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Packaging and containerization of computational methods.
Alser M, Lawlor B, Abdill RJ, Waymost S, Ayyala R, Rajkumar N, LaPierre N, Brito J, Ribeiro-Dos-Santos AM, Almadhoun N, Sarwal V, Firtina C, Osinski T, Eskin E, Hu Q, Strong D, Kim BBD, Abedalthagafi MS, Mutlu O, Mangul S. Alser M, et al. Among authors: brito j. Nat Protoc. 2024 Sep;19(9):2529-2539. doi: 10.1038/s41596-024-00986-0. Epub 2024 Apr 2. Nat Protoc. 2024. PMID: 38565959 Review.
Challenges and recommendations to improve the installability and archival stability of omics computational tools.
Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AK, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R. Mangul S, et al. Among authors: brito j. PLoS Biol. 2019 Jun 20;17(6):e3000333. doi: 10.1371/journal.pbio.3000333. eCollection 2019 Jun. PLoS Biol. 2019. PMID: 31220077 Free PMC article.
Benchmarking of computational error-correction methods for next-generation sequencing data.
Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, Littman E, Shabani T, Enik G, Yao D, Sun R, Schroeder J, Eskin E, Zelikovsky A, Skums P, Pop M, Mangul S. Mitchell K, et al. Among authors: brito jj. Genome Biol. 2020 Mar 17;21(1):71. doi: 10.1186/s13059-020-01988-3. Genome Biol. 2020. PMID: 32183840 Free PMC article.
Critical Assessment of Metagenome Interpretation: the second round of challenges.
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Meyer F, et al. Among authors: brito jj. Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8. Nat Methods. 2022. PMID: 35396482 Free PMC article.
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing.
Peng K, Nowicki TS, Campbell K, Vahed M, Peng D, Meng Y, Nagareddy A, Huang YN, Karlsberg A, Miller Z, Brito J, Nadel B, Pak VM, Abedalthagafi MS, Burkhardt AM, Alachkar H, Ribas A, Mangul S. Peng K, et al. Among authors: brito j. Brief Bioinform. 2023 Jul 20;24(4):bbad220. doi: 10.1093/bib/bbad220. Brief Bioinform. 2023. PMID: 37291798 Free PMC article.
1,330 results