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Publications


A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity


K. Slowikowski, P. Sen, C. Cosgriff, J. Tantivit, T. Eisenhaure, T. J. LaSalle, K. Manakongtreecheep, A. Tirard, B. Y. Arnold, A. Pacheco-Navarro, E. Y. Yang, M. Reyes, A. Gonye, I. Gushterova, B. Russo, M. Rojas-Lopez, N. Sharma, M. F. Thomas, T. Sharova, D. Frederick, K. Lavin-Parsons, B. Lilley, B. Mckaig, C. Lodenstein, H. Khanna, K. Kays, N. Charland, N. Smith, S. Ramesh, T. Delorey, D. Phillips, L. Amir-Zilberstein, E. M. Brown, M. Benson, S.-M. Park, B. Tusi, V. Pokatayev, C. Hecht, N. Pishesha, A. E. Woolley, L. Cosimi, Rozenblatt-Ro

medRxiv, 2025


Immune responses in checkpoint myocarditis across heart, blood and tumour.


S. Blum, Daniel A. Zlotoff, N. Smith, Isabela J. Kernin, Swetha Ramesh, L. Zubiri, Joshua Caplin, Nandini Samanta, Sidney Martin, Mike Wang, Alice Tirard, Yuhui Song, Katherine H Xu, J. Barth, Pritha Sen, Kamil Slowikowski, J. Tantivit, K. Manakongtreecheep, Benjamin Y. Arnold, Mazen Nasrallah, Christopher J. Pinto, D. McLoughlin, Monica Jackson, PuiYee Chan, Aleigha Lawless, William A Michaud, T. Sharova, Linda T. Nieman, Justin F Gainor, Catherine J Wu, D. Juric, M. Mino-Kenudson, Giacomo Oliveira, Ryan J. Sullivan, Genevieve M. Boland, James R. Stone, M. Thomas, T. Neilan, Kerry L. Reynolds, A-C. Villani

Nature, 2024


Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis


Molly Fisher Thomas, Kamil Slowikowski, Kasidet Manakongtreecheep, Pritha Sen, Nandini Samanta, Jessica Tantivit, Mazen Nasrallah, Leyre Zubiri, Neal P Smith, Alice Tirard, Swetha Ramesh, Benjamin Y Arnold, Linda T Nieman, Jonathan H Chen, Thomas Eisenhaure, Karin Pelka, Yuhui Song, Katherine H Xu, Vjola Jorgji, Christopher J Pinto, Tatyana Sharova, Rachel Glasser, Puiyee Chan, Ryan J Sullivan, Hamed Khalili, Dejan Juric, Genevieve M Boland, Michael Dougan, Nir Hacohen, Bo Li, Kerry L Reynolds, Alexandra-Chloé Villani

Nat. Med., vol. 30, Springer Science and Business Media LLC, 2024 May, pp. 1349--1362


A human model of asthma exacerbation reveals transcriptional programs and cell circuits specific to allergic asthma


Jehan Alladina, Neal P Smith, Tristan Kooistra, Kamil Slowikowski, Isabela J Kernin, Jacques Deguine, Henry L Keen, Kasidet Manakongtreecheep, Jessica Tantivit, Rod A Rahimi, Susan L Sheng, Nhan D Nguyen, Alexis M Haring, Francesca L Giacona, Lida P Hariri, Ramnik J Xavier, Andrew D Luster, Alexandra-Chloé Villani, Josalyn L Cho, Benjamin D Medoff

Sci. Immunol., vol. 8, American Association for the Advancement of Science, 2023 May, pp. eabq6352


Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics


Christoph Muus, Malte D Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, Graham Heimberg, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smillie, Karthik A Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L Haber, Hattie Chung, Daniel T Montoro, Taylor Adams, Hananeh Aliee, Samuel J Allon, Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Bécavin, Inbal Benhar, Joseph Bergenstråhle, Ludvig Bergenstråhle, Liam Bolt, Emelie Braun, Linh T Bui, Steven Callori, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M Conlon, Michael S Cuoco, Anna S E Cuomo, Marie Deprez, Grant Duclos, Denise Fine, David S Fischer, Shila Ghazanfar, Astrid Gillich, Bruno Giotti, Joshua Gould, Minzhe Guo, Austin J Gutierrez, Arun C Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Yan Hu, Alok Jaiswal, Lu Ji, Peiyong Jiang, Theodoros S Kapellos, Christin S Kuo, Ludvig Larsson, Michael A Leney-Greene, Kyungtae Lim, Monika Litviňuková, Leif S Ludwig, Soeren Lukassen, Wendy Luo, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Sylvie Leroy, Christoph H Mayr, Ian M Mbano, Alexi M McAdams, Ahmad N Nabhan, Sarah K Nyquist, Lolita Penland, Olivier B Poirion, Sergio Poli, Cancan Qi, Rachel Queen, Daniel Reichart, Ivan Rosas, Jonas C Schupp, Conor V Shea, Xingyi Shi, Rahul Sinha, Rene V Sit, Kamil Slowikowski, Michal Slyper, Neal P Smith, Alex Sountoulidis, Maximilian Strunz, Travis B Sullivan, Dawei Sun, Carlos Talavera-López, Peng Tan, Jessica Tantivit, Kyle J Travaglini, Nathan R Tucker, Katherine A Vernon, Marc H Wadsworth, Julia Waldman, Xiuting Wang, Ke Xu, Wenjun Yan, William Zhao, Carly G K Ziegler

Nature medicine, vol. 27, Nature Publishing Group US, 2021 Mar, pp. 546--559


Archaeal ribosomal proteins possess nuclear localization signal-type motifs: implications for the origin of the cell nucleus


S Melnikov, H Kwok, K Manakongtreecheep, Antonia van den Elzen, Carson C Thoreen, D Söll

bioRxiv, vol. 37, Oxford University Press, 2019 Jun, pp. 124--133


Comprehensive functional genomic resource and integrative model for the human brain


Daifeng Wang, Shuang Liu, Jonathan Warrell, Hyejung Won, Xu Shi, Fabio C P Navarro, Declan Clarke, Mengting Gu, Prashant Emani, Yucheng T Yang, Min Xu, Michael J Gandal, Shaoke Lou, Jing Zhang, Jonathan J Park, Chengfei Yan, Suhn Kyong Rhie, Kasidet Manakongtreecheep, Holly Zhou, Aparna Nathan, Mette Peters, Eugenio Mattei, Dominic Fitzgerald, Tonya Brunetti, Jill Moore, Yan Jiang, Kiran Girdhar, Gabriel E Hoffman, Selim Kalayci, Zeynep H Gümüş, Gregory E Crawford, {PsychENCODE Consortium}, Panos Roussos, Schahram Akbarian, Andrew E Jaffe, Kevin P White, Zhiping Weng, Nenad Sestan, Daniel H Geschwind, James A Knowles, Mark B Gerstein

Science, vol. 362, American Association for the Advancement of Science (AAAS), 2018 Dec, pp. eaat8464


Muller’s ratchet and ribosome degeneration in the obligate intracellular parasites Microsporidia


S Melnikov, K Manakongtreecheep, Keith D Rivera, A Makarenko, D Pappin, D Söll

Int. J. Mol. Sci., vol. 19, MDPI, 2018 Nov, p. 4125


Revising the structural diversity of ribosomal proteins across the three domains of life


S Melnikov, K Manakongtreecheep, D Söll

Mol. Biol. Evol., vol. 35, Oxford University Press, 2018 Jul, pp. 1588--1598

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