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
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
Single cell RNA sequencing in atherosclerosis research
April 2020
Jesse W Williams, Holger Winkels, Christopher P Durant, Konstantin Zaitsev, Yanal Ghosheh, Klaus Ley
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
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
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
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
Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures
May 2019
Konstantin Zaitsev, Monika Bambouskova, Amanda Swain, Maxim N Artyomov
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Ranking Vertices for Active Module Recovery Problem
April 2017
Javlon E. Isomurodov, Alexander A. Loboda, Alexey A. Sergushichev
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
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
Integrating immunometabolism and macrophage diversity
October 2016
Maxim N. Artyomov, Alexey Sergushichev, Joel D. Schilling
Solving Generalized Maximum-Weight Connected Subgraph Problem for Network Enrichment Analysis
August 2016
Alexander A. Loboda, Maxim N. Artyomov, Alexey A. Sergushichev
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
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.
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
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
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