Direct 5 (2010). https://doi.org/10.1186/1745-6150-5-68.
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[40]
2010 | Journal Article | IST-REx-ID: 862
Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” Nature 464, no. 7286 (2010): 279–82. https://doi.org/10.1038/nature08691.
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[39]
2009 | Journal Article | IST-REx-ID: 908
Alkalaeva, Elena, Boris Eliseev, Alexandre Ambrogelly, Peter Vlasov, Fyodor Kondrashov, Sarath Gundllapalli, Ludmila Frolova, Dieter Söll, and Lev Kisselev. “Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters 583, no. 21 (2009): 3455–60. https://doi.org/10.1016/j.febslet.2009.09.044.
View | DOI
 
[38]
2008 | Journal Article | IST-REx-ID: 895
Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology 8, no. 1 (2008). https://doi.org/10.1186/1471-2148-8-180.
View | DOI
 
[37]
2008 | Journal Article | IST-REx-ID: 844
Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics 4, no. 11 (2008). https://doi.org/10.1371/journal.pgen.1000281.
View | DOI
 
[36]
2008 | Journal Article | IST-REx-ID: 907
Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics 24, no. 10 (2008): 475–78. https://doi.org/10.1016/j.tig.2008.08.003.
View | DOI
 
[35]
2007 | Journal Article | IST-REx-ID: 860
Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko, Evgeny Ginter, and Evgeny 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 81, no. 1 (2007): 32–43. https://doi.org/10.1086/518616.
View | DOI
 
[34]
2007 | Journal Article | IST-REx-ID: 904
Bazykin, Georgii, Fyodor Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, and Alexey Kondrashov. “Extensive Parallelism in Protein Evolution.” Biology Direct 2 (2007). https://doi.org/10.1186/1745-6150-2-20.
View | DOI
 
[33]
2007 | Journal Article | IST-REx-ID: 861
Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics 8 (2007). https://doi.org/10.1186/1471-2105-8-441.
View | DOI
 
[32]
2007 | Journal Article | IST-REx-ID: 879
Kondrashov, Fyodor, Tatiana Gurbich, and Peter Vlasov. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics 23, no. 5 (2007): 215–18. https://doi.org/10.1016/j.tig.2007.03.002.
View | DOI
 
[31]
2006 | Journal Article | IST-REx-ID: 903
Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer 6 (2006). https://doi.org/10.1186/1471-2407-6-36.
View | DOI
 
[30]
2006 | Journal Article | IST-REx-ID: 869
Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal of Theoretical Biology 240, no. 4 (2006): 616–26. https://doi.org/10.1016/j.jtbi.2005.10.020.
View | DOI
 
[29]
2006 | Journal Article | IST-REx-ID: 854
Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology 4, no. 3 (2006): 0403–10. https://doi.org/10.1371/journal.pbio.0040073.
View | DOI
 
[28]
2006 | Journal Article | IST-REx-ID: 873
Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology 239, no. 2 (2006): 141–51. https://doi.org/10.1016/j.jtbi.2005.08.033.
View | DOI
 
[27]
2006 | Journal Article | IST-REx-ID: 868
Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct 1 (2006). https://doi.org/10.1186/1745-6150-1-31.
View | DOI
 
[26]
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 50, no. 3 (2005): 389–95.
View | Download (ext.)
 
[25]
2005 | Journal Article | IST-REx-ID: 878
Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics 37, no. 1 (2005): 9–10. https://doi.org/10.1038/ng0105-9.
View | DOI
 
[24]
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 50, no. 3 (2005): 396–403.
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[23]
2005 | Journal Article | IST-REx-ID: 893
Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature 433, no. 7026 (2005): 633–38. https://doi.org/10.1038/nature03306.
View | DOI
 
[22]
2005 | Journal Article | IST-REx-ID: 843
Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics 14, no. 21 (2005): 3191–3201. https://doi.org/10.1093/hmg/ddi350.
View | DOI
 
[21]
2005 | Journal Article | IST-REx-ID: 882
Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics 14, no. 16 (2005): 2415–19. https://doi.org/10.1093/hmg/ddi243.
View | DOI
 
[20]
2004 | Journal Article | IST-REx-ID: 864
Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science 13, no. 4 (2004): 884–92. https://doi.org/10.1110/ps.03465504.
View | DOI
 
[19]
2004 | Journal Article | IST-REx-ID: 889
Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics 36, no. 11 (2004): 1207–12. https://doi.org/10.1038/ng1451.
View | DOI
 
[18]
2004 | Journal Article | IST-REx-ID: 898
Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature 429, no. 6991 (2004): 558–62. https://doi.org/10.1038/nature02601.
View | DOI
 
[17]
2004 | Journal Article | IST-REx-ID: 870
Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research 32, no. 5 (2004): 1731–37. https://doi.org/10.1093/nar/gkh330.
View | DOI
 
[16]
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 20, no. 7 (2004): 287–91. https://doi.org/10.1016/j.tig.2004.05.001.
View | DOI
 
[15]
2004 | Journal Article | IST-REx-ID: 902
Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research 14, no. 5 (2004): 802–11. https://doi.org/10.1101/gr.2195604.
View | DOI
 
[14]
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 19, no. 3 (2003): 115–19. https://doi.org/10.1016/S0168-9525(02)00029-X.
View | DOI
 
[13]
2003 | Journal Article | IST-REx-ID: 847
Sunyaev, Shamil, Fyodor Kondrashov, Peer Bork, and Vasily Ramensky. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics 12, no. 24 (2003): 3325–30. https://doi.org/10.1093/hmg/ddg359.
View | DOI
 
[12]
2002 | Journal Article | IST-REx-ID: 871
Kondrashov, Fyodor, Igor Rogozin, Yuri Wolf, and Eugene Koonin. “Selection in the Evolution of Gene Duplications .” Genome Biology 3, no. 2 (2002). https://doi.org/10.1186/gb-2002-3-2-research0008.
View | DOI
 
[11]
2002 | Journal Article | IST-REx-ID: 859
Perelygin, Andrey, Fyodor Kondrashov, Igor Rogozin, and Margo Brinton. “Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution 55, no. 2 (2002): 202–10. https://doi.org/10.1007/s00239-002-2318-0.
View | DOI
 
[10]
2002 | Journal Article | IST-REx-ID: 885
Kondrashov, Alexey, Shamil Sunyaev, and Fyodor Kondrashov. “Dobzhansky-Muller Incompatibilities in Protein Evolution.” PNAS 99, no. 23 (2002): 14878–83. https://doi.org/10.1073/pnas.232565499.
View | DOI
 
[9]
2002 | Journal Article | IST-REx-ID: 897
Castillo Davis, Cristian, Sergei Mekhedov, Daniel Hartl, Eugene Koonin, and Fyodor Kondrashov. “Selection for Short Introns in Highly Expressed Genes.” Nature Genetics 31, no. 4 (2002): 415–18. https://doi.org/10.1038/ng940.
View | DOI
 
[8]
2001 | Journal Article | IST-REx-ID: 888
Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf, and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology 2, no. 12 (2001). https://doi.org/10.1186/gb-2001-2-12-research0053.
View | DOI
 
[7]
2001 | Journal Article | IST-REx-ID: 841
Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics 17, no. 9 (2001): 499–501. https://doi.org/10.1016/S0168-9525(01)02376-9.
View | DOI
 
[6]
2001 | Journal Article | IST-REx-ID: 874
Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS 98, no. 21 (2001): 12089–92. https://doi.org/10.1073/pnas.211214298.
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[5]
2001 | Journal Article | IST-REx-ID: 855
Rogozin, Igor, Alex Kochetov, Fyodor Kondrashov, Eugene Koonin, and Luciano Milanesi. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics 17, no. 10 (2001): 890–900. https://doi.org/10.1093/bioinformatics/17.10.890.
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[4]
2001 | Journal Article | IST-REx-ID: 867
Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics 10, no. 23 (2001): 2661–69. https://doi.org/10.1093/hmg/10.23.2661.
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[3]
2001 | Journal Article | IST-REx-ID: 851
Rogozin, Igor, Fyodor Kondrashov, and Galina Glazko. “Use of Mutation Spectra Analysis Software.” Human Mutation 17, no. 2 (2001): 83–102. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
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[2]
2000 | Journal Article | IST-REx-ID: 842
Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “No Footprints of Primordial Introns in a Eukaryotic Genome.” Trends in Genetics 16, no. 8 (2000): 333–34. https://doi.org/10.1016/S0168-9525(00)02059-X.
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[1]
1999 | Journal Article | IST-REx-ID: 883
Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative Traits in the Course of Sympatric Speciation.” Nature 400, no. 6742 (1999): 351–54. https://doi.org/10.1038/22514.
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