VGsim: Scalable viral genealogy simulator for global pandemic.
Autorzy:
Shchur V; International laboratory of statistical and computational genomics, HSE University, Moscow, Russia. Spirin V; International laboratory of statistical and computational genomics, HSE University, Moscow, Russia. Sirotkin D; International laboratory of statistical and computational genomics, HSE University, Moscow, Russia. Burovski E; HSE University, Moscow, Russia. DeMaioN; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom. Corbett-Detig R; Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, California, United States of America.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2022 Aug 24; Vol. 18 (8), pp. e1010409. Date of Electronic Publication: 2022 Aug 24 (Print Publication: 2022).
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural
phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.
Autorzy:
DeMaioN; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. Boulton W; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. Weilguny L; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. Walker CR; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.; Department of Genetics, University of Cambridge, Cambridge, United Kingdom. Turakhia Y; Department of Electrical and Computer Engineering, University of California San Diego, San Diego, California, United States of America. Corbett-Detig R; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.; Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America. Goldman N; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2022 Apr 29; Vol. 18 (4), pp. e1010056. Date of Electronic Publication: 2022 Apr 29 (Print Publication: 2022).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
A phylogenetic approach for weighting genetic sequences.
Autorzy:
DeMaioN; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK. . Alekseyenko AV; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA. Coleman-Smith WJ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK. Pardi F; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.; LIRMM, University of Montpellier, CNRS, Montpellier, France. Suchard MA; Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, CA, USA. Tamuri AU; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.; Research IT Services, University College London, London, UK. Truszkowski J; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.; RBC Borealis AI, Waterloo, ON, Canada. Goldman N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2021 May 28; Vol. 22 (1), pp. 285. Date of Electronic Publication: 2021 May 28.
Short-range template switching in great ape genomes explored using pair hidden Markov models.
Autorzy:
Walker CR; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom.; Department of Genetics, University of Cambridge, Cambridge, United Kingdom. Scally A; Department of Genetics, University of Cambridge, Cambridge, United Kingdom. DeMaioN; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom. Goldman N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom.
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Źródło:
PLoS genetics [PLoS Genet] 2021 Mar 02; Vol. 17 (3), pp. e1009221. Date of Electronic Publication: 2021 Mar 02 (Print Publication: 2021).
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.
Autorzy:
Kalkauskas A; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. Perron U; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. Sun Y; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. Goldman N; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. Baele G; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium. Guindon S; Department of Computer Science, LIRMM, CNRS and Université de Montpellier, Montpellier, France. DeMaioN; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2021 Jan 06; Vol. 17 (1), pp. e1008561. Date of Electronic Publication: 2021 Jan 06 (Print Publication: 2021).
Turakhia Y; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America. DeMaioN; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom. Thornlow B; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America. Gozashti L; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America. Lanfear R; Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia. Walker CR; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom.; Department of Genetics, University of Cambridge, Cambridge, United Kingdom. Hinrichs AS; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America. Fernandes JD; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States of America. Borges R; Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria. Slodkowicz G; MRC Laboratory of Molecular Biology, Cambridge, United Kingdom. Weilguny L; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom. Haussler D; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States of America. Goldman N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom. Corbett-Detig R; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America.
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Źródło:
PLoS genetics [PLoS Genet] 2020 Nov 18; Vol. 16 (11), pp. e1009175. Date of Electronic Publication: 2020 Nov 18 (Print Publication: 2020).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
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