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Multiscale PHATE identifies multimodal signatures of COVID-19.
Kuchroo M, Huang J, Wong P, Grenier JC, Shung D, Tong A, Lucas C, Klein J, Burkhardt DB, Gigante S, Godavarthi A, Rieck B, Israelow B, Simonov M, Mao T, Oh JE, Silva J, Takahashi T, Odio CD, Casanovas-Massana A, Fournier J; Yale IMPACT Team; Farhadian S, Dela Cruz CS, Ko AI, Hirn MJ, Wilson FP, Hussin JG, Wolf G, Iwasaki A, Krishnaswamy S. Kuchroo M, et al. Among authors: silva j. Nat Biotechnol. 2022 May;40(5):681-691. doi: 10.1038/s41587-021-01186-x. Epub 2022 Feb 28. Nat Biotechnol. 2022. PMID: 35228707 Free PMC article.
Sex differences in immune responses to SARS-CoV-2 that underlie disease outcomes.
Takahashi T, Wong P, Ellingson MK, Lucas C, Klein J, Israelow B, Silva J, Oh JE, Mao T, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Casanovas-Massana A, Cruz CD, Fournier JB, Odio CD, Farhadian S, Grubaugh ND, Schulz WL, Ko AI, Ring AM, Omer SB, Iwasaki A; Yale IMPACT research team. Takahashi T, et al. Among authors: silva j. medRxiv [Preprint]. 2020 Jun 26:2020.06.06.20123414. doi: 10.1101/2020.06.06.20123414. medRxiv. 2020. Update in: Nature. 2020 Dec;588(7837):315-320. doi: 10.1038/s41586-020-2700-3 PMID: 32577695 Free PMC article. Updated. Preprint.
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets.
Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Catherine Muenker M, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Tokuyama M, Venkataraman A, Weizman OE, Wong P, Yang Y, Cheemarla NR, White EB, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz CS, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND. Vogels CBF, et al. Among authors: silva j. Nat Microbiol. 2020 Oct;5(10):1299-1305. doi: 10.1038/s41564-020-0761-6. Epub 2020 Jul 10. Nat Microbiol. 2020. PMID: 32651556 Free PMC article.
Longitudinal analyses reveal immunological misfiring in severe COVID-19.
Lucas C, Wong P, Klein J, Castro TBR, Silva J, Sundaram M, Ellingson MK, Mao T, Oh JE, Israelow B, Takahashi T, Tokuyama M, Lu P, Venkataraman A, Park A, Mohanty S, Wang H, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Muenker MC, Fournier JB, Campbell M, Odio CD, Casanovas-Massana A; Yale IMPACT Team; Herbst R, Shaw AC, Medzhitov R, Schulz WL, Grubaugh ND, Dela Cruz C, Farhadian S, Ko AI, Omer SB, Iwasaki A. Lucas C, et al. Among authors: silva j. Nature. 2020 Aug;584(7821):463-469. doi: 10.1038/s41586-020-2588-y. Epub 2020 Jul 27. Nature. 2020. PMID: 32717743 Free PMC article.
Sex differences in immune responses that underlie COVID-19 disease outcomes.
Takahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ; Yale IMPACT Research Team; Shaw A, Fournier JB, Odio CD, Farhadian S, Dela Cruz C, Grubaugh ND, Schulz WL, Ring AM, Ko AI, Omer SB, Iwasaki A. Takahashi T, et al. Among authors: silva j. Nature. 2020 Dec;588(7837):315-320. doi: 10.1038/s41586-020-2700-3. Epub 2020 Aug 26. Nature. 2020. PMID: 32846427 Free PMC article.
Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2.
Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI. Wyllie AL, et al. Among authors: silva j. N Engl J Med. 2020 Sep 24;383(13):1283-1286. doi: 10.1056/NEJMc2016359. Epub 2020 Aug 28. N Engl J Med. 2020. PMID: 32857487 Free PMC article. No abstract available.
Kynurenic acid underlies sex-specific immune responses to COVID-19.
Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh J, Silva J, Wong P; Yale IMPACT Research team; Ko AI, Khan SA, Iwasaki A, Johnson CH. Cai Y, et al. Among authors: silva j. medRxiv [Preprint]. 2020 Sep 8:2020.09.06.20189159. doi: 10.1101/2020.09.06.20189159. medRxiv. 2020. Update in: Sci Signal. 2021 Jul 06;14(690):eabf8483. doi: 10.1126/scisignal.abf8483 PMID: 32935119 Free PMC article. Updated. Preprint.
Diverse Functional Autoantibodies in Patients with COVID-19.
Wang EY, Mao T, Klein J, Dai Y, Huck JD, Liu F, Zheng NS, Zhou T, Israelow B, Wong P, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE; Yale IMPACT Team; Cruz CD, Farhadian SF, Schulz WL, Grubaugh ND, Ko AI, Iwasaki A, Ring AM. Wang EY, et al. Among authors: silva j. medRxiv [Preprint]. 2021 Feb 1:2020.12.10.20247205. doi: 10.1101/2020.12.10.20247205. medRxiv. 2021. Update in: Nature. 2021 Jul;595(7866):283-288. doi: 10.1038/s41586-021-03631-y PMID: 33330894 Free PMC article. Updated. Preprint.
Kinetics of antibody responses dictate COVID-19 outcome.
Lucas C, Klein J, Sundaram M, Liu F, Wong P, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Wyllie AL, Vogels CBF, Muenker MC, Casanovas-Massana A, Schulz WL, Zell J, Campbell M, Fournier JB; Yale IMPACT Research Team; Grubaugh ND, Farhadian S, Wisnewski AV, Cruz CD, Omer S, Ko AI, Ring A, Iwasaki A. Lucas C, et al. Among authors: silva j. medRxiv [Preprint]. 2020 Dec 22:2020.12.18.20248331. doi: 10.1101/2020.12.18.20248331. medRxiv. 2020. PMID: 33398304 Free PMC article. Preprint.
Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality.
Silva J, Lucas C, Sundaram M, Israelow B, Wong P, Klein J, Tokuyama M, Lu P, Venkataraman A, Liu F, Mao T, Oh JE, Park A, Casanovas-Massana A, Vogels CBF, Muenker MC, Zell J, Fournier JB, Campbell M, Chiorazzi M, Fuentes ER, Petrone ME, Kalinich CC, Ott IM, Watkins A, Moore AJ, Nakahata M; Yale IMPACT Team; Farhadian S, Cruz CD, Ko AI, Schulz WL, Ring A, Ma S, Omer S, Wyllie AL, Iwasaki A. Silva J, et al. medRxiv [Preprint]. 2021 Jan 10:2021.01.04.21249236. doi: 10.1101/2021.01.04.21249236. medRxiv. 2021. PMID: 33442706 Free PMC article. Preprint.
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