Activities per year
The main objective of the project is to conduct study of stable secondary structures of nucleic acids based on experimental data on DNA/DNA hybridization for complex single-stranded DNA mixtures using a machine learning approach. The development of bioinformatics tools that implement machine learning approaches for calculating the basic thermodynamics of secondary DNA structures as applied to DNA detection and amplification technologies.
The algorithms developed by us will enable to explain the observed artifacts in mega-multiplex DNA amplification and predict thermodynamic prognoses regarding the melting of DNA duplexes. Software to be developed will enable to detect nucleic acid interactions for the design of individual oligonucleotides and their mixtures, which are characterized by the weakest possible cross-interactions. Model experiments in DNA hybridization and determination of melting temperatures using synthetic DNA structures will be carried out. Studies of stable secondary nucleic acid structures will be carried out based on experimental data on DNA/DNA duplexes for complex single-stranded DNA mixtures. Bioinformatics tools implementing a machine learning approaches for calculating the basic thermodynamics of secondary DNA structures as applied to DNA detection and amplification will be developed. Algorithms, which implement machine learning approaches, will be developed for the design of PCR primers, probes, microchips. Online applications will be installed on the server. At least 3 articles will be published in peer-reviewed scientific journals from academic publishing company (Springer Nature, Cell Press, PLOS, PeerJ, MDPI, Oxford Press, Frontiers and Elsevier), included in the Q1-Q3 quartile in the Web of Science database with a CiteScore percentile in the Scopus database not less than 50.
|Effective start/end date||10/1/20 → 12/31/22|
Plos One: Interviews with the lab protocol community — insights from an Academic Editor and a reviewer
Ruslan Kalendar (Invited speaker)Apr 25 2022
Activity: Talk or presentation › Invited talk
Ruslan Kalendar (Speaker)Oct 20 2022 → Oct 21 2022
Activity: Talk or presentation › Oral presentation
Ruslan Kalendar (Participant)Dec 6 2022
Activity: Other activity types › Other
Kalendar, R., Jan 1 2022, In: Methods in Molecular Biology. 2392, p. 223-243 20 p.
Research output: Contribution to journal › Book/Film/Article review › peer-reviewOpen AccessFile
Kalendar, R., Baidyussen, A., Serikbay, D., Zotova, L., Khassanova, G., Kuzbakova, M., Kurishbayev, A., Jatayev, S., Hu, Y-G., Schramm, C., Anderson, P. A., Jenkins, C. L. D., Soole, K. L. & Shavrukov, Y., Jan 10 2022, In: Frontiers in Plant Science. 12, 747886.
Research output: Contribution to journal › Article › peer-reviewOpen AccessFile
DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of AltaiKhapilina, O., Raiser, O., Danilova, A., Shevtsov, V., Turzhanova, A. & Kalendar, R., Jan 8 2021, In: PeerJ. 9, e10674.
Research output: Contribution to journal › Article › peer-reviewOpen Access