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Page 1
Enhanced Feature Selection for Microbiome Data using FLORAL: Scalable Log-ratio Lasso Regression.
Fei T, Funnell T, Waters NR, Raj SS, Sadeghi K, Dai A, Miltiadous O, Shouval R, Lv M, Peled JU, Ponce DM, Perales MA, Gönen M, van den Brink MRM. Fei T, et al. Among authors: waters nr. bioRxiv [Preprint]. 2023 Dec 18:2023.05.02.538599. doi: 10.1101/2023.05.02.538599. bioRxiv. 2023. Update in: Cell Rep Methods. 2024 Nov 18;4(11):100899. doi: 10.1016/j.crmeth.2024.100899 PMID: 37205350 Free PMC article. Updated. Preprint.
Early intestinal microbial features are associated with CD4 T-cell recovery after allogeneic hematopoietic transplant.
Miltiadous O, Waters NR, Andrlová H, Dai A, Nguyen CL, Burgos da Silva M, Lindner S, Slingerland J, Giardina P, Clurman A, Armijo GK, Gomes ALC, Lakkaraja M, Maslak P, Scordo M, Shouval R, Staffas A, O'Reilly R, Taur Y, Prockop S, Boelens JJ, Giralt S, Perales MA, Devlin SM, Peled JU, Markey KA, van den Brink MRM. Miltiadous O, et al. Among authors: waters nr. Blood. 2022 May 5;139(18):2758-2769. doi: 10.1182/blood.2021014255. Blood. 2022. PMID: 35061893 Free PMC article.
Mitigation of gastrointestinal graft-versus-host disease with tocilizumab prophylaxis is accompanied by preservation of microbial diversity and attenuation of enterococcal domination.
Chhabra S, Szabo A, Clurman A, McShane K, Waters N, Eastwood D, Samanas L, Fei T, Armijo G, Abedin S, Longo W, Hari P, Hamadani M, Shah NN, Runaas L, Jerkins JH, Van den Brink M, Peled JU, Drobyski WR. Chhabra S, et al. Haematologica. 2023 Jan 1;108(1):250-256. doi: 10.3324/haematol.2022.281309. Haematologica. 2023. PMID: 36106394 Free PMC article. No abstract available.
Conditioning Regimens are Associated with Distinct Patterns of Microbiota Injury in Allogeneic Hematopoietic Cell Transplantation.
Shouval R, Waters NR, Gomes ALC, Zuanelli Brambilla C, Fei T, Devlin SM, Nguyen CL, Markey KA, Dai A, Slingerland JB, Clurman AG, Fontana E, Amoretti LA, Wright RJ, Hohl TM, Taur Y, Sung AD, Weber D, Hashimoto D, Teshima T, Chao NJ, Holler E, Scordo M, Giralt SA, Perales MA, Peled JU, van den Brink MRM. Shouval R, et al. Among authors: waters nr. Clin Cancer Res. 2023 Jan 4;29(1):165-173. doi: 10.1158/1078-0432.CCR-22-1254. Clin Cancer Res. 2023. PMID: 36322005 Free PMC article.
Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse.
DeWolf S, Elhanati Y, Nichols K, Waters NR, Nguyen CL, Slingerland JB, Rodriguez N, Lyudovyk O, Giardina PA, Kousa AI, Andrlová H, Ceglia N, Fei T, Kappagantula R, Li Y, Aleynick N, Baez P, Murali R, Hayashi A, Lee N, Gipson B, Rangesa M, Katsamakis Z, Dai A, Blouin AG, Arcila M, Masilionis I, Chaligne R, Ponce DM, Landau HJ, Politikos I, Tamari R, Hanash AM, Jenq RR, Giralt SA, Markey KA, Zhang Y, Perales MA, Socci ND, Greenbaum BD, Iacobuzio-Donahue CA, Hollmann TJ, van den Brink MRM, Peled JU. DeWolf S, et al. Among authors: waters nr. Sci Transl Med. 2023 Jul 26;15(706):eabq0476. doi: 10.1126/scitranslmed.abq0476. Epub 2023 Jul 26. Sci Transl Med. 2023. PMID: 37494469 Free PMC article.
Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation.
Elkrief A, Waters NR, Smith N, Dai A, Slingerland J, Aleynick N, Febles B, Gogia P, Socci ND, Lumish M, Giardina PA, Chaft JE, Eng J, Motzer RJ, Mendelsohn RB, Markey KA, Zhuang M, Li Y, Yang Z, Hollmann TJ, Rudin CM, van den Brink MRM, Shia J, DeWolf S, Schoenfeld AJ, Hellmann MD, Babady NE, Faleck DM, Peled JU. Elkrief A, et al. Among authors: waters nr. Cancer Immunol Res. 2024 Mar 4;12(3):308-321. doi: 10.1158/2326-6066.CIR-23-0498. Cancer Immunol Res. 2024. PMID: 38108398 Free PMC article.
Altered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease.
Lindner S, Miltiadous O, Ramos RJF, Paredes J, Kousa AI, Dai A, Fei T, Lauder E, Frame J, Waters NR, Sadeghi K, Armijo GK, Ghale R, Victor K, Gipson B, Monette S, Russo MV, Nguyen CL, Slingerland J, Taur Y, Markey KA, Andrlova H, Giralt S, Perales MA, Reddy P, Peled JU, Smith M, Cross JR, Burgos da Silva M, Campbell C, van den Brink MRM. Lindner S, et al. Among authors: waters nr. Nat Microbiol. 2024 Mar;9(3):614-630. doi: 10.1038/s41564-024-01617-w. Epub 2024 Mar 1. Nat Microbiol. 2024. PMID: 38429422 Free PMC article.
Sugar-rich foods exacerbate antibiotic-induced microbiome injury.
Dai A, Adintori PA, Funnell T, Jogia WP, Fei T, Waters NR, Rangesa M, Ballweg A, Gipson B, Raj S, Hayase E, Markey KA, Burgos da Silva M, Miltiadous O, Brambilla CZ, Buchan ML, Peets T, Gradissimo A, Smith N, Katsamakis Z, Warren A, Amoretti LA, Duan C, Zhang C, Matheis F, Sullivan AP, Slingerland JB, Clurman A, Brereton DG, Giardina PA, Gomes ALC, Johnson AJ, Knights D, Jenq RR, Perales MA, Giralt SA, Schluter J, van den Brink MRM, Peled J. Dai A, et al. Among authors: waters nr. bioRxiv [Preprint]. 2024 Oct 14:2024.10.14.617881. doi: 10.1101/2024.10.14.617881. bioRxiv. 2024. PMID: 39463943 Free PMC article. Preprint.
Scalable log-ratio lasso regression for enhanced microbial feature selection with FLORAL.
Fei T, Funnell T, Waters NR, Raj SS, Baichoo M, Sadeghi K, Dai A, Miltiadous O, Shouval R, Lv M, Peled JU, Ponce DM, Perales MA, Gönen M, van den Brink MRM. Fei T, et al. Among authors: waters nr. Cell Rep Methods. 2024 Nov 18;4(11):100899. doi: 10.1016/j.crmeth.2024.100899. Epub 2024 Nov 7. Cell Rep Methods. 2024. PMID: 39515336 Free PMC article.
13 results