Research group

Bioinformatics Group

Publications

Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging

December 2020

Denis A. Mogilenko, Oleg Shpynov, Prabhakar Sairam Andhey, Laura Arthur, Amanda Swain, Ekaterina Esaulova, Simone Brioschi, Irina Shchukina, Martina Kerndl, Monika Bambouskova, Zhangting Yao, Anwesha Laha, Konstantin Zaitsev, Samantha Burdess, Susan Gillfilan, Sheila A. Stewart, Marco Colonna, Maxim N.Artyomov

Immunity

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Single-cell RNA-seq analysis of human CSF microglia and myeloid cells in neuroinflammation

July 2020

Ekaterina Esaulova, Claudia Cantoni, Irina Shchukina, Konstantin Zaitsev, Robert C Bucelli, Gregory F Wu, Maxim N Artyomov, Anne H Cross, Brian T Edelson

Neurology-Neuroimmunology Neuroinflammation

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Single cell RNA sequencing in atherosclerosis research

April 2020

Jesse W Williams, Holger Winkels, Christopher P Durant, Konstantin Zaitsev, Yanal Ghosheh, Klaus Ley

Circulation research

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Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes

February 2020

Ya-Ting Wang, Konstantin Zaitsev, Qun Lu, Shan Li, W Timothy Schaiff, Ki-Wook Kim, Lindsay Droit, Craig B Wilen, Chandni Desai, Dale R Balce, Robert C Orchard, Anthony Orvedahl, Sunmin Park, Darren Kreamalmeyer, Scott A Handley, John D Pfeifer, Megan T Baldridge, Maxim N Artyomov, Christina L Stallings, Herbert W Virgin

Nature microbiology

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Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

January 2020

Yingyue Zhou, Wilbur M Song, Prabhakar S Andhey, Amanda Swain, Tyler Levy, Kelly R Miller, Pietro L Poliani, Manuela Cominelli, Shikha Grover, Susan Gilfillan, Marina Cella, Tyler K Ulland, Konstantin Zaitsev, Akinori Miyashita, Takeshi Ikeuchi, Makoto Sainouchi, Akiyoshi Kakita, David A Bennett, Julie A Schneider, Michael R Nichols, Sean A Beausoleil, Jason D Ulrich, David M Holtzman, Maxim N Artyomov, Marco Colonna

Nature medicine

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Subsets of ILC3− ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues

August 2019

Marina Cella, Ramya Gamini, Cristiane Sécca, Patrick L Collins, Shanrong Zhao, Vincent Peng, Michelle L Robinette, Jorge Schettini, Konstantin Zaitsev, William Gordon, Jennifer K Bando, Kentaro Yomogida, Victor Cortez, Catrina Fronick, Robert Fulton, Lih-Ling Lin, Susan Gilfillan, Richard A Flavell, Liang Shan, Maxim N Artyomov, Michael Bowman, Eugene M Oltz, Scott A Jelinsky, Marco Colonna

Nature immunology

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Toxoplasma gondii infection drives conversion of NK cells into ILC1-like cells

August 2019

Eugene Park, Swapneel Patel, Qiuling Wang, Prabhakar Andhey, Konstantin Zaitsev, Sophia Porter, Maxwell Hershey, Michael Bern, Beatrice Plougastel-Douglas, Patrick Collins, Marco Colonna, Kenneth M Murphy, Eugene Oltz, Maxim Artyomov, L David Sibley, Wayne M Yokoyama

eLife

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Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures

May 2019

Konstantin Zaitsev, Monika Bambouskova, Amanda Swain, Maxim N Artyomov

Nature communications

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LKB1 expressed in dendritic cells governs the development and expansion of thymus-derived regulatory T cells

April 2019

Leonard R. Pelgrom, Thiago A. Patente, Alexey Sergushichev, Ekaterina Esaulova, Frank Otto, Arifa Ozir-Fazalalikhan, Hendrik J. P. van der Zande, Alwin J. van der Ham, Stefan van der Stel, Maxim N. Artyomov & Bart Everts

Cell Research, volume 29, pages 406–419

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Interferon lambda protects the female reproductive tract against Zika virus infection

January 2019

Elizabeth A Caine, Suzanne M Scheaffer, Nitin Arora, Konstantin Zaitsev, Maxim N Artyomov, Carolyn B Coyne, Kelle H Moley, Michael S Diamond

Nature communications

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Tissue resident CCR2− and CCR2+ cardiac macrophages differentially orchestrate monocyte recruitment and fate specification following myocardial injury

January 2019

Geetika Bajpai, Andrea Bredemeyer, Wenjun Li, Konstantin Zaitsev, Andrew L Koenig, Inessa Lokshina, Jayaram Mohan, Brooke Ivey, His-Min Hsiao, Carla Weinheimer, Attila Kovacs, Slava Epelman, Maxim Artyomov, Daniel Kreisel, Kory J Lavine

Circulation research

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High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy

October 2018

Matthew M. Gubin, Ekaterina Esaulova, Jeffrey P. Ward, Olga N. Malkova, Daniele Runci, Pamela Wong, Takuro Noguchi, Cora D. Arthur, Wei Meng, Elise Alspach, Ruan F.V. Medrano, Catrina Fronick, Michael Fehlings, Evan W. Newell, Robert S. Fulton, Kathleen C.F. Sheehan, Stephen T. Oh, Robert D. Schreiber, Maxim N. Artyomov

Cell

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Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models

October 2018

Kyeongdae Kim , Dahee Shim , Jun Seong Lee , Konstantin Zaitsev , Jesse W. Williams , Ki-Wook Kim , Man-Young Jang , Hyung Seok Jang , Tae Jin Yun , Seung Hyun Lee , Won Kee Yoon , Annik Prat , Nabil G. Seidah , Jungsoon Choi , Seung-Pyo Lee , Sang-Ho Yoon , Jin Wu Nam , Je Kyung Seong , Goo Taeg Oh , Gwendalyn J. Randolph , Maxim N. Artyomov , Cheolho Cheong , and Jae-Hoon Choi

Circulation Research

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An Immunocompetent Mouse Model of Zika Virus Infection

May 2018

Matthew J. Gorman, Elizabeth A. Caine, Konstantin Zaitsev, Matthew C. Begley, James Weger-Lucarelli, Melissa B. Uccellini, Shashank Tripathi, Juliet Morrison, Boyd L. Yount, Kenneth H. Dinnon III, Claudia Rückert, Michael C. Young, Zhe Zhu, Shelly J. Robertson, Kristin L. McNally, Jing Ye, Bin Cao, Indira U. Mysorekar, Gregory D. Ebel, Ralph S. Baric, Sonja M. Best, Maxim N. Artyomov, Adolfo Garcia-Sastre, Michael S. Diamond

Cell Host & Microbe, Volume 23, Issue 5, p672–685.e6

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Electrophilic properties of itaconate and derivatives regulate the IκBζ–ATF3 inflammatory axis

April 2018

Monika Bambouskova, Laurent Gorvel, Vicky Lampropoulou, Alexey Sergushichev, Ekaterina Loginicheva, Kendall Johnson, Daniel Korenfeld, Mary Elizabeth Mathyer, Hyeryun Kim, Li-Hao Huang, Dustin Duncan, Howard Bregman, Abdurrahman Keskin, Andrea Santeford, Rajendra S. Apte, Raghav Sehgal, Britney Johnson, Gaya K. Amarasinghe, Miguel P. Soares, Takashi Satoh, Shizuo Akira, Tsonwin Hai, Cristina de Guzman Strong, Karine Auclair, Thomas P. Roddy, Scott A. Biller, Marko Jovanovic, Eynav Klechevsky, Kelly M. Stewart, Gwendalyn J. Randolph & Maxim N. Artyomov

Nature

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Irg1 expression in myeloid cells prevents immunopathology during M. tuberculosis infection

March 2018

Sharmila Nair, Jeremy P. Huynh, Vicky Lampropoulou, Ekaterina Loginicheva, View ORCID ProfileEkaterina Esaulova, Anshu P. Gounder, View ORCID ProfileAdrianus C.M. Boon, Elizabeth A. Schwarzkopf, Tara R. Bradstreet, Brian T. Edelson, Maxim N. Artyomov, Christina L. Stallings, Michael S. Diamond

Journal of Experimental Medicine

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Targeted sequencing analysis of ACVR2A gene identifies novel risk variants associated with preeclampsia

March 2018

Andrey S. Glotov, Sergey V. Kazakov, Elena S. Vashukova, Vladimir S. Pakin, Maria M. Danilova, Yulia A. Nasykhova, Aleksey E. Masharsky, Elena V. Mozgovaya, Dina R. Eremeeva, Marina S. Zainullina & Vladislav S. Baranov

The Journal of Maternal-Fetal & Neonatal Medicine

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Opposing Roles of Dendritic Cell Subsets in Experimental GN

January 2018

Sebastian Brähler, Bernd H. Zinselmeyer, Saravanan Raju, Maximilian Nitschke, Hani Suleiman, Brian T. Saunders, Michael W. Johnson, Alexander M.C. Böhner, Susanne F. Viehmann, Derek J. Theisen, Nicole M. Kretzer, Carlos G. Briseño, Konstantin Zaitsev, Olga Ornatsky, Qing Chang, Javier A. Carrero, Jeffrey B. Kopp, Maxim N. Artyomov, Christian Kurts, Kenneth M. Murphy, Jeffrey H. Miner and Andrey S. Shaw

1 Journal of the american society of nephrology

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Draft Genome Sequence of Coxiella burnetii Historical Strain Leningrad-2, Isolated from Blood of a Patient with Acute Q Fever in Saint Petersburg, Russia

January 2018

Olga Freylikhman, Artem Kiselev, Sergey Kazakov, Alexey Sergushichev, Yulia Panferova, Nikolay Tokarevich, Anna Kostareva

Genome Announc vol. 6 no. 3 e01464-17

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The microbial metabolite desaminotyrosine protects from influenza through type I interferon

August 2017

Ashley L. Steed, George P. Christophi, Gerard E. Kaiko, Lulu Sun, Victoria M. Goodwin, Umang Jain, Ekaterina Esaulova, Maxim N. Artyomov, David J. Morales, Michael J. Holtzman, Adrianus C. M. Boon, Deborah J. Lenschow, Thaddeus S. Stappenbeck

Science Vol 357, Issue 6350

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TREM2 Maintains Microglial Metabolic Fitness in Alzheimer’s Disease

August 2017

Tyler K. Ulland, Wilbur M. Song, Stanley Ching-Cheng Huang, Jason D. Ulrich, Alexey Sergushichev, Wandy L. Beatty, Alexander A. Loboda, Yingyue Zhou, Nigel J. Cairns, Amal Kambal, Ekaterina Loginicheva, Susan Gilfillan, Marina Cella, Herbert W. Virgin, Emil R. Unanue, Yaming Wang, Maxim N. Artyomov, David M. Holtzman, Marco Colonna

Cell, Volume 170, Issue 4

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Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses

June 2017

Srirupa Chatterjee, Priya Luthra, Ekaterina Esaulova, Eugene Agapov, Benjamin C. Yen, Dominika M. Borek, Megan R. Edwards, Anuradha Mittal, David S. Jordan, Parameshwar Ramanan, Martin L. Moore, Rohit V. Pappu, Michael J. Holtzman, Maxim N. Artyomov, Christopher F. Basler, Gaya K. Amarasinghe & Daisy W. Leung

Nature Microbiology 2, Article number: 17101

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Ranking Vertices for Active Module Recovery Problem

April 2017

Javlon E. Isomurodov, Alexander A. Loboda, Alexey A. Sergushichev

Algorithms for Computational Biology

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Genomic landscape of high-grade meningiomas

April 2017

Wenya Linda Bi, Noah F. Greenwald, Malak Abedalthagafi, Jeremiah Wala, Will J. Gibson, Pankaj K. Agarwalla, Peleg Horowitz, Steven E. Schumacher, Ekaterina Esaulova, Yu Mei, Aaron Chevalier, Matthew A. Ducar, Aaron R. Thorner, Paul van Hummelen, Anat O. Stemmer-Rachamimov, Maksym Artyomov, Ossama Al-Mefty, Gavin P. Dunn, Sandro Santagata, Ian F. Dunn & Rameen Beroukhim

npj Genomic Medicine 2, Article number: 15

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POSTER: Systems Level Characterization of the Epigenomic Changes During Healthy Aging in the Human Blood Monocyte

October 2016

Bagaitkar Juhi, Bambouskova Monica, Oltz Eugene, Porter Sofia, Collins Patrick, Shpynov Oleg, German Demidov, Konstantin Zaytsev

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Integrating immunometabolism and macrophage diversity

October 2016

Maxim N. Artyomov, Alexey Sergushichev, Joel D. Schilling

Seminars in Immunology, Volume 28, Issue 5

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Solving Generalized Maximum-Weight Connected Subgraph Problem for Network Enrichment Analysis

August 2016

Alexander A. Loboda, Maxim N. Artyomov, Alexey A. Sergushichev

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Itaconate Links Inhibition of Succinate Dehydrogenase with Macrophage Metabolic Remodeling and Regulation of Inflammation

July 2016

V. Lampropoulou, A. Sergushichev, M. Bambouskova, S. Nair, E. Vincent, E. Loginicheva, L. Cervantes-Barragan, X. Ma, S. Huang, T. Griss, C. Weinheimer, S. Khader, G. Randolph, E. Pearce, R. G. Jones, A. Diwan, M. Diamond,M. N. Artyomov

Cell Metabolism

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MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data

June 2016

Ulyantsev V.I., Kazakov S.V., Dubinkina V.B., Tyakht A.V., Alexeev D.G.

Bioinformatics

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GAM: a web-service for integrated transcriptional and metabolic network analysis

April 2016

Alexey A. Sergushichev, Alexander A. Loboda, Abhishek K. Jha, Emma E. Vincent, Edward M. Driggers, Russell G. Jones, Edward J. Pearce and Maxim N. Artyomov

Nucleic Acids Research, Vol. 44

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Mitochondrial Phosphoenolpyruvate Carboxykinase Regulates Metabolic Adaptation and Enables Glucose-Independent Tumor Growth

October 2015

E. Vincent, A. Sergushichev, T. Griss, M. Gingras, B. Samborska, T. Ntimbane, P. Coelho, J. Blagih, T. Raissi, L. Choinière, G. Bridon, E. Loginicheva, B. Flynn, E. Thomas, J. Tavaré, D. Avizonis, A. Pause, D. Elder, M. Artyomov, R. Jones

Molecular Cell, Vol. 60, Issue 2, p195–207

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Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization

March 2015

Abhishek K. Jha, Stanley Ching-Cheng Huang, Alexey Sergushichev, Vicky Lampropoulou, Yulia Ivanova, Ekaterina Loginicheva, Karina Chmielewski, Kelly M. Stewart, Juliet Ashall, Bart Everts, Edward J. Pearce, Edward M. Driggers, and Maxim N. Artyomov

Immunity. - Vol. 42, No. 3. - P. 419-430.

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