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.
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.
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.
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.
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.
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.
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.
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.
Gene Set Co-regulation Analysis
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.
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.
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.
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.
Single Cell Navigator allows cross-matching of public scRNA-seq data: study case of tumor immune microenvironments
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Artyomov M.N., Sergushichev A., Schilling J. Integrating immunometabolism and macrophage diversity. Seminars in Immunology. 2016. Vol. 28. No. 5. pp. 417-424.
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.