Marc A Suchard

Marc A Suchard

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Marc A Suchard

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

Stat Med 2019 Sep 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
September 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

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

Pharmacoepidemiol Drug Saf 2019 Jul 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

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

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 2019

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525270PMC
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://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
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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

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

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

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://link.springer.com/10.1007/s00705-014-2262-5
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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

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

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

Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS.

J Gen Virol 2014 Dec 9;95(Pt 12):2784-95. Epub 2014 Sep 9.

Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA

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http://dx.doi.org/10.1099/vir.0.070318-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233634PMC
December 2014

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

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

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

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

High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.

Biostatistics 2014 Apr 4;15(2):207-21. Epub 2013 Oct 4.

Department of Statistics, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1093/biostatistics/kxt043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944969PMC
April 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

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

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

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

Interpreting observational studies: why empirical calibration is needed to correct p-values.

Stat Med 2014 Jan 30;33(2):209-18. Epub 2013 Jul 30.

Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands; Observational Medical Outcomes Partnership, Foundation for the National Institutes of Health, Bethesda, MD, U.S.A.

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http://dx.doi.org/10.1002/sim.5925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285234PMC
January 2014

Discussion: An estimate of the science-wise false discovery rate and application to the top medical literature.

Biostatistics 2014 Jan 25;15(1):36-9; discussion 39-45. Epub 2013 Sep 25.

Observational Medical Outcomes Partnership, Foundation for the National Institutes of Health, Bethesda, MD 20814, USAJanssen Research and Development LLC, Titusville, NJ 08560, USA.

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http://dx.doi.org/10.1093/biostatistics/kxt037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3862211PMC
January 2014

Multiple self-controlled case series for large-scale longitudinal observational databases.

Biometrics 2013 Dec 11;69(4):893-902. Epub 2013 Oct 11.

Department of Statistics, Columbia University, New York, New York, U.S.A.

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http://dx.doi.org/10.1111/biom.12078DOI Listing
December 2013

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

Empirical performance of the self-controlled case series design: lessons for developing a risk identification and analysis system.

Drug Saf 2013 Oct;36 Suppl 1:S83-93

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/10.1007/s40264-013-0100-4DOI Listing
October 2013

A comparison of the empirical performance of methods for a risk identification system.

Drug Saf 2013 Oct;36 Suppl 1:S143-58

Janssen Research and Development LLC, 1125 Trenton-Harbourton Road, Room K30205, PO Box 200, Titusville, NJ, 08560, USA,

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http://dx.doi.org/10.1007/s40264-013-0108-9DOI Listing
October 2013

The impact of drug and outcome prevalence on the feasibility and performance of analytical methods for a risk identification and analysis system.

Drug Saf 2013 Oct;36 Suppl 1:S195-204

AstraZeneca PLC, 35 Gatehouse Drive, Waltham, MA, 02451, USA,

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http://dx.doi.org/10.1007/s40264-013-0112-0DOI Listing
October 2013

Evaluating the impact of database heterogeneity on observational study results.

Am J Epidemiol 2013 Aug 5;178(4):645-51. Epub 2013 May 5.

Department of Statistics, Columbia University, 1255 Amsterdam Avenue, New York, NY 10027, USA.

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http://dx.doi.org/10.1093/aje/kwt010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736754PMC
August 2013

Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees.

Syst Biol 2013 May 15;62(3):439-55. Epub 2013 Feb 15.

Department of Biostatistics, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/sysbio/syt010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622899PMC
May 2013

Stability-mediated epistasis constrains the evolution of an influenza protein.

Elife 2013 May 14;2:e00631. Epub 2013 May 14.

Division of Basic Sciences , Fred Hutchinson Cancer Research Center , Seattle , United States.

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http://dx.doi.org/10.7554/eLife.00631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654441PMC
May 2013

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.

Mol Biol Evol 2013 Mar 22;30(3):713-24. Epub 2012 Nov 22.

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

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http://dx.doi.org/10.1093/molbev/mss265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563973PMC
March 2013

Bayesian selection of nucleotide substitution models and their site assignments.

Mol Biol Evol 2013 Mar 11;30(3):669-88. Epub 2012 Dec 11.

Department of Computer Science, University of Auckland, Auckland, New Zealand.

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http://dx.doi.org/10.1093/molbev/mss258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563969PMC
March 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

Graph hierarchies for phylogeography.

Philos Trans R Soc Lond B Biol Sci 2013 Mar 4;368(1614):20120206. Epub 2013 Feb 4.

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

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http://dx.doi.org/10.1098/rstb.2012.0206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678330PMC
March 2013

Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.

Mol Biol Evol 2013 Feb 22;30(2):239-43. Epub 2012 Oct 22.

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

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http://dx.doi.org/10.1093/molbev/mss243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548314PMC
February 2013

Bayesian phylogenetics with BEAUti and the BEAST 1.7.

Mol Biol Evol 2012 Aug 25;29(8):1969-73. Epub 2012 Feb 25.

Department of Computer Science, University of Auckland, Auckland, New Zealand.

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http://dx.doi.org/10.1093/molbev/mss075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408070PMC
August 2012

A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses.

Comput Biol Chem 2012 Aug 30;39:20-8. Epub 2012 Jun 30.

Graduate Institute of Electrical Engineering, Chang Gung University, Taoyuan, Taiwan.

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https://linkinghub.elsevier.com/retrieve/pii/S14769271120004
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http://dx.doi.org/10.1016/j.compbiolchem.2012.06.004DOI Listing
August 2012

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.

Syst Biol 2012 May 22;61(3):539-42. Epub 2012 Feb 22.

Department of Biodiversity Informatics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden.

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http://dx.doi.org/10.1093/sysbio/sys029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329765PMC
May 2012

A Bayesian model for the common effects of multiple predictors on mixed outcomes.

Interface Focus 2011 Dec 31;1(6):886-94. Epub 2011 Aug 31.

Department of Biostatistics, UCLA School of Public Health, University of California, Los Angeles, CA 90095-1772,USA.

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http://dx.doi.org/10.1098/rsfs.2011.0041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262291PMC
December 2011

Toward a quantitative understanding of viral phylogeography.

Curr Opin Virol 2011 Nov 28;1(5):423-9. Epub 2011 Oct 28.

Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1016/j.coviro.2011.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312803PMC
November 2011