Publications by authors named "Marc A Suchard"

100Publications

Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework.

Wellcome Open Res 2020 30;5:53. Epub 2020 Mar 30.

Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, 695 Charles E. Young Drive, Los Angeles, California, 90095-1766, USA.

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http://dx.doi.org/10.12688/wellcomeopenres.15770.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463299PMC
March 2020

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

Principles of Large-scale Evidence Generation and Evaluation across a Network of Databases (LEGEND).

J Am Med Inform Assoc 2020 Aug;27(8):1331-1337

Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA.

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http://dx.doi.org/10.1093/jamia/ocaa103DOI Listing
August 2020

Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study.

Lancet Rheumatol 2020 Aug 21. Epub 2020 Aug 21.

Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1016/S2665-9913(20)30276-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7442425PMC
August 2020

Large-scale evidence generation and evaluation across a network of databases (LEGEND): assessing validity using hypertension as a case study.

J Am Med Inform Assoc 2020 Aug;27(8):1268-1277

Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, USA.

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http://dx.doi.org/10.1093/jamia/ocaa124DOI Listing
August 2020

Relaxed Random Walks at Scale.

Syst Biol 2020 Jul 20. Epub 2020 Jul 20.

Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, United States.

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http://dx.doi.org/10.1093/sysbio/syaa056DOI Listing
July 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 May 27. Epub 2020 May 27.

Department of Biomathematics, David Geffen School of Medicine.

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http://dx.doi.org/10.1093/molbev/msaa130DOI Listing
May 2020

Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST.

Syst Biol 2020 May 16. Epub 2020 May 16.

Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, United States.

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http://dx.doi.org/10.1093/sysbio/syaa037DOI Listing
May 2020

Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus.

Mol Biol Evol 2020 09;37(9):2641-2654

MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.

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http://dx.doi.org/10.1093/molbev/msaa117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454817PMC
September 2020

COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives.

Trends Mol Med 2020 05 21;26(5):483-495. Epub 2020 Mar 21.

MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China. Electronic address:

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http://dx.doi.org/10.1016/j.molmed.2020.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118693PMC
May 2020

Assessing the role of live poultry trade in community-structured transmission of avian influenza in China.

Proc Natl Acad Sci U S A 2020 03 2;117(11):5949-5954. Epub 2020 Mar 2.

State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, 100875 Beijing, China;

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http://dx.doi.org/10.1073/pnas.1906954117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7084072PMC
March 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

In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography.

Viruses 2020 02 5;12(2). Epub 2020 Feb 5.

Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium.

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http://dx.doi.org/10.3390/v12020182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077180PMC
February 2020

A surrogate ℓ sparse Cox's regression with applications to sparse high-dimensional massive sample size time-to-event data.

Stat Med 2020 03 8;39(6):675-686. Epub 2019 Dec 8.

Department of Preventive Medicine, University of Southern California, Los Angeles, California.

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http://dx.doi.org/10.1002/sim.8438DOI Listing
March 2020

On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model.

J Math Biol 2020 03 21;80(4):1119-1138. Epub 2019 Nov 21.

Departments of Biomathematics, Biostatistics and Human Genetics, University of California, Los Angeles, USA.

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http://dx.doi.org/10.1007/s00285-019-01453-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7033008PMC
March 2020

Divergence dating using mixed effects clock modelling: An application to HIV-1.

Virus Evol 2019 Jul 5;5(2):vez036. Epub 2019 Sep 5.

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

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http://dx.doi.org/10.1093/ve/vez036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6830409PMC
July 2019

Comprehensive comparative effectiveness and safety of first-line antihypertensive drug classes: a systematic, multinational, large-scale analysis.

Lancet 2019 11 24;394(10211):1816-1826. Epub 2019 Oct 24.

Epidemiology Analytics, Janssen Research & Development, Titusville, NJ, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA.

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http://dx.doi.org/10.1016/S0140-6736(19)32317-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924620PMC
November 2019

Comparison of First-Line Dual Combination Treatments in Hypertension: Real-World Evidence from Multinational Heterogeneous Cohorts.

Korean Circ J 2020 Jan 28;50(1):52-68. Epub 2019 Aug 28.

Division of Cardiology, Severance Cardiovascular Hospital and Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea.

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http://dx.doi.org/10.4070/kcj.2019.0173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923236PMC
January 2020

A plea to stop using the case-control design in retrospective database studies.

Stat Med 2019 09 22;38(22):4199-4208. Epub 2019 Aug 22.

Observational Health Data Sciences and Informatics, New York, New York.

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http://dx.doi.org/10.1002/sim.8215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771795PMC
September 2019

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

Comment on "How pharmacoepidemiology networks can manage distributed analyses to improve replicability and transparency and minimize bias".

Pharmacoepidemiol Drug Saf 2019 07 8;28(7):1032-1033. Epub 2019 May 8.

Observational Health Data Sciences and Informatics, New York, NY.

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http://dx.doi.org/10.1002/pds.4798DOI Listing
July 2019

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

Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography.

Virus Evol 2019 Jan 28;5(1):vey043. Epub 2019 Feb 28.

Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA.

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http://dx.doi.org/10.1093/ve/vey043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395475PMC
January 2019

Consistency and convergence rate of phylogenetic inference via regularization.

Ann Stat 2018 Aug 27;46(4):1481-1512. Epub 2018 Jun 27.

Program in Computational Biology Fred Hutchinson Cancer Research Center.

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http://dx.doi.org/10.1214/17-AOS1592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191858PMC
August 2018

Recent advances in computational phylodynamics.

Curr Opin Virol 2018 08 22;31:24-32. Epub 2018 Sep 22.

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

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http://dx.doi.org/10.1016/j.coviro.2018.08.009DOI Listing
August 2018

Improving reproducibility by using high-throughput observational studies with empirical calibration.

Philos Trans A Math Phys Eng Sci 2018 Sep;376(2128)

Observational Health Data Sciences and Informatics (OHDSI), New York, NY 10032, USA.

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http://rsta.royalsocietypublishing.org/lookup/doi/10.1098/rs
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http://dx.doi.org/10.1098/rsta.2017.0356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107542PMC
September 2018

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

Computational methods for birth-death processes.

Wiley Interdiscip Rev Comput Stat 2018 Mar-Apr;10(2). Epub 2018 Jan 2.

Departments of Biomathematics, Biostatistics and Human Genetics, University of California, Los Angeles.

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http://dx.doi.org/10.1002/wics.1423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6014701PMC
January 2018

Evaluating large-scale propensity score performance through real-world and synthetic data experiments.

Int J Epidemiol 2018 12;47(6):2005-2014

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

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http://dx.doi.org/10.1093/ije/dyy120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280944PMC
December 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

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.

Virus Evol 2017 Jul 6;3(2):vex028. Epub 2017 Oct 6.

Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.

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https://academic.oup.com/ve/article/doi/10.1093/ve/vex028/43
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http://dx.doi.org/10.1093/ve/vex028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5632516PMC
July 2017

Phylogenetic Factor Analysis.

Syst Biol 2018 May;67(3):384-399

Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, 650 Charles E. Young Dr. South Los Angeles, CA 90095-1772, USA.

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http://dx.doi.org/10.1093/sysbio/syx066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920329PMC
May 2018

Birth/birth-death processes and their computable transition probabilities with biological applications.

J Math Biol 2018 03 24;76(4):911-944. Epub 2017 Jul 24.

Departments of Biomathematics, Biostatistics and Human Genetics, University of California, Los Angeles, Los Angeles, WA, USA.

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http://dx.doi.org/10.1007/s00285-017-1160-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5783825PMC
March 2018

Hierarchical Models for Multiple, Rare Outcomes Using Massive Observational Healthcare Databases.

Stat Anal Data Min 2016 Aug 17;9(4):260-268. Epub 2016 Jul 17.

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/sam.11324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423675PMC
August 2016

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

Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation.

Microb Genom 2016 06 24;2(6):e000057. Epub 2016 Jun 24.

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

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http://dx.doi.org/10.1099/mgen.0.000057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320644PMC
June 2016

The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia.

Sci Rep 2017 03 21;7:44947. Epub 2017 Mar 21.

KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium.

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http://dx.doi.org/10.1038/srep44947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359580PMC
March 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 phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.

PLoS Comput Biol 2017 02 7;13(2):e1005389. Epub 2017 Feb 7.

Department of Biomedical Informatics, Arizona State University, Tempe, Arizona, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321473PMC
February 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

A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution.

Syst Biol 2017 05;66(3):299-319

Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/sysbio/syw093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075548PMC
May 2017

Identifying predictors of time-inhomogeneous viral evolutionary processes.

Virus Evol 2016 Jul 6;2(2):vew023. Epub 2016 Sep 6.

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

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http://dx.doi.org/10.1093/ve/vew023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072463PMC
July 2016

Host ecology determines the dispersal patterns of a plant virus.

Virus Evol 2015 16;1(1):vev016. Epub 2015 Dec 16.

Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium.

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http://dx.doi.org/10.1093/ve/vev016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014491PMC
December 2015

Robust empirical calibration of p-values using observational data.

Stat Med 2016 09;35(22):3883-8

Department of Biomathematics and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, U.S.A.

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http://dx.doi.org/10.1002/sim.6977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5108459PMC
September 2016

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates.

Syst Biol 2016 Nov 1;65(6):1041-1056. Epub 2016 Jul 1.

Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/sysbio/syw050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066065PMC
November 2016

Characterizing treatment pathways at scale using the OHDSI network.

Proc Natl Acad Sci U S A 2016 07 6;113(27):7329-36. Epub 2016 Jun 6.

Observational Health Data Sciences and Informatics, New York, NY 10032; Department of Statistics, Columbia University, New York, NY 10027.

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http://dx.doi.org/10.1073/pnas.1510502113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941483PMC
July 2016

Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada.

Proc Natl Acad Sci U S A 2016 07 6;113(29):8057-63. Epub 2016 Jun 6.

Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064; University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064

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http://dx.doi.org/10.1073/pnas.1601077113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961175PMC
July 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

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.

PLoS Comput Biol 2016 Mar 3;12(3):e1004789. Epub 2016 Mar 3.

Department of Statistics, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777449PMC
March 2016

Pioglitazone Use and Risk of Bladder Cancer.

JAMA 2015 Dec;314(23):2567-8

Department of Biomathematics, University of California, Los Angeles.

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http://dx.doi.org/10.1001/jama.2015.13912DOI Listing
December 2015

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty.

Syst Biol 2016 Mar 1;65(2):250-64. Epub 2015 Nov 1.

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

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http://dx.doi.org/10.1093/sysbio/syv083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009437PMC
March 2016

SEX, LIES AND SELF-REPORTED COUNTS: BAYESIAN MIXTURE MODELS FOR HEAPING IN LONGITUDINAL COUNT DATA VIA BIRTH-DEATH PROCESSES.

Ann Appl Stat 2015;9(2):572-596

Department of Biostatistics, UCLA Fielding School of Public Health ; Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA.

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http://dx.doi.org/10.1214/15-AOAS809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617556PMC
January 2015

Contribution of Epidemiological Predictors in Unraveling the Phylogeographic History of HIV-1 Subtype C in Brazil.

J Virol 2015 Dec 30;89(24):12341-8. Epub 2015 Sep 30.

Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.

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http://jvi.asm.org/lookup/doi/10.1128/JVI.01681-15
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http://dx.doi.org/10.1128/JVI.01681-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665240PMC
December 2015

Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals.

AIDS 2015 Sep;29(15):2045-52

aKU Leuven, Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics biMinds Medical IT cKU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium dPortuguese Society of Rheumatology eLaboratório de Microbiologia Clínica e Biologia Molecular, Serviço de Patologia Clínica, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Rua da Junqueira, Lisbon fCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Sul, Campus Universitário, Quinta da Granja, Monte de Caparica, Caparica, Portugal gDepartment of Biomathematics hDepartment of Human Genetics, David Geffen School of Medicine at UCLA iDepartment of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, California, USA jGlobal Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lsboa, Portugal.

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http://dx.doi.org/10.1097/QAD.0000000000000811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570689PMC
September 2015

Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1.

Mol Biol Evol 2015 Dec 3;32(12):3264-75. Epub 2015 Sep 3.

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

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http://dx.doi.org/10.1093/molbev/msv185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831561PMC
December 2015

Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages.

J Virol 2015 Nov 26;89(22):11275-83. Epub 2015 Aug 26.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

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http://dx.doi.org/10.1128/JVI.01571-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4645657PMC
November 2015

Analysis of Viral Genetics for Estimating Diffusion of Influenza A H6N1.

AMIA Jt Summits Transl Sci Proc 2015 23;2015:36-40. Epub 2015 Mar 23.

University of Washington, Seattle, WA.

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August 2015

Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution.

AIDS 2015 Jul;29(12):1549-56

aDepartment of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium bCentro de Malária e Outras Doenças Tropicais Instituto de Higiene e Medicina Tropical and Unidade de Microbiologia, Universidade Nova de Lisboa, Lisboa, Portugal cDepartment of Biomathematics dDepartment of Human Genetics, David Geffen School of Medicine at UCLA eDepartment of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, California, USA.

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http://dx.doi.org/10.1097/QAD.0000000000000731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348249PMC
July 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

Generalized linear models for identifying predictors of the evolutionary diffusion of viruses.

AMIA Jt Summits Transl Sci Proc 2014 7;2014:23-8. Epub 2014 Apr 7.

Arizona State University, Tempe, AZ, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333690PMC
February 2015

Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion.

Arch Virol 2015 Jan 30;160(1):215-24. Epub 2014 Oct 30.

Department of Biomedical Informatics, Arizona State University, 13212 E. Shea Blvd., Scottsdale, 85259, AZ, USA.

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http://dx.doi.org/10.1007/s00705-014-2262-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398335PMC
January 2015

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid.

Proc Natl Acad Sci U S A 2014 Nov 21;111(44):E4736-42. Epub 2014 Oct 21.

Ecology, Evolution, and Marine Biology Department, University of California, Santa Barbara, CA 93106;

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http://dx.doi.org/10.1073/pnas.1416574111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226117PMC
November 2014

Estimation for general birth-death processes.

J Am Stat Assoc 2014 Apr;109(506):730-747

Department of Biomathematics, University of California Los Angeles, 6558 Gonda Building, Los Angeles, CA 90095-1766 USA ; Department of Biostatistics, University of California Los Angeles, 6558 Gonda Building, Los Angeles, CA 90095-1766 USA ; Department of Human Genetics, University of California Los Angeles, 6558 Gonda Building, Los Angeles, CA 90095-1766 USA.

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http://dx.doi.org/10.1080/01621459.2013.866565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196218PMC
April 2014

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

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA.

Mol Ecol Resour 2015 Jan 4;15(1):81-6. Epub 2014 Jul 4.

School of Biological Sciences, University of Sydney, Edgeworth David building A11, Science Road, 2006, Sydney, NSW, Australia; Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.

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http://dx.doi.org/10.1111/1755-0998.12295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270920PMC
January 2015

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

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

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

On the biogeography of Centipeda: a species-tree diffusion approach.

Syst Biol 2014 Mar 12;63(2):178-91. Epub 2013 Dec 12.

Department of Botany, Swedish Museum of Natural History, Svante Arrhenius väg 7, SE-104 05 Stockholm, Sweden; Department of Microbiology and Immunology, KU Leuven, Minderbroederstraat 10 blok x, box 1030 BE-3000 Leuven, Belgium; School of Biological Sciences, Bangor University, Deiniol Road Bangor Gwynedd, Bangor, LL57 2UW UK; Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, BOX 951766, University of California, Los Angeles, CA 90095-1766, USA; Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095-1772, USA; Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22 B, SE-413 19 Gothenburg, Sweden; and National Herbarium of Victoria, Birdwood Avenue, South Yarra 3141, Australia.

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http://dx.doi.org/10.1093/sysbio/syt102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926304PMC
March 2014

The spread of type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: a phylogeographic approach.

Virology 2013 Dec 27;447(1-2):146-54. Epub 2013 Sep 27.

Sydney Emerging Infections & Biosecurity Institute, School of Biological Sciences and Sydney Medical School, The University of Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1016/j.virol.2013.08.028DOI Listing
December 2013