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Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.
Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG Jr, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Chen X, et al. Nat Comput Sci. 2023 Jul;3(7):644-657. doi: 10.1038/s43588-023-00476-5. Epub 2023 Jul 25. Nat Comput Sci. 2023. PMID: 37974651 Free PMC article.
Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature.
Cappuccio A, Chawla DG, Chen X, Rubenstein AB, Cheng WS, Mao W, Burke TW, Tsalik EL, Petzold E, Henao R, McClain MT, Woods CW, Chikina M, Troyanskaya OG, Sealfon SC, Kleinstein SH, Zaslavsky E. Cappuccio A, et al. Among authors: chen x. Cell Syst. 2022 Dec 21;13(12):989-1001.e8. doi: 10.1016/j.cels.2022.11.008. Cell Syst. 2022. PMID: 36549275 Free article.
Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise.
Rubenstein AB, Smith GR, Zhang Z, Chen X, Chambers TL, Ruf-Zamojski F, Mendelev N, Cheng WS, Zamojski M, Amper MAS, Nair VD, Marderstein AR, Montgomery SB, Troyanskaya OG, Zaslavsky E, Trappe T, Trappe S, Sealfon SC. Rubenstein AB, et al. Among authors: chen x. bioRxiv [Preprint]. 2023 Oct 9:2023.09.26.558914. doi: 10.1101/2023.09.26.558914. bioRxiv. 2023. PMID: 37808658 Free PMC article. Preprint.
Automated single-cell omics end-to-end framework with data-driven batch inference.
Wang Y, Thistlethwaite W, Tadych A, Ruf-Zamojski F, Bernard DJ, Cappuccio A, Zaslavsky E, Chen X, Sealfon SC, Troyanskaya OG. Wang Y, et al. Among authors: chen x. bioRxiv [Preprint]. 2024 Jun 20:2023.11.01.564815. doi: 10.1101/2023.11.01.564815. bioRxiv. 2024. Update in: Cell Syst. 2024 Oct 16;15(10):982-990.e5. doi: 10.1016/j.cels.2024.09.003 PMID: 37961197 Free PMC article. Updated. Preprint.
Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data.
Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG Jr, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Chen X, et al. Nat Comput Sci. 2023 Sep;3(9):805. doi: 10.1038/s43588-023-00523-1. Nat Comput Sci. 2023. PMID: 38177788 Free PMC article. No abstract available.
Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders.
Zhou B, Arthur JG, Guo H, Kim T, Huang Y, Pattni R, Wang T, Kundu S, Luo JXJ, Lee H, Nachun DC, Purmann C, Monte EM, Weimer AK, Qu PP, Shi M, Jiang L, Yang X, Fullard JF, Bendl J, Girdhar K, Kim M, Chen X; PsychENCODE Consortium; Greenleaf WJ, Duncan L, Ji HP, Zhu X, Song G, Montgomery SB, Palejev D, Zu Dohna H, Roussos P, Kundaje A, Hallmayer JF, Snyder MP, Wong WH, Urban AE. Zhou B, et al. Among authors: chen x. Cell. 2024 Nov 14;187(23):6687-6706.e25. doi: 10.1016/j.cell.2024.09.014. Epub 2024 Sep 30. Cell. 2024. PMID: 39353437
A systematic review of left unilateral electroconvulsive therapy.
Kellner CH, Farber KG, Chen XR, Mehrotra A, Zipursky GDN. Kellner CH, et al. Among authors: chen xr. Acta Psychiatr Scand. 2017 Aug;136(2):166-176. doi: 10.1111/acps.12740. Epub 2017 Apr 19. Acta Psychiatr Scand. 2017. PMID: 28422271 Review.
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