Publications by authors named "Andrew Rambaut"

100Publications

The emergence of SARS-CoV-2 in Europe and North America.

Science 2020 Sep 10. Epub 2020 Sep 10.

KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium.

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http://dx.doi.org/10.1126/science.abc8169DOI Listing
September 2020

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic.

Nat Microbiol 2020 11 28;5(11):1408-1417. Epub 2020 Jul 28.

MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.

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http://dx.doi.org/10.1038/s41564-020-0771-4DOI Listing
November 2020

Evolution and epidemic spread of SARS-CoV-2 in Brazil.

Science 2020 09 23;369(6508):1255-1260. Epub 2020 Jul 23.

Department of Zoology, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1126/science.abd2161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402630PMC
September 2020

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.

Nat Microbiol 2020 11 15;5(11):1403-1407. Epub 2020 Jul 15.

Department of Zoology, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/s41564-020-0770-5DOI Listing
November 2020

The emergence of SARS-CoV-2 in Europe and the US.

bioRxiv 2020 May 23. Epub 2020 May 23.

KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium.

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http://dx.doi.org/10.1101/2020.05.21.109322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265688PMC
May 2020

Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics.

Mol Biol Evol 2020 Oct;37(10):3047-3060

Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA.

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http://dx.doi.org/10.1093/molbev/msaa130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7530611PMC
October 2020

The proximal origin of SARS-CoV-2.

Nat Med 2020 04;26(4):450-452

Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA.

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http://dx.doi.org/10.1038/s41591-020-0820-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095063PMC
April 2020

Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction.

Mol Biol Evol 2020 06;37(6):1832-1842

Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1093/molbev/msaa047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253210PMC
June 2020

High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE.

Methods Mol Biol 2019 ;1910:691-722

Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1007/978-1-4939-9074-0_23DOI Listing
January 2020

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates.

Mol Biol Evol 2019 08;36(8):1793-1803

Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium.

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https://academic.oup.com/mbe/advance-article/doi/10.1093/mol
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http://dx.doi.org/10.1093/molbev/msz094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657730PMC
August 2019

PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa.

Curr Opin HIV AIDS 2019 05;14(3):173-180

Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1097/COH.0000000000000542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629166PMC
May 2019

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.

Virus Evol 2019 Jan 8;5(1):vez003. Epub 2019 Mar 8.

Laboratory Clinical and Evolutionary Virology, Rega Institute for Medical Research - KU Leuven, Leuven, Belgium.

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https://academic.oup.com/ve/article/doi/10.1093/ve/vez003/53
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http://dx.doi.org/10.1093/ve/vez003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407609PMC
January 2019

Tracking virus outbreaks in the twenty-first century.

Nat Microbiol 2019 01 13;4(1):10-19. Epub 2018 Dec 13.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

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http://www.nature.com/articles/s41564-018-0296-2
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http://dx.doi.org/10.1038/s41564-018-0296-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345516PMC
January 2019

Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building.

Epidemics 2019 03 23;26:116-127. Epub 2018 Oct 23.

Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda MD, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S17554365183002
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http://dx.doi.org/10.1016/j.epidem.2018.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105018PMC
March 2019

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

Virus Evol 2018 Jan 8;4(1):vey016. Epub 2018 Jun 8.

Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, EH9 3FL UK.

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http://dx.doi.org/10.1093/ve/vey016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007674PMC
January 2018

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak.

Nat Commun 2018 06 8;9(1):2222. Epub 2018 Jun 8.

Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium.

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http://dx.doi.org/10.1038/s41467-018-03763-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993714PMC
June 2018

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.

Syst Biol 2018 09;67(5):901-904

Department of Human Genetics, University of California, Los Angeles, 695 Charles E. Young Dr., Los Angeles, CA 90095, USA.

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https://academic.oup.com/sysbio/article/67/5/901/4989127
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http://dx.doi.org/10.1093/sysbio/syy032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101584PMC
September 2018

MERS-CoV spillover at the camel-human interface.

Elife 2018 01 16;7. Epub 2018 Jan 16.

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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http://dx.doi.org/10.7554/eLife.31257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777824PMC
January 2018

Lorenzo-Redondo et al. reply.

Nature 2017 11;551(7681):E10

Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60011, USA.

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http://dx.doi.org/10.1038/nature24635DOI Listing
November 2017

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Nature 2017 06 24;546(7658):401-405. Epub 2017 May 24.

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature22400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536180PMC
June 2017

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Nature 2017 04 12;544(7650):309-315. Epub 2017 Apr 12.

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.

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http://dx.doi.org/10.1038/nature22040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712493PMC
April 2017

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.

Bioinformatics 2017 Jun;33(12):1798-1805

Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044345PMC
June 2017

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

Syst Biol 2017 01;66(1):e47-e65

Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1093/sysbio/syw054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837209PMC
January 2017

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.

Stat Med 2018 Jan 18;37(2):195-206. Epub 2017 Jan 18.

Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.

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http://dx.doi.org/10.1002/sim.7196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515700PMC
January 2018

Modelling the impact of co-circulating low pathogenic avian influenza viruses on epidemics of highly pathogenic avian influenza in poultry.

Epidemics 2016 12 19;17:27-34. Epub 2016 Oct 19.

Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. Electronic address:

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http://dx.doi.org/10.1016/j.epidem.2016.10.005DOI Listing
December 2016

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen).

Virus Evol 2016 Jan 9;2(1):vew007. Epub 2016 Apr 9.

Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

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http://dx.doi.org/10.1093/ve/vew007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989882PMC
January 2016

The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study.

Virus Evol 2016 Jan 2;2(1):vew003. Epub 2016 Mar 2.

Institute of Evolutionary Biology, University of Edinburgh EH9 3FL, Edinburgh, UK,; Centre for Immunity, Infection and Evolution, University of Edinburgh EH9 3FL, Edinburgh, UK and; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892-2220, USA.

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http://academic.oup.com/ve/article/doi/10.1093/vew003/175343
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http://dx.doi.org/10.1093/ve/vew003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989886PMC
January 2016

MERS-CoV recombination: implications about the reservoir and potential for adaptation.

Virus Evol 2016 Jan 20;2(1):vev023. Epub 2016 Jan 20.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK,; Centre for Immunology, Infection and Evolution at the University of Edinburgh, Edinburgh, UK and; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1093/ve/vev023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989901PMC
January 2016

The evolution of Ebola virus: Insights from the 2013-2016 epidemic.

Nature 2016 10;538(7624):193-200

The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, San Diego, California 92037, USA.

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http://dx.doi.org/10.1038/nature19790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580494PMC
October 2016

Comment on "Mutation rate and genotype variation of Ebola virus from Mali case sequences".

Science 2016 Aug 11;353(6300):658. Epub 2016 Aug 11.

The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA 92037, USA. Scripps Translational Science Institute, La Jolla, CA 92037, USA. Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.aaf3823DOI Listing
August 2016

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

Mol Biol Evol 2016 08 23;33(8):2167-9. Epub 2016 Apr 23.

Department of Microbiology and Immunology, KU Leuven - University of Leuven, Rega Institute, Leuven, Belgium.

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http://dx.doi.org/10.1093/molbev/msw082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398721PMC
August 2016

The effect of genetic structure on molecular dating and tests for temporal signal.

Methods Ecol Evol 2016 Jan 22;7(1):80-89. Epub 2015 Sep 22.

Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK.

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http://dx.doi.org/10.1111/2041-210X.12466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832290PMC
January 2016

Real-time, portable genome sequencing for Ebola surveillance.

Authors:
Joshua Quick Nicholas J Loman Sophie Duraffour Jared T Simpson Ettore Severi Lauren Cowley Joseph Akoi Bore Raymond Koundouno Gytis Dudas Amy Mikhail Nobila Ouédraogo Babak Afrough Amadou Bah Jonathan Hj Baum Beate Becker-Ziaja Jan-Peter Boettcher Mar Cabeza-Cabrerizo Alvaro Camino-Sanchez Lisa L Carter Juiliane Doerrbecker Theresa Enkirch Isabel Graciela García Dorival Nicole Hetzelt Julia Hinzmann Tobias Holm Liana Eleni Kafetzopoulou Michel Koropogui Abigail Kosgey Eeva Kuisma Christopher H Logue Antonio Mazzarelli Sarah Meisel Marc Mertens Janine Michel Didier Ngabo Katja Nitzsche Elisa Pallash Livia Victoria Patrono Jasmine Portmann Johanna Gabriella Repits Natasha Yasmin Rickett Andrea Sachse Katrin Singethan Inês Vitoriano Rahel L Yemanaberhan Elsa G Zekeng Racine Trina Alexander Bello Amadou Alpha Sall Ousmane Faye Oumar Faye N'Faly Magassouba Cecelia V Williams Victoria Amburgey Linda Winona Emily Davis Jon Gerlach Franck Washington Vanessa Monteil Marine Jourdain Marion Bererd Alimou Camara Hermann Somlare Abdoulaye Camara Marianne Gerard Guillaume Bado Bernard Baillet Déborah Delaune Koumpingnin Yacouba Nebie Abdoulaye Diarra Yacouba Savane Raymond Bernard Pallawo Giovanna Jaramillo Gutierrez Natacha Milhano Isabelle Roger Christopher J Williams Facinet Yattara Kuiama Lewandowski Jamie Taylor Philip Rachwal Daniel Turner Georgios Pollakis Julian A Hiscox David A Matthews Matthew K O'Shea Andrew McD Johnston Duncan Wilson Emma Hutley Erasmus Smit Antonino Di Caro Roman Woelfel Kilian Stoecker Erna Fleischmann Martin Gabriel Simon A Weller Lamine Koivogui Boubacar Diallo Sakoba Keita Andrew Rambaut Pierre Formenty Stephan Gunther Miles W Carroll

Nature 2016 Feb 3;530(7589):228-232. Epub 2016 Feb 3.

The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany.

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http://dx.doi.org/10.1038/nature16996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817224PMC
February 2016

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.

PLoS Comput Biol 2015 Dec 30;11(12):e1004613. Epub 2015 Dec 30.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701012PMC
December 2015

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management.

Sci Transl Med 2015 Sep;7(307):307rv5

Wellcome Trust Sanger Institute, Cambridge CB10 1RQ, UK. Division of Infection & Immunity, University College London, London WC1E 6BT, UK.

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http://dx.doi.org/10.1126/scitranslmed.aab0191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819730PMC
September 2015

Relationship between haemagglutination inhibition titre and immunity to influenza in ferrets.

Vaccine 2015 Oct 3;33(41):5380-5385. Epub 2015 Sep 3.

Institute of Evolutionary Biology, University of Edinburgh, UK; Fogarty International Center, National Institute of Health, Bethesda, MD, USA; Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.

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http://dx.doi.org/10.1016/j.vaccine.2015.08.065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582772PMC
October 2015

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Cell 2015 Jun;161(7):1516-26

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503805PMC
June 2015

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.

Authors:
Miles W Carroll David A Matthews Julian A Hiscox Michael J Elmore Georgios Pollakis Andrew Rambaut Roger Hewson Isabel García-Dorival Joseph Akoi Bore Raymond Koundouno Saïd Abdellati Babak Afrough John Aiyepada Patience Akhilomen Danny Asogun Barry Atkinson Marlis Badusche Amadou Bah Simon Bate Jan Baumann Dirk Becker Beate Becker-Ziaja Anne Bocquin Benny Borremans Andrew Bosworth Jan Peter Boettcher Angela Cannas Fabrizio Carletti Concetta Castilletti Simon Clark Francesca Colavita Sandra Diederich Adomeh Donatus Sophie Duraffour Deborah Ehichioya Heinz Ellerbrok Maria Dolores Fernandez-Garcia Alexandra Fizet Erna Fleischmann Sophie Gryseels Antje Hermelink Julia Hinzmann Ute Hopf-Guevara Yemisi Ighodalo Lisa Jameson Anne Kelterbaum Zoltan Kis Stefan Kloth Claudia Kohl Miša Korva Annette Kraus Eeva Kuisma Andreas Kurth Britta Liedigk Christopher H Logue Anja Lüdtke Piet Maes James McCowen Stéphane Mély Marc Mertens Silvia Meschi Benjamin Meyer Janine Michel Peter Molkenthin César Muñoz-Fontela Doreen Muth Edmund N C Newman Didier Ngabo Lisa Oestereich Jennifer Okosun Thomas Olokor Racheal Omiunu Emmanuel Omomoh Elisa Pallasch Bernadett Pályi Jasmine Portmann Thomas Pottage Catherine Pratt Simone Priesnitz Serena Quartu Julie Rappe Johanna Repits Martin Richter Martin Rudolf Andreas Sachse Kristina Maria Schmidt Gordian Schudt Thomas Strecker Ruth Thom Stephen Thomas Ekaete Tobin Howard Tolley Jochen Trautner Tine Vermoesen Inês Vitoriano Matthias Wagner Svenja Wolff Constanze Yue Maria Rosaria Capobianchi Birte Kretschmer Yper Hall John G Kenny Natasha Y Rickett Gytis Dudas Cordelia E M Coltart Romy Kerber Damien Steer Callum Wright Francis Senyah Sakoba Keita Patrick Drury Boubacar Diallo Hilde de Clerck Michel Van Herp Armand Sprecher Alexis Traore Mandiou Diakite Mandy Kader Konde Lamine Koivogui N'Faly Magassouba Tatjana Avšič-Županc Andreas Nitsche Marc Strasser Giuseppe Ippolito Stephan Becker Kilian Stoecker Martin Gabriel Hervé Raoul Antonino Di Caro Roman Wölfel Pierre Formenty Stephan Günther

Nature 2015 Aug 17;524(7563):97-101. Epub 2015 Jun 17.

1] The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany [2] Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany [3] German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany.

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http://dx.doi.org/10.1038/nature14594DOI Listing
August 2015

Global migration of influenza A viruses in swine.

Nat Commun 2015 Mar 27;6:6696. Epub 2015 Mar 27.

Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1038/ncomms7696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380236PMC
March 2015

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution.

Methods Ecol Evol 2015 Jan;6(1):67-82

Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-1766, USA ; Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095-1766, USA.

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http://dx.doi.org/10.1111/2041-210X.12293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358766PMC
January 2015

Real-time digital pathogen surveillance - the time is now.

Genome Biol 2015 07 30;16(1):155. Epub 2015 Jul 30.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 2FL, UK.

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http://dx.doi.org/10.1186/s13059-015-0726-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531805PMC
July 2015

Reassortment between influenza B lineages and the emergence of a coadapted PB1-PB2-HA gene complex.

Mol Biol Evol 2015 Jan 15;32(1):162-72. Epub 2014 Oct 15.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom Fogarty International Center, National Institutes of Health, Bethesda, MD Centre for Immunology, Infection and Evolution at the University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msu287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271528PMC
January 2015

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.

Science 2014 10 2;346(6205):56-61. Epub 2014 Oct 2.

KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium.

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http://dx.doi.org/10.1126/science.1256739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254776PMC
October 2014

Possible footprints of APOBEC3F and/or other APOBEC3 deaminases, but not APOBEC3G, on HIV-1 from patients with acute/early and chronic infections.

J Virol 2014 Nov 27;88(21):12882-94. Epub 2014 Aug 27.

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom

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http://dx.doi.org/10.1128/JVI.01460-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248940PMC
November 2014

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.

BMC Bioinformatics 2014 May 7;15:133. Epub 2014 May 7.

Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1186/1471-2105-15-133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020384PMC
May 2014

Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus.

Proc Natl Acad Sci U S A 2014 Jun 28;111(22):8107-12. Epub 2014 Apr 28.

Institute of Evolutionary Biology andCentre for Infection, Immunity, and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom; andFogarty International Center, National Institutes of Health, Bethesda, MD 20892.

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http://dx.doi.org/10.1073/pnas.1324197111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050607PMC
June 2014

BEAST 2: a software platform for Bayesian evolutionary analysis.

PLoS Comput Biol 2014 Apr 10;10(4):e1003537. Epub 2014 Apr 10.

Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand; Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand.

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http://dx.doi.org/10.1371/journal.pcbi.1003537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985171PMC
April 2014

Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.

Syst Biol 2014 Jul 12;63(4):493-504. Epub 2014 Mar 12.

Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA;Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.

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http://dx.doi.org/10.1093/sysbio/syu015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055869PMC
July 2014

Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2.

PLoS Pathog 2014 Feb 20;10(2):e1003932. Epub 2014 Feb 20.

Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America ; Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1003932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930559PMC
February 2014

A synchronized global sweep of the internal genes of modern avian influenza virus.

Nature 2014 Apr 16;508(7495):254-7. Epub 2014 Feb 16.

1] Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK [2] Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1038/nature13016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098125PMC
April 2014

Integrating influenza antigenic dynamics with molecular evolution.

Elife 2014 4;3:e01914. Epub 2014 Feb 4.

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.7554/eLife.01914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3909918PMC
November 2015

Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility.

Lancet Infect Dis 2014 Jan 13;14(1):50-56. Epub 2013 Nov 13.

MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK. Electronic address:

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http://dx.doi.org/10.1016/S1473-3099(13)70304-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895322PMC
January 2014

Multiple introductions of salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture.

J Gen Virol 2014 Jan 23;95(Pt 1):52-59. Epub 2013 Sep 23.

University of Edinburgh, Edinburgh, UK.

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http://dx.doi.org/10.1099/vir.0.057455-0DOI Listing
January 2014

Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus.

mBio 2013 Aug 13;4(4). Epub 2013 Aug 13.

The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, United Kingdom.

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http://dx.doi.org/10.1128/mBio.00356-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747577PMC
August 2013

Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.

Philos Trans R Soc Lond B Biol Sci 2013 Mar 4;368(1614):20120196. Epub 2013 Feb 4.

Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1098/rstb.2012.0196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678322PMC
March 2013

Estimating the rate of intersubtype recombination in early HIV-1 group M strains.

J Virol 2013 Feb 12;87(4):1967-73. Epub 2012 Dec 12.

University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1128/JVI.02478-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571495PMC
February 2013

Relaxed phylogenetics and the palaeoptera problem: resolving deep ancestral splits in the insect phylogeny.

Syst Biol 2013 Mar 5;62(2):285-97. Epub 2012 Dec 5.

Department of Biology, University of York, York YO10 5DD, UK.

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https://academic.oup.com/sysbio/article/62/2/285/1670647
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http://dx.doi.org/10.1093/sysbio/sys093DOI Listing
March 2013