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Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data.
Sci Transl Med. 2023 Jan 25;15(680):eabn7979. doi: 10.1126/scitranslmed.abn7979. Epub 2023 Jan 25.
Sci Transl Med. 2023.
PMID: 36346321
Free PMC article.
Recent advances in inferring viral diversity from high-throughput sequencing data.
Posada-Cespedes S, Seifert D, Beerenwinkel N.
Posada-Cespedes S, et al.
Virus Res. 2017 Jul 15;239:17-32. doi: 10.1016/j.virusres.2016.09.016. Epub 2016 Sep 28.
Virus Res. 2017.
PMID: 27693290
Free article.
Review.
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Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020.
Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D; WHO European Region sequencing laboratories and GISAID EpiCoV group; WHO European Region sequencing laboratories and GISAID EpiCoV group*.
Alm E, et al.
Euro Surveill. 2020 Aug;25(32):2001410. doi: 10.2807/1560-7917.ES.2020.25.32.2001410.
Euro Surveill. 2020.
PMID: 32794443
Free PMC article.
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V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data.
Posada-Céspedes S, Seifert D, Topolsky I, Jablonski KP, Metzner KJ, Beerenwinkel N.
Posada-Céspedes S, et al.
Bioinformatics. 2021 Jul 19;37(12):1673-1680. doi: 10.1093/bioinformatics/btab015.
Bioinformatics. 2021.
PMID: 33471068
Free PMC article.
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Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C.
Posada-Céspedes S, Van Zyl G, Montazeri H, Kuipers J, Rhee SY, Kouyos R, Günthard HF, Beerenwinkel N.
Posada-Céspedes S, et al.
PLoS Comput Biol. 2021 Sep 7;17(9):e1008363. doi: 10.1371/journal.pcbi.1008363. eCollection 2021 Sep.
PLoS Comput Biol. 2021.
PMID: 34491984
Free PMC article.
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Global disparities in SARS-CoV-2 genomic surveillance.
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C; Bulgarian SARS-CoV-2 sequencing group; Communicable Diseases Genomics Network (Australia and New Zealand); COVID-19 Impact Project; Danish Covid-19 Genome Consortium; Fiocruz COVID-19 Genomic Surveillance Network; GISAID core curation team; Network for Genomic Surveillance in South Africa (NGS-SA); Swiss SARS-CoV-2 Sequencing Consortium; Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR.
Brito AF, et al.
Nat Commun. 2022 Nov 16;13(1):7003. doi: 10.1038/s41467-022-33713-y.
Nat Commun. 2022.
PMID: 36385137
Free PMC article.
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Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies.
Rollin J, Bester R, Brostaux Y, Caglayan K, De Jonghe K, Eichmeier A, Foucart Y, Haegeman A, Koloniuk I, Kominek P, Maree H, Onder S, Posada Céspedes S, Roumi V, Šafářová D, Schumpp O, Ulubas Serce C, Sõmera M, Tamisier L, Vainio E, van der Vlugt RA, Massart S.
Rollin J, et al. Among authors: posada cespedes s.
PeerJ. 2023 Aug 16;11:e15816. doi: 10.7717/peerj.15816. eCollection 2023.
PeerJ. 2023.
PMID: 37601254
Free PMC article.
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Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.
Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M.
Ibrahim B, et al. Among authors: posada cespedes s.
Viruses. 2018 May 14;10(5):256. doi: 10.3390/v10050256.
Viruses. 2018.
PMID: 29757994
Free PMC article.
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