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Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Mavian C, et al. Among authors: stamatakis a. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381734 Free PMC article. No abstract available.
Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult.
Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki EG, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A. Morel B, et al. Among authors: stamatakis a. Mol Biol Evol. 2021 May 4;38(5):1777-1791. doi: 10.1093/molbev/msaa314. Mol Biol Evol. 2021. PMID: 33316067 Free PMC article.
Want to track pandemic variants faster? Fix the bioinformatics bottleneck.
Hodcroft EB, De Maio N, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C. Hodcroft EB, et al. Among authors: stamatakis a. Nature. 2021 Mar;591(7848):30-33. doi: 10.1038/d41586-021-00525-x. Nature. 2021. PMID: 33649511 No abstract available.
The phylogenetic likelihood library.
Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A. Flouri T, et al. Among authors: stamatakis a. Syst Biol. 2015 Mar;64(2):356-62. doi: 10.1093/sysbio/syu084. Epub 2014 Oct 30. Syst Biol. 2015. PMID: 25358969 Free PMC article.
Two C++ libraries for counting trees on a phylogenetic terrace.
Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A. Biczok R, et al. Among authors: stamatakis a. Bioinformatics. 2018 Oct 1;34(19):3399-3401. doi: 10.1093/bioinformatics/bty384. Bioinformatics. 2018. PMID: 29746618 Free PMC article.
217 results