Отдел международной аспирантуры и докторантуры

Управление подготовки кадров высшей квалификации

Научные руководители

Артемов Максим


PhD, химические науки
martomov@itmo.ru
Структурное подразделение:
факультет информационных технологий и программирования
Должность:
профессор (исследователь)
Профиль:
05.13.10 - Управление в социальных и экономических системах
05.13.11 - Математическое и программное обеспечение вычислительных машин, комплексов и компьютерных сетей
05.13.18 - Математическое моделирование, численные методы и комплексы программ
05.13.17 - Теоретические основы информатики
2.3.5. - Математическое и программное обеспечение вычислительных систем, комплексов и компьютерных сетей
2.3.8. - Информатика и информационные процессы
1.2.2. - Математическое моделирование, численные методы и комплексы программ
1.2.3. - Теоретическая информатика, кибернетика
2.3.4. - Управление в организационных системах

Область интересов:
Кластеризации в графовом и корреляционном пространствах, визуальный и интерактивный анализ экспрессии генов, идентификация метаболических модулей и др., применение технологий NLP в задаче предсказания связывающей способности белков молекул MHC.
Рабочий язык:
Английский, Русский

Публикации руководителя
Выходные данные Год Индексирование в БД
Kleverov M., Zenkova D., Kamenev V., Sablina M., Artyomov M.N., Sergushichev A.A. Phantasus, a web application for visual and interactive gene expression analysis//eLife, 2024, Vol. 13, pp. e85722 2024 Scopus, Web of Science, Белый список
Клеверов Д.А., Шалыто А.А., Артемов М. Метод построения интерпретируемых скрытых марковских моделей для задачи поиска связываемых участков пептидов в последовательностях белков [A method for constructing interpretable hidden Markov models for the task of identifying binding cores in sequences] // Научно-технический вестник информационных технологий, механики и оптики [Scientific and Technical Journal of Information Technologies, Mechanics and Optics] -2023. - Т. 23. - № 5(147). - С. 989-1000 2023 RSCI, Scopus, Белый список, ВАК, РИНЦ
Terekhova M., Swain A., Aladyeva E., Arthur L., Mogilenko D.A., Burdess S., Sukhov V., Kleverov D., Echalar B., Tsurinov P., Chernyatchik R., Husarcikova K., Artemov M.N. Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB-CD8+memory T cells and accumulation of type 2 memory T cells//Immunity, 2023, Vol. 56, No. 12, pp. 2836-2854.e9 2023 Scopus, Web of Science, Белый список
Emelianova M., Gainullina A., Poperechnyi N., Loboda A.A., Artyomov M., Sergushichev A. Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks//Nucleic Acids Research, 2022, Vol. 50, No. 1, pp. W690-W696 2022 Scopus, Web of Science
Koenig A., Shchukina I., Amrute J., Andhey P., Zaitsev K., Lai L., Bajpai G., Bredemeyer A., Smith G., Jones C., Terrebonne E., Rentschler S.L., Artyomov M.N., Lavine K. Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure//Nature Cardiovascular Research, 2022, Vol. 1, No. 3, pp. 263-280 2022 Scopus, Web of Science
Rodriguez-Hernandez C.J., Sokoloski K.J., Stocke K.S., Dukka H., Jin S., Metzler M.A., Zaitsev K., Shpak B., Shen D., Miller D.P., Artyomov M.N., Lamont R.J., Bagaitkar J. Microbiome-mediated incapacitation of interferon lambda production in the oral mucosa//Proceedings of the National Academy of Sciences of the United States of America, 2021, Vol. 118, No. 51, pp. e2105170118 2021 Scopus, Web of Science
Daemen S., Gainullina A.N., Kalugotla G., He L., Chan M.M., Beals J.W., Liss K.H., Klein S., Feldstein A.F., Finck B.N., Artyomov M., Schilling J.D. Dynamic Shifts in the Composition of Resident and Recruited Macrophages Influence Tissue Remodeling in NASH//Cell Reports, 2021, Vol. 34, No. 2, pp. 108626 2021 Scopus, Web of Science
Miller H., Andhey P., Swiecki M., Rosa B.A., Zaitsev K., Villani A., Mitreva M., Artyomov M., Gilfillan S., Cella M., Colonna M. Altered ratio of dendritic cell subsets in skin-draining lymph nodes promotes Th2-driven contact hypersensitivity//Proceedings of the National Academy of Sciences of the United States of America, 2021, Vol. 118, No. 3, pp. e2021364118 2021 Scopus, Web of Science
Shpynov O., Dievskii A., Chernyatchik R., Tsurinov P., Artyomov M.N. Semi-supervised peak calling with SPAN and JBR Genome Browser//Bioinformatics, 2021, Vol. 37, No. 22, pp. 4235-4237 2021 Scopus, Web of Science
Shpynov O., Chernyatchik R., Tsurinov P., Artyomov M.N. SPAN and JBR - tools for semi-supervised peak calling//Proceedings of the 10th Moscow Conference on Computational Molecular Biology, MCCMB'21, 2021 2021
Shchukina I., Bagaitkar J., Shpynov O., Loginicheva E., Porter S., Mogilenko D.A., Wolin E., Collins P., Demidov G., Artomov M., Zaitsev K., Sidorov S., Camell C., Bambouskova M., Laura A., Swain A., Panteleeva A., Dievskii A., Kurbatsky E., Tsurinov P., Chernyatchik R., Dixit V.D., Jovanovic M., Stewart S.A., Daly M., Dmitriev S., Oltz E.M., Artyomov M.N. Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome//Nature Aging, 2021, Vol. 1, No. 1, pp. 124-141 2021 Scopus, Web of Science
Merlin J., Ivanov S., Dumont A., Sergushichev A.A., Gall J., Stunault M.I., Ayrault M., Vaillant N., Castiglione A., Swain A., Orange F., Gallerand A., Berton T., Martin J., Carobbio S., Masson J., Gaisler-Salomon I., Maechler P., Rayport S., Sluimer J., Biessen E., Guinamard R.R., Gautier E., Thorp E.B., Artyomov M.N., Yvan-Charvet L. Non-canonical glutamine transamination sustains efferocytosis by coupling redox buffering to oxidative phosphorylation//Nature Metabolism, 2021, Vol. 3, No. 10, pp. 1313-1326 2021 Scopus, Web of Science
Zhou Y., Song W., Andhey P., Swain A., Levy T., Miller K., Poliani P., Cominelli M., Grover S., Gilfillan S., Cella M., Ulland T.K., Zaitsev K., Miyashita A., Ikeuchi T., Sainouchi M., Kakita A., Bennett D., Schneider J., Nichols M., Beausoleil S., Ulrich J.D., Holtzman D.M., Artyomov M.N., Colonna M. Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer's disease//Nature medicine, 2020, Vol. 26, No. 1, pp. 131-142 2020 Scopus, Web of Science
Zhou Y., Song W., Andhey P., Swain A., Levy T., Miller K., Poliani P., Cominelli M., Grover S., Gilfillan S., Cella M., Ulland T.K., Zaitsev K., Miyashita A., Ikeuchi T., Sainouchi M., Kakita A., Bennett D., Schneider J., Nichols M., Beausoleil S., Ulrich J.D., Holtzman D.M., Artyomov M.N., Colonna M. Author Correction: Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease (Nature Medicine, (2020), 26, 1, (131-142), 10.1038/s41591-019-0695-9)//Nature medicine, 2020, Vol. 26, No. 6, pp. 981 2020 Scopus, Web of Science
Aguilar S., Aguilar O., Allan R., Amir E., Angeli V., Artyomov M.N., Asinovski N., Astarita J., Austen K., Bajpai G., Barrett N., Baysoy A., Benoist C., Bellemare-Pelletier A., Berg B., Best A., Bezman N., Blair D., Blander J., Bogunovic M., Brennan P., Brenner M., Brown B., Buechler M., Buenrostro J., Casanova M., Choi K., Chow A., Chudnovskiy A., Cipoletta D., Cohen N., Collins J., Colonna M., Cook A., Costello J., Cremasco V., Crowl T., Crozat K., Cruse R., D’Angelo J., Dalod M., Davis S., Demiralp C., Deng T., Desai J., Desland F., Dhainaut M., Ding J., Doedens A., Dominguez C., Doran G., Dress R., Dustin M., Dwyer D., Dzhagalov I., Elpek K., Ergun A., Ericson J., Esomonu E., Fairfax K., Fletcher A., Frascoli M., Fuchs A., Gainullina A., Gal-Oz S., Gallagher M., Gautier E., Gazit R., Gibbings S., Giraud M., Ginhoux F., Goldrath A., Gotthardt D., Gray D., Greter M., Grieshaber-Bouyer R., Guilliams M., Haidermota S., Hardy R., Hashimoto D., Helft J., Hendricks D., Heng T., Hill J., Hyatt G., Idoyaga J., Jakubzick C., Jarjoura J., Jepson D., Jia B., Jianu R., Johanson T., Jordan S., Jojic V., Kamimura Y., Kana V., Kang J., Kapoor V., Kenigsberg E., Kent A., Kim C., Kim E., Kim F., Kim J., Kim K., Kiner E., Knell J., Koller D., Krchma K., Kozinn L., Kreslavsky T., Kronenberg M., Kwan W., Laidlaw D., Lam V., Lanier L., Laplace C., Lareau C., Lavin Y., Lavine K., Leader A., Leboeuf M., Lee J., Lee J., Li B., Li H., Li Y., Lionakis M., Luche H., Lynch L., Magen A., Maier B., Malhotra D., Malhotra N., Malissen M., Maslova A., Mathis D., Mcfarland A., Merad M., Meunier E., Miller J., Milner J., Mingueneau M., Min-Oo G., Monach P., Moodley D., Mortha A., Morvan M., Mostafavi S., Muller S., Muus C., Nabekura T., Nageswara Rao T., Narang V., Narayan K., Ner-Gaon H., Nguyen Q., Nigrovic P., Novakovsky G., Nutt S., Omilusik K., Ortiz-Lopez A., Paidassi H., Paik H., Painter M., Paynich M., Peng V., Potempa M., Pradhan R., Price J., Qi Y., Qi Y., Quon S., Ramirez R., Ramanan D., Randolph G., Regev A., Rhoads A., Robinette M., Rose S., Rossi D., Rothamel K., Sachidanandam R., Sathe P., Scott C., Seddu K., See P., Sergushichev A., Shaw L., Shay T., Shemesh A., Shinton S., Shyer J., Sieweke M., Smillie C., Spel L., Spidale N., Stifano G., Subramanian A., Sun J., Sylvia K., Tellier J., This S., Tomasello E., Todorov H., Turley S., Vijaykumar B., Wagers A., Wakamatsu E., Wang C., Wang P., Wroblewska A., Wu J., Yang E., Yang L., Yim A., Yng L., Yoshida H., Yu B., Zhou Y., Zhu Y., Ziemkiewicz C. ImmGen at 15//Nature Immunology, 2020, Vol. 21, No. 7, pp. 700-703 2020 Scopus, Web of Science
Гайнуллина А.Н., Артемов М., Сергушичев А.А. Модификация метода совместной кластеризации в графовом и корреляционном пространствах [Method of joint clustering in network and correlation spaces] // Научно-технический вестник информационных технологий, механики и оптики [Scientific and Technical Journal of Information Technologies, Mechanics and Optics] -2020. - Т. 20. - № 6(130). - С. 807-814 2020 RSCI, Scopus, ВАК, РИНЦ
Williams J.W., Zaitsev K., Kim K., Ivanov S., Saunders B.T., Schrank P., Kim K., Elvington A., Kim S., Tucker C., Wohltmann M., Fife B., Epelman S., Artyomov M., Lavine K.J., Zinselmeyer B.H., Choi J.H., Randolph G.J. Limited proliferation capacity of aortic intima resident macrophages requires monocyte recruitment for atherosclerotic plaque progression//Nature Immunology, 2020, Vol. 21, No. 10, pp. 1194-1204 2020 Scopus, Web of Science
Esaulova E., Cantoni C., Shchukina I., Zaitsev K., Bucelli R., Wu G., Artyomov M., Cross A., Edelson B. Single-cell RNA-seq analysis of human CSF microglia and myeloid cells in neuroinflammation//Neurology: Neuroimmunology and NeuroInflammation, 2020, Vol. 7, No. 4, pp. e732 2020 Scopus, Web of Science
Park E., Patel S., Wang Q., Andhey P., Zaitsev K., Porter S., Hershey M., Bern M., Plougastel-Douglas B., Collins P.L., Colonna M., Murphy K.M., Oltz E.M., Artyomov M.N., Sibley L., Yokoyama W. Toxoplasma gondii infection drives conversion of NK cells into ILC1-like cells//eLife, 2019, Vol. 8, pp. e47605 2019 Scopus, Web of Science
Zaitsev K., Bambouskova M., Swain A., Artyomov M.N. Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures//Nature Communications, 2019, Vol. 10, pp. 2209 2019 Scopus, Web of Science
Cella M., Gamini R., Secca C., Collins P.L., Zhao S., Peng V., Robinette M.L., Schettini J., Zaitsev K., Gordon W., Bando J.K., Yomogida K., Cortez V., Fronick C., Fulton R.S., Lin L., Gilfillan S., Flavell R.A., Shan L., Artyomov M.N., Bowman M., Oltz E.M., Jelinsky S.A., Colonna M. Publisher Correction: Subsets of ILC3?ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues (Nature Immunology, (2019), 20, 8, (980-991), 10.1038/s41590-019-0425-y)//Nature Immunology, 2019, Vol. 20, No. 10, pp. 1405 2019 Scopus, Web of Science
Kim K., Shim D., Lee J.S., Zaitsev K., Williams J.W., Kim K.W., Jang M.Y., Jang H.S., Yun T.J., Lee S.H., Yoon W.K., Prat A., Seidah N.G., Choi J., Lee S.P., Yoon S.H., Nam J.W., Seong J.K., Oh G.T., Randolph G.J., Artyomov M.N., Cheong C., Choi J.H. Transcriptome Analysis Reveals NonFoamy Rather than Foamy Plaque Macrophages Are ProInflammatory in Atherosclerotic Murine Models//Circulation Research, 2018, Vol. 123, No. 10, pp. 1127-1142 2018 Scopus, Web of Science
Gorman M.J., Caine E.A., Zaitsev K., Begley M.C., Weger-Lucarelli J., Uccellini M.B., Tripathi S., Morrison J., Yount B.L., Dinnon K.H., Ruckert C., Young M.C., Zhu Z., Robertson S.J., Mcnally K.L., Ye J., Cao B., Mysorekar I.U., Ebel G.D., Baric R.S., Best S.M., Artyomov M.N., Garcia-Sastre A., Diamond M.S. An Immunocompetent Mouse Model of Zika Virus Infection//Cell Host and Microbe, 2018, Vol. 23, No. 5, pp. 672-685 2018 Scopus, Web of Science
Gubin M.M., Esaulova E., Ward J.P., Malkova O.N., Runci D., Wong P., Noguchi T., Arthur C.D., Meng W., Alspach E., Medrano R.F., Fronick C., Fehlings M., Newell E.W., Fulton R.S., Sheehan K.C., Oh S.T., Schreiber R.D., Artyomov M.N. High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy//Cell, 2018, Vol. 175, No. 4, pp. 1014-1030.e19 2018 Scopus, Web of Science
Brahler S., Zinselmeyer B.H., Raju S., Nitschke M., Suleiman H., Saunders B.T., Johnson M.W., Bohner A.M., Viehmann S.F., Theisen D.J., Kretzer N.M., Briseno C.G., Zaitsev K., Ornatsky O.I., Chang Q., Carrero J.A., Kopp J.B., Artyomov M.N., Kurts C., Murphy K.M., Miner J.H., Shaw A.S. Opposing roles of dendritic cell subsets in experimental GN//Journal of the American Society of Nephrology, 2018, Vol. 29, No. 1, pp. 138-154 2018 Scopus, Web of Science
Ulland T.K., Song W., Huang S.C., Ulrich J.D., Sergushichev A.A., Beatty W.L., Loboda A.A., Zhou Y., Cairns N.J., Kambal A., Loginicheva E., Gilfillan S., Cella M., Virgin H.W., Unanue E.R., Wang Y., Artyomov M.N., Holtzman D.M., Colonna M. TREM2 Maintains Microglial Metabolic Fitness in Alzheimer's Disease//Cell, 2017, Vol. 170, No. 4, pp. 649-663.e13 2017 Scopus, Web of Science
Steed A.L., Christophides G.K., Kaiko G.E., Sun L., Goodwin V.M., Jain U., Esaulova E., Artyomov M.N., Morales D.J., Holtzman M.J., Boon A.C., Lenschow D.J., Stappenbeck T.S. The microbial metabolite desaminotyrosine protects from influenza through type I interferon//Science, 2017, Vol. 357, No. 6350, pp. 498-502 2017 Scopus, Web of Science
Bi W.L., Greenwald N.F., Abedalthagafi M., Wala J., Gibson W.J., Agarwalla P.K., Horowitz P., Schumacher S.E., Esaulova E., Mei Y., Chevalier A., Ducar M.A., Thorner A.R., Van Hummelen P., Stemmer-Rachamimov A.O., Artemov M., Al-Mefty O., Dunn G.P., Santagata S., Dunn I.F., Beroukhim R. Genomic landscape of high-grade meningiomas//NPJ Genomic Medicine, 2017, Vol. 2, pp. 15 2017 Scopus, Web of Science
Chatterjee S., Luthra P., Esaulova E., Agapov E., Yen B., Borek D.M., Edwards M.R., Mittal A., Jordan D.S., Ramanan P., Moore M.L., Pappu R.V., Holtzman M.J., Artyomov M., Basler C.F., Amarasinghe G.K., Leung D.W. Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses//Nature Microbiology, 2017, Vol. 2, No. 9, pp. 17101 2017 Scopus, Web of Science
Bi W.L., Greenwald N.F., Abedalthagafi M., Wala J., Gibson W.J., Agarwalla P.K., Horowitz P., Schumacher S.E., Esaulova E., Mei Y., Chevalier A., Ducar M.A., Thorner A.R., Van Hummelen P., Stemmer-Rachamimov A.O., Artemov M., Al-Mefty O., Dunn G.P., Santagata S., Dunn I.F., Beroukhim R. Erratum: Genomic landscape of high-grade meningiomas//NPJ Genomic Medicine, 2017, Vol. 2, pp. 26 2017 Scopus, Web of Science
Loboda A.A., Artyomov M.N., Sergushichev A.A. Solving generalized maximum-weight connected subgraph problem for network enrichment analysis//Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2016, Vol. 9838, pp. 210-221 2016 Scopus, Web of Science
Artyomov M.N., Sergushichev A., Schilling J. Integrating immunometabolism and macrophage diversity//Seminars in Immunology, 2016, Vol. 28, No. 5, pp. 417-424 2016 Scopus, Web of Science
Sergushichev A.A., Loboda A.A., Jha A.K., Vincent E.E., Driggers E.M., Jones R.G., Pearce E.J., Artyomov M.N. GAM: a web-service for integrated transcriptional and metabolic network analysis//Nucleic Acids Research, 2016, Vol. 44, No. 1, pp. W194-W200 2016 Scopus, Web of Science