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A human model of asthma exacerbation reveals transcriptional programs and cell circuits specific to allergic asthma.
Alladina J, Smith NP, Kooistra T, Slowikowski K, Kernin IJ, Deguine J, Keen HL, Manakongtreecheep K, Tantivit J, Rahimi RA, Sheng SL, Nguyen ND, Haring AM, Giacona FL, Hariri LP, Xavier RJ, Luster AD, Villani AC, Cho JL, Medoff BD. Alladina J, et al. Sci Immunol. 2023 May 12;8(83):eabq6352. doi: 10.1126/sciimmunol.abq6352. Epub 2023 May 5. Sci Immunol. 2023. PMID: 37146132 Free PMC article.
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.
Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. Delorey TM, et al. Nature. 2021 Jul;595(7865):107-113. doi: 10.1038/s41586-021-03570-8. Epub 2021 Apr 29. Nature. 2021. PMID: 33915569 Free PMC article.
Immune Responses in Checkpoint Myocarditis Across Heart, Blood, and Tumor.
Blum SM, Zlotoff DA, Smith NP, Kernin IJ, Ramesh S, Zubiri L, Caplin J, Samanta N, Martin SC, Tirard A, Sen P, Song Y, Barth J, Slowikowski K, Nasrallah M, Tantivit J, Manakongtreecheep K, Arnold BY, McGuire J, Pinto CJ, McLoughlin D, Jackson M, Chan P, Lawless A, Sharova T, Nieman LT, Gainor JF, Juric D, Mino-Kenudsen M, Sullivan RJ, Boland GM, Stone JR, Thomas MF, Neilan TG, Reynolds KL, Villani AC. Blum SM, et al. bioRxiv [Preprint]. 2023 Nov 29:2023.09.15.557794. doi: 10.1101/2023.09.15.557794. bioRxiv. 2023. Update in: Nature. 2024 Dec;636(8041):215-223. doi: 10.1038/s41586-024-08105-5 PMID: 37790460 Free PMC article. Updated. Preprint.
scTab: Scaling cross-tissue single-cell annotation models.
Fischer F, Fischer DS, Mukhin R, Isaev A, Biederstedt E, Villani AC, Theis FJ. Fischer F, et al. Nat Commun. 2024 Aug 4;15(1):6611. doi: 10.1038/s41467-024-51059-5. Nat Commun. 2024. PMID: 39098889 Free PMC article.
Gene-based association study of rare variants in children of diverse ancestries implicates TNFRSF21 in the development of allergic asthma.
Clay S, Alladina J, Smith NP, Visness CM, Wood RA, O'Connor GT, Cohen RT, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Rivera-Spoljaric K, Robison RG, Gergen PJ, Busse WW, Villani AC, Cho JL, Medoff BD, Gern JE, Jackson DJ, Ober C, Dapas M. Clay S, et al. J Allergy Clin Immunol. 2024 Mar;153(3):809-820. doi: 10.1016/j.jaci.2023.10.023. Epub 2023 Nov 7. J Allergy Clin Immunol. 2024. PMID: 37944567 Free PMC article.
Soluble and cell-based markers of immune checkpoint inhibitor-associated nephritis.
Sise ME, Wang Q, Seethapathy H, Moreno D, Harden D, Smith RN, Rosales IA, Colvin RB, Chute S, Cornell LD, Herrmann SM, Fadden R, Sullivan RJ, Yang NJ, Barmettler S, Wells S, Gupta S, Villani AC, Reynolds KL, Farmer J. Sise ME, et al. J Immunother Cancer. 2023 Jan;11(1):e006222. doi: 10.1136/jitc-2022-006222. J Immunother Cancer. 2023. PMID: 36657813 Free PMC article.
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2.
Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. Delorey TM, et al. bioRxiv [Preprint]. 2021 Feb 25:2021.02.25.430130. doi: 10.1101/2021.02.25.430130. bioRxiv. 2021. PMID: 33655247 Free PMC article. Preprint.