Maria Poptsova
- Laboratory Head:Faculty of Computer Science / Big Data and Information Retrieval School / International Laboratory of Bioinformatics
- Associate Professor:Faculty of Computer Science / Big Data and Information Retrieval School
- Programme Academic Supervisor:Data Analysis in Biology and Medicine
- Maria Poptsova has been at HSE University since 2016.
Education and Degrees
- 2004
Candidate of Sciences* (PhD) in Biophysics
Lomonosov Moscow State University
Thesis Title: Transformation of autowaves in local inhomogeneous active media - 1995
Degree in Physics
Lomonosov Moscow State University
According to the International Standard Classification of Education (ISCED) 2011, Candidate of Sciences belongs to ISCED level 8 - "doctoral or equivalent", together with PhD, DPhil, D.Lit, D.Sc, LL.D, Doctorate or similar. Candidate of Sciences allows its holders to reach the level of the Associate Professor.
Continuing education / Professional retraining / Internships / Study abroad experience
1993 Amsterdam University, Netherlands
2005-2009 University of Connecticut, USA
2010-2011 Cornell University, USA
Courses (2022/2023)
- Bioinformatics (Bachelor’s programme; Faculty of Computer Science; 3 year, 1, 2 module)Rus
- Bioinformatics of DNA, RNA and Proteins (Minor; Faculty of Computer Science; 1, 2 module)Rus
- Machine Learning in Bioinformatics (Master’s programme; Faculty of Computer Science; 1 year, 1, 2 module)Eng
- Medical Bioinformatics (Minor; Faculty of Computer Science; 3, 4 module)Rus
- Research Seminar "Data Analysis in the Natural Sciences" (Bachelor’s programme; Faculty of Computer Science; 4 year, 1-3 module)Eng
- Past Courses
Courses (2021/2022)
- Bioinformatics (Bachelor’s programme; Faculty of Computer Science; 3 year, 1, 2 module)Rus
- Bioinformatics of DNA, RNA and Proteins (Minor; Faculty of Computer Science; 1, 2 module)Rus
- Medical bioinformatics (Minor; Faculty of Computer Science; 3, 4 module)Rus
- Modern Methods of Data Analysis (Master’s programme; Faculty of Computer Science; 1 year, 1, 2 module)Eng
- Molecular Evolution (Master’s programme; Faculty of Computer Science; 1 year, 4 module)Rus
Courses (2020/2021)
- Applied Statistics in Bioinformatics (Master’s programme; Faculty of Computer Science; 1 year, 3, 4 module)Eng
- Bioinformatics of DNA, RNA and Proteins (Minor; Faculty of Computer Science; 1, 2 module)Rus
- Medical bioinformatics (Minor; Faculty of Computer Science; 3, 4 module)Rus
- Modern Methods of Data Analysis (Master’s programme; Faculty of Computer Science; 1 year, 1, 2 module)Eng
Courses (2019/2020)
- Bioinformatics of DNA, RNA and Proteins (Minor; Faculty of Computer Science; 3, 4 module)Rus
- Elementary Genomics (Minor; Faculty of Computer Science; 1, 2 module)Rus
- Modern Methods of Data Analysis (Master’s programme; Faculty of Computer Science; 1 year, 1, 2 module)Eng
Courses (2018/2019)
- Applied Bioinformatics (Master’s programme; Faculty of Computer Science; 1 year, 3, 4 module)Rus
- Modern Methods of Data Analysis (Master’s programme; Faculty of Computer Science; 1 year, 1, 2 module)Eng
Publications32
- Article Herbert A., Pavlov F., Dmitrii Konovalov, Poptsova M. Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations // International Journal of Molecular Sciences. 2023. Vol. 24. Article 4884. doi (in press)
- Article Zhang T., Yin C., Fedorov A., Qiao L., Bao H., Beknazarov N., Wang S., Gautam A., Williams M. R., Crawford J. C., Peri S., Studitsky V., Beg A. A., Thomas P. G., Walkley C., Xu Y., Poptsova M., Herbert A., Balachandran S. ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis // Nature. 2022. Vol. 606. No. 7914. P. 594-602. doi
- Article Herbert A., Fedorov A., Poptsova M. Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus // International Journal of Molecular Sciences. 2022. Vol. 23. No. 6. Article 3079. doi
- Article Herbert A., Fedorov A., Poptsova M. Mono a Mano: ZBP1’s Love–Hate Relationship with the Kissing Virus // International Journal of Molecular Sciences. 2022. Vol. 23. No. 6 doi
- Article Herbert A., Poptsova M. Z-RNA and the Flipside of the SARS Nsp13 Helicase: Is There a Role for Flipons in Coronavirus-Induced Pathology? // Frontiers in Immunology. 2022. Vol. 13. Article 912717. doi
- Article Cheloshkina K., Poptsova M. Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements // PLoS Computational Biology. 2021. Vol. 17. No. 3. Article e1008749. doi
- Article Cheloshkina K., Bzhikhatlov I., Poptsova M. Randomness in Cancer Breakpoint Prediction // Journal of Computational Biology. 2021. Vol. 28. No. 7. P. 716-731. doi
- Article Herbert A., Karapetyan S., Poptsova M., Vasquez K., Vicens, Q., Vogeli B. Special Issue: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA // International Journal of Molecular Sciences. 2021. Vol. 22. No. 14. Article 7686. doi
- Chapter Cheloshkina K., Bzhikhatlov I., Poptsova M. Cancer Breakpoint Hotspots Versus Individual Breakpoints Prediction by Machine Learning Models, in: Proceedings 16th International Symposium, ISBRA 2020, Moscow, Russia, December 1–4, 2020. Lecture Notes in Computer Science Vol. 12304. Springer Publishing Company, 2020. doi P. 217-228. doi
- Article Beknazarov N., Jin S., Poptsova M. Deep learning approach for predicting functional Z-DNA regions using omics data // Scientific Reports. 2020. Vol. 10. P. 19134. doi
- Article Mirzaev K., Abdullaev S., Akmalova K., Sozaeva J., Grishina E., Shuev G., Bolieva L., Sozaeva M., Zhuchkova S., Gimaldinova N., Sidukova E., Serebrova S., Asoskova A., Шеин А. В., Poptsova M., Suleymanov S., Burashnikova I., Shikaleva A., Kachanova A., Fedorinov D., Sychev D. Interethnic differences in the prevalence of main cardiovascular pharmacogenetic biomarkers // Pharmacogenomics. 2020. Vol. 21. No. 10. P. 677-694. doi
- Chapter Pavlov F., Poptsova M. Recognition of DNA Secondary Structures as Nucleosome Barriers with Deep Learning Methods, in: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Seul : IEEE, 2020. doi P. 2800-2805. doi
- Article Cheloshkina K., Poptsova M. Understanding cancer breakpoint determinants with omics data // Integrative Cancer Science and Therapeutics. 2020. Vol. 7. P. 1-5. doi
- Chapter Tevanyan E., Poptsova M. Machine Learning Applications for Genomic Pattern Recognition Problem, in: Proceedings of the MACSPro Workshop 2019 / Ed. by Irina Lomazova, Anna Kalenkova, Р. Яворский. Vol. 2478: CEUR Workshop Proceedings. CEUR-WS.org, 2019. P. 139-148.
- Article Шеин А. В., Zaikin A., Poptsova M. Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models // Scientific Reports. 2019. Vol. 9. No. 7211. P. 1-16. doi
- Chapter Tevanyan E., Poptsova M. SEARCHING FOR NON-B-DNA STRUCTURES AS NUCLEOSOME BARRIERS WITH MACHINE LEARNING METHODS, in: The proceedings of International congress «Biotechnology: state of the art and perspectives» FEBRUARY 25 - 27, 2019. LLC “RED GROUP”, 2019. P. 363-364.
- Chapter Poptsova M., Шеин А. В., Zaikin A. SEQUENCE-BASED AND STRUCTURE-BASED MACHINE-LEARNING MODELS FOR RECOGNITION OF 3’-END L1 AND ALU STEM-LOOPS IN HUMAN GENOME, in: The proceedings of International congress «Biotechnology: state of the art and perspectives» FEBRUARY 25 - 27, 2019. LLC “RED GROUP”, 2019. P. 356-356.
- Article Cheloshkina K., Poptsova M. Tissue-specific impact of stem-loops and quadruplexes on cancer breakpoints formation // BMC Cancer. 2019. Vol. 19. No. 434. P. 1-17. doi
- Chapter Коновалов Д. Л., Попцова М. С. Роль CpG метилирования квадруплексов в эпигенетической регуляции. // В кн.: Сборник трудов 43-й междисциплинарной школы-конференции ИППИ РАН "Информационные технологии и системы 2019". [б.и.], 2019. (in press)
- Chapter Cheloshkina K., Poptsova M. Machine-learning models for cancer breakpoints prediction based on DNA structure distributions, in: Сборник трудов 42-й междисциплинарной школы-конференции ИППИ РАН "Информационные технологии и системы 2018". Институт проблем передачи информации им. А.А. Харкевича РАН, 2018. P. 1-5.
- Chapter Шеин А. В., Poptsova M. Recognition of 3’ UTR stem-loop in LINE transposons across the tree of life by machine learning methods, in: Сборник трудов 42-й междисциплинарной школы-конференции ИППИ РАН "Информационные технологии и системы 2018". Институт проблем передачи информации им. А.А. Харкевича РАН, 2018. P. 1-5.
- Chapter Tevanyan E., Poptsova M. Recognizing Patterns of Nucleosome and DNA Structures Positioning, in: Сборник трудов 42-й междисциплинарной школы-конференции ИППИ РАН "Информационные технологии и системы 2018". Институт проблем передачи информации им. А.А. Харкевича РАН, 2018. P. 1-10.
- Chapter Tevanyan E., Poptsova M. Recognizing Patterns of Nucleosome and DNA Structures Positioning, in: Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine. Madrid : IEEE, 2018. P. 2808-2809. doi
- Chapter Маткаримов О. О., Поливода Д. Э., Попцова М. С. Поиск паттернов ассоциации между функциональными элементами генома // В кн.: Доклады Международной конференции "Математическая биология и биоинформатика" / Под общ. ред.: В. Д. Лахно. Т. 7. Пущино : Государственное учреждение Институт математических проблем биологии РАН, 2018. Гл. 57. С. 1-3. doi
- Chapter Коновалов Д. Л., Попцова М. С. Построение модели машинного обучения, распознающей G-квадруплексы на основе физико-химических свойств ДНК // В кн.: Материалы Международного молодежного научного форума «ЛОМОНОСОВ-2018». М. : МАКС Пресс, 2018. (in press)
- Article Попцова М. С., Гречишникова Д. А. The Physical and Geometric Properties of Human Transposon Stem–Loop Structures under Natural Selection // Биофизика. 2017. Т. 62. № 6. С. 857-864. doi
- Article Гречишникова Д. А., Попцова М. С. Распознавание структур стебель-петля транспозонов человека и прогнозирование их функции при помощи модели машинного обучения. // Известия высших учебных заведений. Северо-Кавказский регион. Серия: Естественные науки. 2017. Т. 4. № 1. С. 63-69. doi
- Article Нечипуренко Ю., Ильичева И., Попцова М. С., Гроховский С. Физико-химические свойства ДНК в регуляторных участках генома // Актуальные вопросы биологической физики и химии. 2017. Т. 2. № 1. С. 339-340.
- Article Poptsova M., Grechishnikova D. Conserved 3' UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition // BMC Genomics. 2016. Vol. 17. No. 1. P. 992. doi
- Chapter Попцова М. С., Гречишникова Д. DNAStructProfiler: автоматизированное построение профилей консервативности вторичных структур ДНК/РНК // В кн.: Сборник докладов VI Международной конференции "Математическая биология и биоинформатика" / Под общ. ред.: В. Д. Лахно. М. : Государственное учреждение Институт математических проблем биологии РАН, 2016. С. 134-135.
- Article Il'icheva I., Khodikov M., Nechipurenko D., Nechipurenko YD Y., Grokhovsky S., Poptsova M. Structural features of DNA that determine RNA polymerase II core promoter // BMC Genomics. 2016. Vol. 17. No. 1. P. 973. doi
- Chapter Попцова М. С., Заикин А. В. Отбор структур стебель-петля в промоторных областях транскрипционных факторов с помощью эволюционного алгоритма // В кн.: Сборник докладов VI Международной конференции "Математическая биология и биоинформатика" / Под общ. ред.: В. Д. Лахно. М. : Государственное учреждение Институт математических проблем биологии РАН, 2016.
Editorial board membership
2007: Guest Editor, Bioinformatics.
2007: Guest Editor, BMC Bioinformatics.
2007: Guest Editor, Nucleic Acids Research.
2007: Guest Editor, PLoS Computational Biology.
2007: Guest Editor, PLoS ONE (Plos One).
New gene regulation mechanism discovered
Article published in the International Journal of Molecular Science
Published a chapter in the book Z-DNA
The long-awaited publication of the chapter on DeepZ by M. Poptsova and N. Beknazarov was published in the book "Z-DNA" by Kyeong Kim Kim, Vinod Kumar Subramani
Annual Student Conference School on Bioinformatics Takes Place
On 16–20 February the student conference school Information Technologies and Systems. Bioinformatics took place. More than 100 students from HSE University, Kharkevich Institute for Information Transmission Problems, Skoltech, MSU, MIPT took part in it.
Winning the Competition for Young Scientists' Research Projects on Digital Technology and Digital Transformation
Konstantin Burkin and Alexander Kirdeev, research interns at the International Laboratory of Bioinformatics, won the competition for young scientists' research projects on digital technologies and transformation. For the 2023 year implementation, this project became part of the strategic work "Digital Transformation: Technologies, Impact, Efficiency".
International Conference "Data Analysis, Optimization and their Applications"
On January 30-31, 2023, the Moscow Institute of Physics and Technology hosted the International Conference "Data Analysis, Optimization and their Applications"
Maria Poptsova live on Radio Zvezda
The world around us through the eyes of a scientist
School "Genetics and Epigenetics: Mechanisms, Structure, Function" at the Biology Department of Moscow State University, October 29-30, 2022
The International Laboratory of Bioinformatics participated in the School for young scientists "Genetics and Epigenetics: Mechanisms, Structure, Function" which was held at the Biology Department of Lomonosov Moscow State University from October 29 to 30, 2022.
The results of the International Laboratory of Bioinformatics were reported by Kommersant
There has been a quantum leap in the creation of scientific zoom collaborations around the world.
HSE University Hosts Third Summer School on Machine Learning in Bioinformatics
Between August 23rd and 25th, the HSE Faculty of Computer Science held its annual summer school on machine learning in bioinformatics. After two years of being held online, the school returned to an offline format for this year. Over three days, more than 120 participants attended lectures and seminars by leading experts in the field from institutions such as HSE University, Skoltech, AIRI, MSU, MIPT, Genotek, and Sber Artificial Intelligence Laboratory.
Interdisciplinary forum "Cardiogenetics and Bioinformatics: Realities of 2022"
On September 2, the second event of the consortium "Genetics of Cardiovascular Diseases" — an interdisciplinary forum "Cardiogenetics and Bioinformatics: Realities of 2022" — was held at the Higher School of Economics, which continued the work of the consortium between the organizations that are part of the consortium. The forum was attended by heads and representatives of scientific centers and institutes from Moscow, St. Petersburg, Novosibirsk, Arkhangelsk, Tyumen, and Surgut.
ABZ2022 International Conference: Structure, Function and Genetics of Z-DNA and Z-RNA
On May 25, 2022, an online conference ABZ2022 was held at the Faculty of Computer Science.
Scientists Propose New Way to Fight Cancer
A team of researchers that includes experts from the International Laboratory of Bioinformatics of the Faculty of Computer Science, HSE University has presented a new way to fight melanoma. The scientists discovered that a form of DNA molecule entering cancer cells is able to induce an immune response similar to the body's response to a virus. As a result, the cells that support tumour growth are killed and the patient begins to respond to anti-cancer therapy again. The results of the study have been published in the Nature.
The Nature journal published an article by Alexander Fedorov, Nazar Beknazarov, Alan Herbert, and Maria Poptsova
The article "ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis" by Alexander Fedorov, Nazar Beknazarov, Alan Herbert, and Maria Poptsova was published in Nature on May 25, 2022.
Russian Congress on Clinical Pharmacogenomics, Moscow, February 4-5, 2022
The International Laboratory of Bioinformatics participated in the Russian Congress on Clinical Pharmacogenomics in Moscow on February 4-5, 2022.
Maria Poptsova spoke at the Sber AI Community Conference on January 28, 2022
The AI Community conference, which was held online, was attended by leading international and Russian experts in the field of AI, as well as business representatives.
"I think that it is right to study in different universities"
Mark Garnitsky, a student of the Data Analysis in Biology and Medicine master's programme is studying for one year at Ghent University in Belgium. We asked Mark to tell us about his story at the Faculty of Computer Science, his academic mobility experience and the social life during the pandemic.
The First International Forum of Genomic and Biomedical Technologies "From birth to active longevity" was held on December 2-3, 2021
On December 2, 2021, the First International Forum of Genomic and Biomedical Technologies "From birth to active longevity" was inaugurated at Surgut State University with the participation of the governor of Yugra Natalia Komarova, as well as the director of the District Department of Education and Youth Policy Alexey Drenin. Its organizers are the government of the district, the Ugra Development Fund and Surgut State University.
Genetics of Cardiovascular Diseases Consortium Holds First Event
In early September, the first event of the Genetics of Cardiovascular Diseases consortium - an interdisciplinary forum "Cardiogenetics and Bioinformatics: Realities 2021" - was held at HSE University. The forum marked the start of the consortium after signing an agreement on scientific cooperation between the participating organizations. The forum was attended by heads and representatives of scientific centres and institutes from Moscow, St. Petersburg, Novosibirsk, Arkhangelsk, Tyumen and Surgut.
Genetics of Cardiovascular Diseases Consortium Opens at HSE University
The Genetics of Cardiovascular Diseases Consortium, the first of this kind in Russia, was unveiled at HSE University at Cardiogenetics and Bioinformatics: 2021 Realities, an interdisciplinary forum. The consortium aims to compile a centralized and complete catalogue of the Russian population’s genomic mutations.
Summer School on Machine Learning in Bioinformatics Held at HSE University
The second international Summer School on Machine Learning in Bioinformatics took place on August 23–27. This year’s school featured 533 participants from 53 countries.
The Moscow Conference on Computational Molecular Biology (MCCMB) 07/30/2021 - 08/02/2021
The Moscow Conference on Computational Molecular Biology (MCCMB) took place on 07/30/2021 - 08/02/2021
ABZ 2021 Meeting: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA
The ABZ 2021 Meeting was held virtually on May 19, 2021, at the Faculty. The first of its kind, this international conference gathered more than 200 scientists from many disciplines to specifically address progress in research involving Z-DNA and Z-RNA.
The HSE Look April Issue
The second issue of 2021 presents interviews about knowledge production and exchange from various angles.
International Laboratory of Bioinformatics Opens at the Faculty of Computer Science
On January 25, 2021, an International Laboratory of Bioinformatics opened at the Faculty of Computer Science. The main goal of the laboratory is to determine the role of alternative DNA structures in the genome.
Round table: «Genetics of Cardiovascular Disease»
On February 2, 2021 an online round table "Genetics of cardiovascular diseases" was held. It was dedicated to the genetics of cardiovascular diseases, the formation of a consortium in this research area and preparations for the signing of an agreement on scientific cooperation.
Maria Poptsova presented at the AI Journey 2020
Maria Poptsova, head of the International Laboratory of Bioinformatics and associate professor of the Big Data and Information Retrieval School, spoke at the AI Journey 2020 conference on artificial intelligence with a presentation “Deep Learning in Genomics”.
HSE Researchers Use Neural Networks to Study DNA
HSE scientists have proposed a way to improve the accuracy of finding Z-DNA, or DNA regions that are twisted to the left instead of to the right. To do this, they used neural networks and a dataset of more than 30,000 experiments conducted by different laboratories around the world. Details of the study are published in Scientific Reports.
Winners of the HSE International Laboratory Proposal Competition Announced
This year’s HSE competition for the creation of international laboratories which considered proposals for the period of January 1, 2021 – December 21, 2023, was conducted from June 15 to December 15, 2020.
Faculty of Computer Science Hosts First School on Machine Learning in Bioinformatics
Laboratory of Bioinformatics organised the first international summer school in bioinformatics. The school was held online on August 24-28.
Podcasts of the program "Physics and Lyrics", radio station "Mayak"
Head of the lab Maria Poptsova - guest on the radio station "Mayak"
HSE Showcases Innovations in Urbanism and Neural Networks at Russia’s Geek Picnic 2020
This year, Russia’s largest science and technology festival, Geek Picnic, was held online for the first time. Despite the new format, the festival programme included all of the event’s usual key features: expert lectures, workshops, competitions, and opportunities to socialize and network with fellow tech and science enthusiasts. HSE University once again served as the festival’s content partner.
GEEK PICNIC 2020
Head of the lab Maria Poptsova give a lecture at Geek Picnic 2020
Third Russian Winter School for Young Scientists and Doctors in Pharmacogenetics and Personalized Therapy
Head of the lab Maria Poptsova - participant and moderator of the round table at the Winter School of Young Scientists and Doctors on Pharmacogenetics and Personalized Therapy
Winter School 2020
Head of the lab Maria Poptsova give a lecture at the Computer Science Winter School for Graduate Students
International Congress "Genetics and Heart"
Head of the laboratory Maria Poptsova - congress co-chair
Lecture hall "University Saturdays at HSE"
Head of the lab Maria Poptsova is a lecturer on University Saturdays
Seminar "Myocardial diseases of predominantly hereditary origin"
Head of the laboratory Maria Poptsova - participant of the seminar
School-conference "Information Technologies and Systems" 2019
Laboratory staff - conference participants
Moscow Conference on Computational Molecular Biology (MCCMB)
Laboratory staff - conference participants
DNA Secondary Structures Lead to Gene Mutations that Increase the Risk of Cancer
Сancer Сells Will Become Vulnerable
"Worldwide Conversation on Women’s Higher Education and Equality in the Workplace"
On November 26, the HSE Faculty of Computer Science held the ‘IT Girls Night’ for the fifth time. This year the event was organized within the University of London’s campaign ‘Worldwide Conversation on Women’s Higher Education and Equality in the Workplace’. This campaign celebrates 150 years since the University of London opened up its ‘Special Examinations for Women’, the first university-level examinations offered for women in the UK. Ten years later, this step led to the University of London becoming the first institution of higher education in the UK to open up full degrees for women.
Results of Competition for Research and Teaching Laboratories Announced
This year, HSE has supported the founding of 10 new Research and Teaching Laboratories (RTLs) in various fields, from cognitive psychology and computer modeling, to international justice and economics of sports.