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Page 1
Single-cell integration reveals metaplasia in inflammatory gut diseases.
Oliver AJ, Huang N, Bartolome-Casado R, Li R, Koplev S, Nilsen HR, Moy M, Cakir B, Polanski K, Gudiño V, Melón-Ardanaz E, Sumanaweera D, Dimitrov D, Milchsack LM, FitzPatrick MEB, Provine NM, Boccacino JM, Dann E, Predeus AV, To K, Prete M, Chapman JA, Masi AC, Stephenson E, Engelbert J, Lobentanzer S, Perera S, Richardson L, Kapuge R, Wilbrey-Clark A, Semprich CI, Ellams S, Tudor C, Joseph P, Garrido-Trigo A, Corraliza AM, Oliver TRW, Hook CE, James KR, Mahbubani KT, Saeb-Parsy K, Zilbauer M, Saez-Rodriguez J, Høivik ML, Bækkevold ES, Stewart CJ, Berrington JE, Meyer KB, Klenerman P, Salas A, Haniffa M, Jahnsen FL, Elmentaite R, Teichmann SA. Oliver AJ, et al. Among authors: sumanaweera d. Nature. 2024 Nov;635(8039):699-707. doi: 10.1038/s41586-024-07571-1. Epub 2024 Nov 20. Nature. 2024. PMID: 39567783 Free PMC article.
A prenatal skin atlas reveals immune regulation of human skin morphogenesis.
Gopee NH, Winheim E, Olabi B, Admane C, Foster AR, Huang N, Botting RA, Torabi F, Sumanaweera D, Le AP, Kim J, Verger L, Stephenson E, Adão D, Ganier C, Gim KY, Serdy SA, Deakin C, Goh I, Steele L, Annusver K, Miah MU, Tun WM, Moghimi P, Kwakwa KA, Li T, Basurto Lozada D, Rumney B, Tudor CL, Roberts K, Chipampe NJ, Sidhpura K, Englebert J, Jardine L, Reynolds G, Rose A, Rowe V, Pritchard S, Mulas I, Fletcher J, Popescu DM, Poyner E, Dubois A, Guy A, Filby A, Lisgo S, Barker RA, Glass IA, Park JE, Vento-Tormo R, Nikolova MT, He P, Lawrence JEG, Moore J, Ballereau S, Hale CB, Shanmugiah V, Horsfall D, Rajan N, McGrath JA, O'Toole EA, Treutlein B, Bayraktar O, Kasper M, Progatzky F, Mazin P, Lee J, Gambardella L, Koehler KR, Teichmann SA, Haniffa M. Gopee NH, et al. Among authors: sumanaweera d. Nature. 2024 Nov;635(8039):679-689. doi: 10.1038/s41586-024-08002-x. Epub 2024 Oct 16. Nature. 2024. PMID: 39415002 Free PMC article.
Gene-level alignment of single-cell trajectories.
Sumanaweera D, Suo C, Cujba AM, Muraro D, Dann E, Polanski K, Steemers AS, Lee W, Oliver AJ, Park JE, Meyer KB, Dumitrascu B, Teichmann SA. Sumanaweera D, et al. Nat Methods. 2024 Sep 19. doi: 10.1038/s41592-024-02378-4. Online ahead of print. Nat Methods. 2024. PMID: 39300283
Author Correction: Human SARS-CoV-2 challenge uncovers local and systemic response dynamics.
Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L, Polanski K, Allen-Hyttinen J, Mehta P, Sumanaweera D, Boccacino JM, Sungnak W, Elmentaite R, Huang N, Mamanova L, Kapuge R, Bolt L, Prigmore E, Killingley B, Kalinova M, Mayer M, Boyers A, Mann A, Swadling L, Woodall MNJ, Ellis S, Smith CM, Teixeira VH, Janes SM, Chambers RC, Haniffa M, Catchpole A, Heyderman R, Noursadeghi M, Chain B, Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. Lindeboom RGH, et al. Among authors: sumanaweera d. Nature. 2024 Aug;632(8025):E3. doi: 10.1038/s41586-024-07838-7. Nature. 2024. PMID: 39090314 Free PMC article. No abstract available.
Human SARS-CoV-2 challenge uncovers local and systemic response dynamics.
Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L, Polanski K, Allen-Hyttinen J, Mehta P, Sumanaweera D, Boccacino JM, Sungnak W, Elmentaite R, Huang N, Mamanova L, Kapuge R, Bolt L, Prigmore E, Killingley B, Kalinova M, Mayer M, Boyers A, Mann A, Swadling L, Woodall MNJ, Ellis S, Smith CM, Teixeira VH, Janes SM, Chambers RC, Haniffa M, Catchpole A, Heyderman R, Noursadeghi M, Chain B, Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. Lindeboom RGH, et al. Among authors: sumanaweera d. Nature. 2024 Jul;631(8019):189-198. doi: 10.1038/s41586-024-07575-x. Epub 2024 Jun 19. Nature. 2024. PMID: 38898278 Free PMC article.
On the reliability and the limits of inference of amino acid sequence alignments.
Rajapaksa S, Sumanaweera D, Lesk AM, Allison L, Stuckey PJ, Garcia de la Banda M, Abramson D, Konagurthu AS. Rajapaksa S, et al. Among authors: sumanaweera d. Bioinformatics. 2022 Jun 24;38(Suppl 1):i255-i263. doi: 10.1093/bioinformatics/btac247. Bioinformatics. 2022. PMID: 35758808 Free PMC article.
Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.
Kueffner R, Zach N, Bronfeld M, Norel R, Atassi N, Balagurusamy V, Di Camillo B, Chio A, Cudkowicz M, Dillenberger D, Garcia-Garcia J, Hardiman O, Hoff B, Knight J, Leitner ML, Li G, Mangravite L, Norman T, Wang L; ALS Stratification Consortium; Xiao J, Fang WC, Peng J, Yang C, Chang HJ, Stolovitzky G. Kueffner R, et al. Sci Rep. 2019 Jan 24;9(1):690. doi: 10.1038/s41598-018-36873-4. Sci Rep. 2019. PMID: 30679616 Free PMC article.