Browsing by Author "Kondrashov, Fyodor A., 1979-"

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  • A structural perspective of compensatory evolution
    Ivankov, Dmitry N.; Finkelstein, Alexei V.; Kondrashov, Fyodor A., 1979- (Elsevier, 2014)
    The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, ...
  • Acrocephalus orinus: a case of mistaken identity
    Koblik, Evgeny A.; Red'kin, Yaroslav A.; Meer, Margarita V., 1986-; Derelle, Romain; Golenkina, Sofia A.; Kondrashov, Fyodor A., 1979-; Arkhipov, Vladimir Y. (Public Library of Science (PLoS), 2011)
    Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical ...
  • An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape
    Pokusaeva, Victoria O.; Usmanova, Dinara R.; Putintseva, Ekaterina V.; Espinar, Lorena; Sarkisyan, Karen S.; Mishin, Alexander S.; Bogatyreva, Natalya S.; Ivankov, Dmitry N.; Akopyan, Arseniy V.; Avvakumov, Sergey Ya; Povolotskaya, Inna, 1986-; Filion, Guillaume; Carey, Lucas, 1980-; Kondrashov, Fyodor A., 1979- (Public Library of Science (PLoS), 2019)
    Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the ...
  • Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R)
    Derelle, Romain; Kondrashov, Fyodor A., 1979-; Arkhipov, Vladimir Y.; Corbel, Hélène; Frantz, Adrien; Gasparini, Julien; Jacquin, Lisa; Jacob, Gwenaël; Thibault, Sophie; Baudry, Emmanuelle (BioMed Central, 2013)
    Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic ...
  • Estimating the rate of irreversibility in protein evolution
    Söylemez, Onuralp, 1985-; Kondrashov, Fyodor A., 1979- (Oxford University Press, 2012)
    Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the ...
  • HypercubeME: two hundred million combinatorially complete datasets from a single experiment
    Esteban, Laura Avino; Lonishin, Lyubov R.; Bobrovskiy, Daniil; Leleytner, Gregory; Bogatyreva, Natalya S.; Kondrashov, Fyodor A., 1979-; Ivankov, Dmitry N. (Oxford University Press, 2020)
    Motivation: Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference ...
  • Long-term asymmetrical acceleration of protein evolution after gene duplication
    Pich Roselló, Oriol, 1992-; Kondrashov, Fyodor A., 1979- (Oxford University Press, 2014)
    Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate ...
  • Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions
    Rivkina, Elizaveta; Petrovskaya, Lada; Vishnivetskaya, Tatiana; Krivushin, Kirill; Shmakova, Lyubov; Tutukina, Maria; Meyers, Arthur; Kondrashov, Fyodor A., 1979- (European Geosciences Union (EGU), 2016)
    A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial ...
  • Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
    Zapata Ortiz, Luis, 1985-; Pich, Oriol; Serrano Pubull, Luis, 1982-; Kondrashov, Fyodor A., 1979-; Ossowski, Stephan; Schaefer, Martin H. (BioMed Central, 2018)
    Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic ...
  • Rate of sequence divergence under constant selection
    Kondrashov, Alexey S.; Povolotskaya, Inna, 1986-; Ivankov, Dmitry N.; Kondrashov, Fyodor A., 1979- (BioMed Central, 2010)
    BACKGROUND: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence ...
  • Recent origin of the methacrylate redox system in geobacter sulfurreducens AM-1 through horizontal gene transfer
    Arkhipova, Oksana V.; Meer, Margarita V., 1986-; Mikoulinskaia, Galina V.; Zakharova, Marina V.; Galushko, Alexander S.; Akimenko, Vasilii K.; Kondrashov, Fyodor A., 1979- (Public Library of Science (PLoS), 2015)
    The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century ...
  • Saturation of recognition elements blocks evolution of new tRNA identities
    Saint-Léger, Adélaïde; Bello, Carla, 1990-; Dans, Pablo D.; Gabriel Torres, Adrian; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A., 1979-; Ribas de Pouplana, Lluís (American Association for the Advancement of Science (AAAS), 2016)
    Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific ...
  • Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation
    Usmanova, Dinara R.; Bogatyreva, Natalya S.; Ariño Bernad, Joan; Eremina, Aleksandra A.; Gorshkova, Anastasiya A.; Kanevskiy, German M.; Lonishin, Lyubov R.; Meister, Alexander V.; Yakupova, Alisa G.; Kondrashov, Fyodor A., 1979-; Ivankov, Dmitry N. (Oxford University Press, 2018)
    Motivation: Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic ...
  • Stop codons in bacteria are not selectively equivalent
    Povolotskaya, Inna, 1986-; Kondrashov, Fyodor A., 1979-; Ledda, Alice; Vlasov, Peter K. (BioMed Central, 2012)
    Background: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of ...
  • Structure and evolutionary history of a large family of NLR proteins in the zebrafish
    Howe, Kerstin; Schiffer, Philipp H.; Zielinski, Julia; Wiehe, Thomas; Laird, Gavin K.; Marioni, John C.; Söylemez, Onuralp, 1985-; Kondrashov, Fyodor A., 1979-; Leptin, Maria (Royal Society, 2016)
    Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small ...
  • The ctenophore genome and the evolutionary origins of neural systems
    Moroz, Leonid L.; Povolotskaya, Inna, 1986-; Derelle, Romain; Kondrashov, Fyodor A., 1979-; Kohn, Andrea B. (Nature Publishing Group, 2014)
    The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have ...
  • The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner
    Antipov, Sergey S.; Tutukina, Maria; Preobrazhenskaya, Elena V.; Kondrashov, Fyodor A., 1979-; Patrushev, Maksim Vladimirovich; Toshchakov, Stepan; Dominova, Irina N.; Shvyreva, Uliana S.; Vrublevskaya, Veronika V.; Morenkov, Oleg S.; Sukharicheva, Natalya A.; Panyukov, Valeriy V.; Ozoline, Olga N. (Public Library of Science (PLoS), 2017)
    Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs ...
  • Two metagenomes from late pleistocene northeast siberian permafrost
    Krivushin, Kirill; Kondrashov, Fyodor A., 1979-; Shmakova, Lyubov; Tutukina, Maria; Petrovskaya, Lada; Rivkina, Elizaveta (American Society for Microbiology, 2015)
    The present study reports metagenomic shotgun sequencing of microbial communities of two ancient permafrost horizons of the Russian Arctic. Results demonstrate a significant difference in microbial community structure of ...

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