Персона: Короткова, Мария Александровна
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Институт интеллектуальных кибернетических систем
Цель ИИКС и стратегия развития - это подготовка кадров, способных противостоять современным угрозам и вызовам, обладающих знаниями и компетенциями в области кибернетики, информационной и финансовой безопасности для решения задач разработки базового программного обеспечения, повышения защищенности критически важных информационных систем и противодействия отмыванию денег, полученных преступным путем, и финансированию терроризма.
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- ПубликацияТолько метаданныеSearch for Tandem Repeats in the First Chromosome from the Rice Genome(2020) Kamionskaya, A. M.; Korotkov, E. V.; Korotkova, M. A.; Коротков, Евгений Вадимович; Короткова, Мария Александровна© 2020, Springer Nature Switzerland AG.Using the RPWM method, we searched for tandem repeats of 2 to 50 nucleotides long in the rice genome. We compared the effectiveness of the RPWM method with Mreps, T-reks, Tandem Repeat Finder and ATR Hunter. About 70% of the tandem repeats found could not be found by other algorithms. The correlation of dispersed repeats and transposons with tandem repeats was studied in this work. We assumed that some of the dispersed repeats and transposons originated from tandem repeats
- ПубликацияОткрытый доступДиалоговая система поиска логического вывода(1986) Короткова, М. А.; Щукин, Б. А.; Короткова, Мария Александровна; Щукин, Борис Алексеевич
- ПубликацияТолько метаданныеGraphLabs Extendable Module System for Education Support(2020) Korotkova, M. A.; Carpow, G.; Zakhryapin, S. O.; Короткова, Мария Александровна© 2020, Springer Nature Switzerland AG.The paper reviews program module system of GraphLabs software environment. Component instantiation and inheritance of prototypes are shown to be used for module extension. An extendable module system is used to improve the development and the maintenance processes of the software package. The necessity of system adaptation to the user is proved in the article. Two approaches for metadata recalculating are considered. A model for system behavior adjustment is suggested. The model is based on metadata of student actions in the system. It proposes the way to indicate optimal and inaccurate tracks of student behavior in the module. The model is generalized to Mealy machine. The estimation criterion of student metadata is provided in the paper. The affecting parameters on the resulting criterion are revealed. Approaches to parameter implementation are discussed in the article. Variant issuing is described using the evaluated criterion value. Prototype-based programming is used while organizing software component inheritance.
- ПубликацияОткрытый доступДИСПЕРСНЫЕ ПОВТОРЫ В ГЕНОМАХ РАЗЛИЧНЫХ БАКТЕРИЙ(НИЯУ МИФИ, 2025) КОРОТКОВ, Е. В.; КОРОТКОВА, М. А.; Короткова, Мария Александровна; Коротков, Евгений ВадимовичМы выполнили поиск дисперсных повторов IP методом в геномах бактерий из 39 phyla. В каждом геноме было выявлено семейство повторов с числом копий от 103 до 1,4x104 в зависимости от генома бактерии. Длины повторов лежат в диапазоне от 450 до 580 оснований. Более 90% найденных повторов наложены как мотив на кодирующие последовательности и повторы занимают от 30 до 50% бактериального генома. Повторы содержат консервативные островки которые чередуются слабо подобными районами. Мы предполагаем, что обнаруженные семейства повторов могут принимать участие в образовании бактериального нуклеоида.
- ПубликацияТолько метаданныеMultiple alignment of promoter sequences from the human genome(2020) Kamionskaya, A. M.; Korotkov, E. V.; Korotkova, M. A.; Коротков, Евгений Вадимович; Короткова, Мария Александровна© 2020.A new algorithm for multiple alignment of nucleotide sequences of MAHDS has been developed. A statistically significant multiple alignment of promoter sequences from the human genome was first created using this algorithm. Based on the constructed alignments, 25 classes of promoter sequences were created with the volume of each class exceeding 100 sequences. The classes of promoters can be used to search for promoter sequences in eukaryotic genomes.
- ПубликацияОткрытый доступSearch for Dispersed Repeats in Bacterial Genomes Using an Iterative Procedure(2023) Korotkov, E.; Suvorova, Y.; Kostenko, D.; Korotkova, M. A.; Короткова, Мария АлександровнаWe have developed a de novo method for the identification of dispersed repeats based on the use of random position-weight matrices (PWMs) and an iterative procedure (IP). The created algorithm (IP method) allows detection of dispersed repeats for which the average number of substitutions between any two repeats per nucleotide (x) is less than or equal to 1.5. We have shown that all previously developed methods and algorithms (RED, RECON, and some others) can only find dispersed repeats for x ≤ 1.0. We applied the IP method to find dispersed repeats in the genomes of E. coli and nine other bacterial species. We identify three families of approximately 1.09 Г— 106, 0.64 Г— 106, and 0.58 Г— 106 DNA bases, respectively, constituting almost 50% of the complete E. coli genome. The length of the repeats is in the range of 400 to 600 bp. Other analyzed bacterial genomes contain one to three families of dispersed repeats with a total number of 103 to 6 Г— 103 copies. The existence of such highly divergent repeats could be associated with the presence of a single-type triplet periodicity in various genes or with the packing of bacterial DNA into a nucleoid.
- ПубликацияОткрытый доступMathematical algorithm for identification of eukaryotic promoter sequences(2021) Korotkov, E. V.; Suvorova, Y. M.; Nezhdanova, A. V.; Gaidukova, S. E.; Korotkova, M. A.; Короткова, Мария Александровна© 2021 by the authors. Licensee MDPI, Basel, Switzerland.Identification of promoter sequences in the eukaryotic genome, by computer methods, is an important task of bioinformatics. However, this problem has not been solved since the best algorithms have a false positive probability of 10−3–10−4 per nucleotide. As a result of full genome analysis, there may be more false positives than annotated gene promoters. The probability of a false positive should be reduced to 10−6–10−8 to reduce the number of false positives and increase the reliability of the prediction. The method for multi alignment of the promoter sequences was developed. Then, mathematical methods were developed for calculation of the statistically important classes of the promoter sequences. Five promoter classes, from the rice genome, were created. We developed promoter classes to search for potential promoter sequences in the rice genome with a false positive number less than 10−8 per nucleotide. Five classes of promoter sequences contain 1740, 222, 199, 167 and 130 promoters, respectively. A total of 145,277 potential promoter sequences (PPSs) were identified. Of these, 18,563 are promoters of known genes, 87,233 PPSs intersect with transposable elements, and 37,390 PPSs were found in previously unannotated sequences. The number of false positives for a randomly mixed rice genome is less than 10−8 per nucleotide. The method developed for detecting PPSs was compared with some previously used approaches. The developed mathematical method can be used to search for genes, transposable elements, and transcript start sites in eukaryotic genomes.
- ПубликацияОткрытый доступКЛЮЧЕВЫЕ СВОЙСТВА МЕТОДА ПОСТРОЕНИЯ И ОЦЕНКИ МНОЖЕСТВЕННЫХ ВЫРАВНИВАНИЙ MAHDS(НИЯУ МИФИ, 2026) КОСТЕНКО, Д. О.; КОРОТКОВ, Е. В.; КОРОТКОВА, М. А.; Коротков, Евгений Вадимович; Короткова, Мария АлександровнаПредставлена концепция разработанного нами метода построения MSA - MAHDS. Рассмотрены статистические свойства и динамика ключевых показателей, рассчитывающихся при применении метода. Показано, что основные свойства метода MAHDS сохраняются независимо от использующихся параметров и модификаций.
- ПубликацияОткрытый доступMultiple alignment of promoter sequences from the arabidopsis thaliana l. Genome(2021) Korotkov, E. V.; Suvorova, Y. M.; Kostenko, D. O.; Korotkova, M. A.; Короткова, Мария Александровна© 2021 by the authors. Licensee MDPI, Basel, Switzerland.In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position (x). We generated sets of artificial DNA sequences with x ranging from 0 to 4.4 and applied MAHDS as well as currently used multiple sequence alignment algorithms, including ClustalW, MAFFT, T-Coffee, Kalign, and Muscle to these sets. The results indicated that most of the existing methods could produce statistically significant alignments only for the sets with x < 2.5, whereas MAHDS could operate on sequences with x = 4.4. We also used MAHDS to analyze a set of promoter sequences from the Arabidopsis thaliana genome and discovered many conserved regions upstream of the transcription initiation site (from −499 to +1 bp); a part of the downstream region (from +1 to +70 bp) also significantly contributed to the obtained alignments. The possibilities of applying the newly developed method for the identification of promoter sequences in any genome are discussed. A server for multiple alignment of nucleotide sequences has been created.
- ПубликацияОткрытый доступDeveloping mathematical method for multi alignment of DNA sequences with weak similarity(2019) Korotkov, E. V.; Korotkova, M. A.; Коротков, Евгений Вадимович; Короткова, Мария Александровна© 2019 Published under licence by IOP Publishing Ltd.A new mathematical method is proposed for constructing multiple alignment of weakly similar amino acid or nucleotide sequences. The method uses a multiple alignment representation in the form of position-weight matrices (PWM) and global dynamic programming. An optimization procedure for PWM is developed with the aim of finding a multiple alignment with maximum statistical significance. The method allows to find multiple alignment of sequences with the number of nucleotide or amino acid substitutions more than 2.5. The developed approach is applied to obtain multiple alignment of promoter sequences of 600 DNA bases length.