Browsing by Author "Bogatyreva, Natalya S."

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  • 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 ...
  • 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 ...
  • Machine learning: how much does it tell about protein folding rates?
    Corrales, Marc; Cuscó, Pol; Usmanova, Dinara R.; Chen, Heng-Chang; Bogatyreva, Natalya S.; Filion, Guillaume; Ivankov, Dmitry N. (Public Library of Science (PLoS), 2015)
    The prediction of protein folding rates is a necessary step towards understanding the principles of protein folding. Due to the increasing amount of experimental data, numerous protein folding models and predictors of ...
  • SABR : a stochastic volatility model in practice
    Bogatyreva, Natalya S.; Grandez, Rodrigo; Rodríguez Apolinar, Sergio; Soldevilla, Abraham (2019)
    The Black and Scholes model (BS) assumes that the volatility of an asset is constant over the trading period. As a result, BS returns a flat volatility surface. This assumption fails to capture the asset’s volatility ...
  • 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 ...

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