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Page 1
Systematic benchmarking of omics computational tools.
Mangul S, Martin LS, Hill BL, Lam AK, Distler MG, Zelikovsky A, Eskin E, Flint J. Mangul S, et al. Nat Commun. 2019 Mar 27;10(1):1393. doi: 10.1038/s41467-019-09406-4. Nat Commun. 2019. PMID: 30918265 Free PMC article. Review.
Eleven grand challenges in single-cell data science.
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowska A, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Lähnemann D, et al. Genome Biol. 2020 Feb 7;21(1):31. doi: 10.1186/s13059-020-1926-6. Genome Biol. 2020. PMID: 32033589 Free PMC article. Review.
Repeat-aware evaluation of scaffolding tools.
Mandric I, Knyazev S, Zelikovsky A. Mandric I, et al. Bioinformatics. 2018 Aug 1;34(15):2530-2537. doi: 10.1093/bioinformatics/bty131. Bioinformatics. 2018. PMID: 29547882 Free PMC article.
Technology dictates algorithms: recent developments in read alignment.
Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal PI, Yang HT, Xue V, Knyazev S, Singer BD, Balliu B, Koslicki D, Skums P, Zelikovsky A, Alkan C, Mutlu O, Mangul S. Alser M, et al. Genome Biol. 2021 Aug 26;22(1):249. doi: 10.1186/s13059-021-02443-7. Genome Biol. 2021. PMID: 34446078 Free PMC article. Review.
Unlocking capacities of viral genomics for the COVID-19 pandemic response.
Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Knyazev S, et al. ArXiv [Preprint]. 2021 Apr 28:arXiv:2104.14005v3. ArXiv. 2021. Update in: Nat Methods. 2022 Apr;19(4):374-380. doi: 10.1038/s41592-022-01444-z. PMID: 33948451 Free PMC article. Updated. Preprint.
Automated quality control for a molecular surveillance system.
Sims S, Longmire AG, Campo DS, Ramachandran S, Medrzycki M, Ganova-Raeva L, Lin Y, Sue A, Thai H, Zelikovsky A, Khudyakov Y. Sims S, et al. BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):358. doi: 10.1186/s12859-018-2329-5. BMC Bioinformatics. 2018. PMID: 30343674 Free PMC article.
44 results