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Year Number of Results
2015 1
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2020 3
2021 12
2022 5
2023 2
2024 1

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27 results

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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. Among authors: knyazev s. Genome Biol. 2021 Aug 26;22(1):249. doi: 10.1186/s13059-021-02443-7. Genome Biol. 2021. PMID: 34446078 Free PMC article. Review.
Repeat-aware evaluation of scaffolding tools.
Mandric I, Knyazev S, Zelikovsky A. Mandric I, et al. Among authors: knyazev s. Bioinformatics. 2018 Aug 1;34(15):2530-2537. doi: 10.1093/bioinformatics/bty131. Bioinformatics. 2018. PMID: 29547882 Free PMC article.
Unlocking capacities of genomics for the COVID-19 response and future pandemics.
Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Knyazev S, et al. Nat Methods. 2022 Apr;19(4):374-380. doi: 10.1038/s41592-022-01444-z. Nat Methods. 2022. PMID: 35396471 Free PMC article.
Using earth mover's distance for viral outbreak investigations.
Melnyk A, Knyazev S, Vannberg F, Bunimovich L, Skums P, Zelikovsky A. Melnyk A, et al. Among authors: knyazev s. BMC Genomics. 2020 Dec 16;21(Suppl 5):582. doi: 10.1186/s12864-020-06982-4. BMC Genomics. 2020. PMID: 33327932 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: knyazev s. Genome Biol. 2020 Mar 17;21(1):71. doi: 10.1186/s13059-020-01988-3. Genome Biol. 2020. PMID: 32183840 Free PMC article.
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.
Sonrel A, Luetge A, Soneson C, Mallona I, Germain PL, Knyazev S, Gilis J, Gerber R, Seurinck R, Paul D, Sonder E, Crowell HL, Fanaswala I, Al-Ajami A, Heidari E, Schmeing S, Milosavljevic S, Saeys Y, Mangul S, Robinson MD. Sonrel A, et al. Among authors: knyazev s. Genome Biol. 2023 May 17;24(1):119. doi: 10.1186/s13059-023-02962-5. Genome Biol. 2023. PMID: 37198712 Free PMC article.
27 results