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Distinguishing features of long COVID identified through immune profiling.
Klein J, Wood J, Jaycox JR, Dhodapkar RM, Lu P, Gehlhausen JR, Tabachnikova A, Greene K, Tabacof L, Malik AA, Silva Monteiro V, Silva J, Kamath K, Zhang M, Dhal A, Ott IM, Valle G, Peña-Hernández M, Mao T, Bhattacharjee B, Takahashi T, Lucas C, Song E, McCarthy D, Breyman E, Tosto-Mancuso J, Dai Y, Perotti E, Akduman K, Tzeng TJ, Xu L, Geraghty AC, Monje M, Yildirim I, Shon J, Medzhitov R, Lutchmansingh D, Possick JD, Kaminski N, Omer SB, Krumholz HM, Guan L, Dela Cruz CS, van Dijk D, Ring AM, Putrino D, Iwasaki A. Klein J, et al. Nature. 2023 Nov;623(7985):139-148. doi: 10.1038/s41586-023-06651-y. Epub 2023 Sep 25. Nature. 2023. PMID: 37748514 Free PMC article.
Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones.
Collora JA, Liu R, Pinto-Santini D, Ravindra N, Ganoza C, Lama JR, Alfaro R, Chiarella J, Spudich S, Mounzer K, Tebas P, Montaner LJ, van Dijk D, Duerr A, Ho YC. Collora JA, et al. Immunity. 2022 Jun 14;55(6):1013-1031.e7. doi: 10.1016/j.immuni.2022.03.004. Epub 2022 Mar 22. Immunity. 2022. PMID: 35320704 Free PMC article.
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19.
Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C Jr, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K; Yale IMPACT Research Team; Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Unterman A, et al. Nat Commun. 2022 Jan 21;13(1):440. doi: 10.1038/s41467-021-27716-4. Nat Commun. 2022. PMID: 35064122 Free PMC article.
Cell2Sentence: Teaching Large Language Models the Language of Biology.
Levine D, Rizvi SA, Lévy S, Pallikkavaliyaveetil N, Zhang D, Chen X, Ghadermarzi S, Wu R, Zheng Z, Vrkic I, Zhong A, Raskin D, Han I, de Oliveira Fonseca AH, Caro JO, Karbasi A, Dhodapkar RM, van Dijk D. Levine D, et al. bioRxiv [Preprint]. 2024 Oct 29:2023.09.11.557287. doi: 10.1101/2023.09.11.557287. bioRxiv. 2024. PMID: 39554079 Free PMC article. Preprint.