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Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome.
Sulaiman I, Chung M, Angel L, Tsay JJ, Wu BG, Yeung ST, Krolikowski K, Li Y, Duerr R, Schluger R, Thannickal SA, Koide A, Rafeq S, Barnett C, Postelnicu R, Wang C, Banakis S, Perez-Perez L, Jour G, Shen G, Meyn P, Carpenito J, Liu X, Ji K, Collazo D, Labarbiera A, Amoroso N, Brosnahan S, Mukherjee V, Kaufman D, Bakker J, Lubinsky A, Pradhan D, Sterman DH, Weiden M, Hegu A, Evans L, Uyeki TM, Clemente JC, De Wit E, Schmidt AM, Shopsin B, Desvignes L, Wang C, Li H, Zhang B, Forst CV, Koide S, Stapleford KA, Khanna KM, Ghedin E, Segal LN. Sulaiman I, et al. Among authors: banakis s. medRxiv [Preprint]. 2021 Feb 26:2021.02.23.21252221. doi: 10.1101/2021.02.23.21252221. medRxiv. 2021. PMID: 33655261 Free PMC article. Updated. Preprint.
Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism.
Sulaiman I, Wu BG, Li Y, Tsay JC, Sauthoff M, Scott AS, Ji K, Koralov SB, Weiden M, Clemente JC, Jones D, Huang YJ, Stringer KA, Zhang L, Geber A, Banakis S, Tipton L, Ghedin E, Segal LN. Sulaiman I, et al. Among authors: banakis s. Eur Respir J. 2021 Jul 29;58(1):2003434. doi: 10.1183/13993003.03434-2020. Print 2021 Jul. Eur Respir J. 2021. PMID: 33446604 Free PMC article.
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.
Sulaiman I, Chung M, Angel L, Tsay JJ, Wu BG, Yeung ST, Krolikowski K, Li Y, Duerr R, Schluger R, Thannickal SA, Koide A, Rafeq S, Barnett C, Postelnicu R, Wang C, Banakis S, Pérez-Pérez L, Shen G, Jour G, Meyn P, Carpenito J, Liu X, Ji K, Collazo D, Labarbiera A, Amoroso N, Brosnahan S, Mukherjee V, Kaufman D, Bakker J, Lubinsky A, Pradhan D, Sterman DH, Weiden M, Heguy A, Evans L, Uyeki TM, Clemente JC, de Wit E, Schmidt AM, Shopsin B, Desvignes L, Wang C, Li H, Zhang B, Forst CV, Koide S, Stapleford KA, Khanna KM, Ghedin E, Segal LN. Sulaiman I, et al. Among authors: banakis s. Nat Microbiol. 2021 Oct;6(10):1245-1258. doi: 10.1038/s41564-021-00961-5. Epub 2021 Aug 31. Nat Microbiol. 2021. PMID: 34465900 Free PMC article.
Successful lung transplantation using an allograft from a COVID-19-recovered donor: a potential role for subgenomic RNA to guide organ utilization.
Saharia KK, Ramelli SC, Stein SR, Roder AE, Kreitman A, Banakis S, Chung JY, Burbelo PD, Singh M, Reed RM, Patel V, Rabin J, Krupnick AS, Cohen JI, de Wit E, Ghedin E, Hewitt SM, Vannella KM, Chertow DS, Grazioli A. Saharia KK, et al. Among authors: banakis s. Am J Transplant. 2023 Jan;23(1):101-107. doi: 10.1016/j.ajt.2022.09.001. Epub 2023 Jan 11. Am J Transplant. 2023. PMID: 36695611 Free PMC article.
Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data.
Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Chung M, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lässig M, Luksza M, Das S, Gresham D, Ghedin E. Roder AE, et al. Among authors: banakis s. mBio. 2023 Aug 31;14(4):e0104623. doi: 10.1128/mbio.01046-23. Epub 2023 Jun 30. mBio. 2023. PMID: 37389439 Free PMC article.
CD4+ and CD8+ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment.
Kar M, Johnson KEE, Vanderheiden A, Elrod EJ, Floyd K, Geerling E, Stone ET, Salinas E, Banakis S, Wang W, Sathish S, Shrihari S, Davis-Gardner ME, Kohlmeier J, Pinto A, Klein R, Grakoui A, Ghedin E, Suthar MS. Kar M, et al. Among authors: banakis s. bioRxiv [Preprint]. 2024 Jan 24:2024.01.23.576505. doi: 10.1101/2024.01.23.576505. bioRxiv. 2024. PMID: 38410446 Free PMC article. Preprint.
Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.
Roder AE, Johnson K, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Åuksza M, Das S, Gresham D, Ghedin E. Roder AE, et al. Among authors: banakis s. bioRxiv [Preprint]. 2022 Aug 16:2021.05.05.442873. doi: 10.1101/2021.05.05.442873. bioRxiv. 2022. PMID: 36656775 Free PMC article. Updated. Preprint.
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion.
Nussenblatt V, Roder AE, Das S, de Wit E, Youn JH, Banakis S, Mushegian A, Mederos C, Wang W, Chung M, Pérez-Pérez L, Palmore T, Brudno JN, Kochenderfer JN, Ghedin E. Nussenblatt V, et al. Among authors: banakis s. medRxiv [Preprint]. 2021 Oct 5:2021.10.02.21264267. doi: 10.1101/2021.10.02.21264267. medRxiv. 2021. PMID: 34642697 Free PMC article. Updated. Preprint.
Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome.
Sulaiman I, Chung M, Angel L, Koralov S, Wu B, Yeung S, Krolikowski K, Li Y, Duerr R, Schluger R, Thannickal S, Koide A, Rafeq S, Barnett C, Postelnicu R, Wang C, Banakis S, Perez-Perez L, Jour G, Shen G, Meyn P, Carpenito J, Liu X, Ji K, Collazo D, Labarbiera A, Amoroso N, Brosnahan S, Mukherjee V, Kaufman D, Bakker J, Lubinsky A, Pradhan D, Sterman D, Heguy A, Uyeki T, Clemente J, de Wit E, Schmidt AM, Shopsin B, Desvignes L, Wang C, Li H, Zhang B, Forst C, Koide S, Stapleford K, Khanna K, Ghedin E, Weiden M, Segal L. Sulaiman I, et al. Among authors: banakis s. Res Sq [Preprint]. 2021 Mar 29:rs.3.rs-266050. doi: 10.21203/rs.3.rs-266050/v1. Res Sq. 2021. PMID: 33791687 Free PMC article. Updated. Preprint.