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Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.
Microb Genom. 2024 May;10(5). doi: 10.1099/mgen.0.001249.
Microb Genom. 2024.
PMID: 38785221
Free article.
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.
Skums P, Mohebbi F, Tsyvina V, Baykal PI, Nemira A, Ramachandran S, Khudyakov Y.
Skums P, et al. Among authors: baykal pi.
Cell Syst. 2022 Oct 19;13(10):844-856.e4. doi: 10.1016/j.cels.2022.07.005.
Cell Syst. 2022.
PMID: 36265470
Free PMC article.
Item in Clipboard
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. Among authors: baykal pi.
Nat Methods. 2022 Apr;19(4):374-380. doi: 10.1038/s41592-022-01444-z.
Nat Methods. 2022.
PMID: 35396471
Free PMC article.
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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: baykal pi.
Genome Biol. 2021 Aug 26;22(1):249. doi: 10.1186/s13059-021-02443-7.
Genome Biol. 2021.
PMID: 34446078
Free PMC article.
Review.
Item in Clipboard
Analysis of heterogeneous genomic samples using image normalization and machine learning.
Basodi S, Baykal PI, Zelikovsky A, Skums P, Pan Y.
Basodi S, et al. Among authors: baykal pi.
BMC Genomics. 2020 Dec 21;21(Suppl 6):405. doi: 10.1186/s12864-020-6661-6.
BMC Genomics. 2020.
PMID: 33349236
Free PMC article.
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Global transmission network of SARS-CoV-2: from outbreak to pandemic.
Skums P, Kirpich A, Baykal PI, Zelikovsky A, Chowell G.
Skums P, et al. Among authors: baykal pi.
medRxiv [Preprint]. 2020 Mar 27:2020.03.22.20041145. doi: 10.1101/2020.03.22.20041145.
medRxiv. 2020.
PMID: 32511620
Free PMC article.
Preprint.
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