Vladimir Shchur
- Laboratory Head, Senior Research Fellow:International Laboratory of Statistical and Computational Genomics
- Associate Professor:HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE) / School of Applied Mathematics
- Vladimir Shchur has been at HSE University since 2018.
Continuing education / Professional retraining / Internships / Study abroad experience
PhD thesis in Mathematics at l’Université Paris-Sud and at l’Ecole Normale
Supérieure (Paris, France), advisor professor P. Pansu, 2009-2013.
PhD (Diplome National de Docteur Mathematiques, mention tres honorable), Universite Paris XI, 08/07/2013
ATER, Department of Mathematics, University Paris Sud 11, Orsay, France.
Postdoc fellow at Durbin’s group Wellcome Trust Sanger Institute, Cambridge, UK, 2013-2016.
Postdoctoral researcher at Nielsen’s lab at UC Berkeley, Berkeley, USA, 2016-2019.
Young Faculty Support Program (Group of Young Academic Professionals)
Category "New Lecturers" (2020)
Courses (2022/2023)
- Population Models in Genomics (Master’s programme; Faculty of Computer Science; 1 year, 3 module)Eng
- Population Models in Genomics (Mago-Lego; 3 module)Eng
- Population Models in Genomics (Master’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 3 module)Eng
- Probability Theory and Mathematical Statistics (Bachelor’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 2 year, 2-4 module)Rus
- Past Courses
Courses (2021/2022)
- Calculus (Bachelor’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 2 year, 1, 2 module)Rus
- Population models in genomics (Master’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 3 module)Eng
Courses (2020/2021)
- Calculus (Bachelor’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 2 year, 1, 2 module)Rus
- Calculus (Bachelor’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 1-4 module)Rus
- Population models in genomics (Master’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 3 module)Eng
Courses (2019/2020)
- Calculus (Bachelor’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 1-4 module)Rus
- Computational Methods of Genomics (Master’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 1, 2 module)Eng
- Probability Theory and Mathematical Statistics (Bachelor’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 2 year, 2-4 module)Rus
Courses (2018/2019)
- Research Seminar (Master’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 1-4 module)Rus
- Research Seminar "Supercomputer Modeling in Science and Engineering" (Master’s programme; HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE); 1 year, 1-4 module)Rus
Publications30
- Article Shchur V. Accuracy of the SMC' approximation of structured coalescent // Lobachevskii Journal of Mathematics. 2022. Vol. 43. No. 12 (in press)
- Article Shchur V., Arzymatov K., Khomutov E. Deep learning for inferring distribution of time to the last common ancestor from a diploid genome // Lobachevskii Journal of Mathematics. 2022
- Preprint Shchur V., Brandt D. Y., Ilina A., Nielsen R. Estimating population split times and migration rates from historical effective population sizes / Cold Spring Harbor Laboratory. Series 005140 "Biorxiv". 2022. doi
- Article Liang M., Shishkin M., Mikhailova A., Shchur V., Nielsen R. Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium // PLoS Genetics. 2022. Vol. 18. No. 7. Article e1010281. doi
- Preprint Bazykin G. A., Danilenko D. M., Komissarov A. B., Yolshin N., Shneider O. V., Nabieva E., Klink G. V., Shvyrev N., Konovalova N., Zheltukhina A., Fadeev A., Komissarova K., Ksenafontov A., Musaeva T., Eder V., Shchur V., Lioznov D. SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia / Research Square Company. Series ResearchSquare "Research Square". 2022. doi
- Article Guskova M., Burovski E., Shchur V., Shchur L. Simulation of the Particle Dynamics in the Two-Dimensional Poiseuille Flow with Low Reynolds Number // Lobachevskii Journal of Mathematics. 2022. Vol. 43. No. 2. P. 381-385. doi
- Article Klink G. V., Safina K. R., Nabieva E., Shvyrev N., Garushyants S., Alekseeva E., Komissarov A. B., Danilenko D. M., Pochtovyi A. A., Divisenko E. V., Vasilchenko L. A., Shidlovskaya E. V., Kuznetsova N. A., Speranskaya A. S., Samoilov A. E., Неверов А. Д., Popova A. V., Fedonin G. G., Akimkin V. G., Lioznov D., Gushchin V. A., Shchur V., Bazykin G. A. The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia // Virus Evolution. 2022. Vol. 8. No. 1. Article veac017. doi
- Article Shchur V., Spirin V., Sirotkin D., Burovski E., De Maio N., Corbett-Detig R. VGsim: Scalable viral genealogy simulator for global pandemic // PLoS Computational Biology. 2022. Vol. 18. No. 8. Article e1010409. doi
- Article Khomutov E., Arzymatov K., Shchur V. Deep learning based methods for estimating distribution of coalescence rates from genome-wide data // Journal of Physics: Conference Series. 2021. Vol. 1740. Article 012031. doi
- Article Jin Y., Brandt D. Y., Li J., Wo Y., Tong H., Shchur V. Elevation as a selective force on mitochondrial respiratory chain complexes of the Phrynocephalus lizards in the Tibetan plateau // Current Zoology. 2021. Vol. 67. No. 2. P. 191-199. doi
- Preprint Liang M., Shishkin M., Mikhailova A., Shchur V., Nielsen R. Estimating the timing of multiple admixture events using 3-locus Linkage Disequilibrium / Cold Spring Harbor Laboratory. Series New Results "BioRxiv". 2021. doi
- Article Komissarov A. B., Safina K. R., Garushyants S. K., Fadeev A. V., Sergeeva M. V., Ivanova A. A., Danilenko D. M., Lioznov D., Shneider O. V., Shvyrev N., Spirin V., Glyzin D., Shchur V., Bazykin G. A. Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia // Nature Communications. 2021. Vol. 12. P. 1-13. doi
- Preprint Vicuña L., Mikhailova A., Norambuena T., Ilina A., Klimenkova O., Eyheramendy S., Shchur V. Genomic insights into the recent population history of Mapuche Native Americans / Cold Spring Harbor Laboratory. Series New Results "BioRxiv". 2021. doi
- Article Svedberg J., Shchur V., Reinman S., Nielsen R., Corbett-Detig R. Inferring Adaptive Introgression Using Hidden Markov Models // Molecular Biology and Evolution. 2021. Vol. 38. No. 5. P. 2152-2165. doi
- Preprint Klink G. V., Safina K. R., Nabieva E., Shvyrev N., Garushyants S., Alekseeva E. I., Komissarov A. B., Danilenko D. M., Pochtovyy A. A., Divisenko E. V., Vasilchenko L. A., Shidlovskaya E. V., Kuznetsova N. A., Samoilov A. E., Neverov A., Popova A., Fedonin G., Akimkin V. G., Lioznov D., Gushchin V., Shchur V., Bazykin G. A. The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia / Cold Spring Harbor Laboratory. Series 005140 "Medrxiv". 2021. doi
- Preprint Shchur V., Spirin V., Pokrovskiy V., Burovski E., De Maio N., Corbett-Detig R. VGsim: scalable viral genealogy simulator for global pandemic / Cold Spring Harbor Laboratory. Series 005140 "Medrxiv". 2021.
- Preprint Komissarov A. B., Safina K. R., Garushyants S. K., Fadeev A. V., Sergeeva M. V., Ivanova A. A., Danilenko D. M., Lioznov D., Shneider O. V., Shvyrev Nikita, Spirin V., Glyzin D., Shchur V., Bazykin G. A. Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia / Cold Spring Harbor Laboratory. Series 005140 "Medrxiv". 2020. doi
- Preprint Svedberg J., Shchur V., Reinman S., Nielsen R., Corbett-Detig R. Inferring Adaptive Introgression Using Hidden Markov Models / Cold Spring Harbor Laboratory. Series 005140 "Biorxiv". 2020. doi
- Article Shchur V., Svedberg J., Medina P., Corbett-Detig R., Nielsen R. On the Distribution of Tract Lengths During Adaptive Introgression // G3: Genes, Genomes, Genetics. 2020. Vol. 10. No. 10. P. 3663-3673. doi
- Article Vicuña L., Klimenkova O., Norambuena T., Martinez F. I., Fernandez M. I., Shchur V., Eyheramendy S. Post-Admixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense Against Pathogens // Genome Biology and Evolution. 2020. Vol. 12. No. 8. P. 1459-1470. doi
- Article Guskova M., Shchur V., Shchur L. Simulation of drop oscillation using the lattice Boltzmann method // Lobachevskii Journal of Mathematics. 2020. Vol. 41. No. 6. P. 992-995. doi
- Article Gouezel S., Shchur V. A corrected quantitative version of the Morse lemma // Journal of Functional Analysis. 2019. Vol. 277. No. 4. P. 1258-1268. doi
- Preprint Vladimir Shchur, Svedberg J., Medina P., Corbett-Detig R., Nielsen R. On the distribution of tract lengths during adaptive introgression / Cold Spring Harbor Laboratory. Series New Results "BioRxiv". 2019. No. 724815. doi
- Article Skov L., Hui R., Щур В. Л., Hobolth A., Scally A., Schierup M. H., Durbin R. Detecting archaic introgression using an unadmixed outgroup // PLoS Genetics. 2018. Т. 14. № e1007641. С. 1-15. doi
- Preprint Shchur V., Ziganurova L., Durbin R. Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure / Cold Spring Harbor Laboratory. Series New Results "BioRxiv". 2018. doi
- Article Shchur V., Nielsen R. On the number of siblings and p-th cousins in a large population sample // Journal of Mathematical Biology. 2018. Vol. 77. No. 5. P. 1279-1298. doi
- Article Shchur V. On the quantitative quasi-isometry problem: Transport of Poincaré inequalities and different types of quasi-isometric distortion growth // Journal of Functional Analysis. 2015. Vol. 269. No. 10. P. 3147-3194. doi
- Article Shchur V. A quantitative version of the Morse lemma and quasi-isometries fixing the ideal boundary // Journal of Functional Analysis. 2013. Vol. 264. No. 3. P. 815-836. doi
- Article Shchur V. Some properties of Frobenius numbers and a fraction of symmetric semigroups in the weak limit for n=3 // Functional Analysis and Other Mathematics. 2010. Vol. 3. No. 1. P. 97-101. doi
- Article Shchur V., Sinai Y., Ustinov A. Limiting distribution of Frobenius numbers for n=3 // Journal of Number Theory. 2009. Vol. 129. No. 11. P. 2778-2789. doi
Conferences
- 2019Probabilistic Modeling in Genomics (Aussois). Presentation: ngsPSMC: genotype likelihood-based PSMC for analysis of low coverage NGS data
- Moscow Conference on Computational Molecular Biology (Москва). Presentation: ngsPSMC: genotype likelihood-based PSMC for analysis of low coverage NGS data
- Bay Area Population Genomics (Stanford). Presentation: On the distribution of tract lengths during adaptive introgression
- MiSTI: method for correction of PSMC trajectories of admixed populations (Москва). Presentation: MiSTI: method for correction of PSMC trajectories of admixed populations
- MiSTI: method for correction of PSMC trajectories of admixed populations (Santa Cruz). Presentation: MiSTI: method for correction of PSMC trajectories of admixed populations
- 2018ProbGen “Probabilistic Modeling In Genomics” (Cold Spring, NY). Presentation: Estimation of population split times and migration rates with variable population sizes
Grants
RSCF
20-71-00143 Developing methods for the inference of historic population structure from full-genome sequences using deep learning approaches (2020-2022)
RFBR
20-29-01028 Methods for population analysis of ancient and modern DNA with genotype likelihoods (2021-2023)
19-07-00515 Method and algorithm for the local ancestry estimation during adaptive introgression based on the Hidden Markov Models (2019-2021)
HSE Researchers Develop New Method for Analysing Genetic Admixture of Populations
Researchers of the HSE International Laboratory of Statistical and Computational Genomics together with their international colleagues have proposed a new statistical method for analysing population admixture that makes it possible to determine the time and number of migration waves more accurately. The history of Colombians and Mexicans (descendants of Native Americans, Spaniards and Africans) features two episodes of admixture that occurred about 350 and 200 years ago for Mexicans and 400 and 100 years ago for Colombians. The results were published in the Plos Genetics journal.
Statistical and Computational Genomics Projects at HSE University
Vladimir Shchur, the Head and a Senior Research Fellow at the International Laboratory of Statistical and Computational Genomics, talks about the lab, its research projects and their practical applications.
HSE University Creates the Viral Genealogy Simulator to Model the Spread of COVID-19
Researchers of HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM), in cooperation with their colleagues from the University of California, Santa Cruz (UCSC), and The European Bioinformatics Institute (EMBL-EBI), have developed software to model the spread of the COVID-19 global pandemic. This is the world’s fastest Viral Genealogy Simulator (VGsim). For more details about this scalable simulator, read the reprint on medRxiv. The code is freely available at GitHub.
Nature Communications Journal Publishes a Study by Russian Scholars Involving HSE MIEM Students
Biologists and mathematicians from HSE University, Skoltech and the RAS Kharkevich Institute have studied the spread of COVID-19 in Russia. The main part of the study was completed in late June, but until October, the team was working with data following the reviewers’ recommendations. The paper was published on January 28, 2021 in the journal Nature Communications. MIEM students spoke about their contribution to the research.
New Online School on Population Genetics and Analysis
The HSE International Laboratory of Statistical and Computational Genomics has launched an online school for applied population genetics and analysis. The school does not require special knowledge in biology and is aimed at students, graduate students, and postdocs in mathematics, physics, and computer programming.
Scientists Are Taking Their Research Seminars Online
The first research seminar of the International Laboratory of Statistical and Computational Genomics had been postponed almost a month due to COVID-19. In April, however, the event finally took place. Laboratory Head Vladimir Shchur discusses what life is like for scientists in self-isolation during the pandemic, what genomics is, and why gesturing is important when teaching online.
HSE Launches New International Laboratories
For ten years now, HSE has been holding an annual grant competition for researchers who wish to start new international laboratories at HSE in collaboration with leading foreign scholars and scientists. The most recent competition reached its conclusion this past November, and now some of the selected proposed labs have already begun operation. Who are the competition winners and what kind of research will they be doing?
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Projects have won the competition for the creation of international laboratories at HSE University for the period from December 1, 2019 to December 31, 2022.