Артемов Максим

Статья

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.. doi: 10.7554/eLife.85722

Статья

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.. doi: 10.17586/2226-1494-2023-23-5-989-1000

Статья

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.. doi: 10.1016/j.immuni.2023.10.013

Статья

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.. doi: 10.1093/nar/gkac427

Статья

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.. doi: 10.1038/s44161-022-00028-6

Тезисы

Single Cell Navigator allows cross-matching of public scRNA-seq data: study case of tumor immune microenvironments

Статья

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.. doi: 10.1073/pnas.2021364118

Статья

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.. doi: 10.1093/bioinformatics/btab376

Статья

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.. doi: 10.1038/s43587-020-00002-6

Статья

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.

Статья

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.. doi: 10.1038/s42255-021-00471-y

Тезисы

Gene Set Co-regulation Analysis

Статья

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.. doi: 10.1016/j.celrep.2020.108626

Статья

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.. doi: 10.1073/pnas.2105170118

Статья

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.. doi: 10.1212/NXI.0000000000000732

Статья

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.. doi: 10.1038/s41590-020-0768-4

Статья

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.. doi: 10.1038/s41591-019-0695-9

Статья

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.. doi: 10.1038/s41591-020-0922-4

Статья

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.. doi: 10.1038/s41590-020-0687-4

Статья

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.. doi: 10.17586/2226-1494-2020-20-6-807-814

Статья

Artomov M., Loboda A.A., Artyomov M., Daly M. A platform for case-control matching enables association studies without genotype sharing. BioRxiv [база препринтов]. 2019. pp. 1-26.. doi: 10.1101/470450

Статья

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.. doi: 10.1038/s41590-019-0474-2

Статья

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. No. 1. pp. 2209.. doi: 10.1038/s41467-019-09990-5

Статья

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.. doi: 10.7554/eLife.47605

Тезисы

Public platform with 42,291 exome control samples enables association studies without genotype sharing (Abstract/Program #98). Presented at the 69th Annual Meeting of The American Society of Human Genetics, October 17, Houston.

Статья

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.. doi: 10.1016/j.cell.2018.09.030

Статья

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.. doi: 10.1681/ASN.2017030270

Статья

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.. doi: 10.1161/CIRCRESAHA.118.312804

Статья

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.. doi: 10.1016/j.chom.2018.04.003

Статья

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.. doi: 10.1038/nmicrobiol.2017.101

Статья

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.. doi: 10.1038/s41525-017-0023-6

Статья

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.. doi: 10.1016/j.cell.2017.07.023

Статья

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.. doi: 10.1038/s41525-017-0014-7

Статья

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.. doi: 10.1126/science.aam5336

Статья

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.. doi: 10.1093/nar/gkw266

Статья

Artyomov M.N., Sergushichev A., Schilling J. Integrating immunometabolism and macrophage diversity. Seminars in Immunology. 2016. Vol. 28. No. 5. pp. 417-424.. doi: 10.1016/j.smim.2016.10.004

Статья

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.. doi: 10.1007/978-3-319-43681-4_17