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Items: 1 to 50 of 196

1.

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

Yang Q, Zhao X, Lemey P, Suchard MA, Bi Y, Shi W, Liu D, Qi W, Zhang G, Stenseth NC, Pybus OG, Tian H.

Proc Natl Acad Sci U S A. 2020 Mar 17;117(11):5949-5954. doi: 10.1073/pnas.1906954117. Epub 2020 Mar 2.

2.

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction.

Gill MS, Lemey P, Suchard MA, Rambaut A, Baele G.

Mol Biol Evol. 2020 Feb 26. pii: msaa047. doi: 10.1093/molbev/msaa047. [Epub ahead of print]

PMID:
32101295
3.

Comparison of Cardiovascular and Safety Outcomes of Chlorthalidone vs Hydrochlorothiazide to Treat Hypertension.

Hripcsak G, Suchard MA, Shea S, Chen R, You SC, Pratt N, Madigan D, Krumholz HM, Ryan PB, Schuemie MJ.

JAMA Intern Med. 2020 Feb 17. doi: 10.1001/jamainternmed.2019.7454. [Epub ahead of print]

4.

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

Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G.

Viruses. 2020 Feb 5;12(2). pii: E182. doi: 10.3390/v12020182.

5.

Symptom evolution following the emergence of maize streak virus.

Monjane AL, Dellicour S, Hartnady P, Oyeniran KA, Owor BE, Bezuidenhout M, Linderme D, Syed RA, Donaldson L, Murray S, Rybicki EP, Kvarnheden A, Yazdkhasti E, Lefeuvre P, Froissart R, Roumagnac P, Shepherd DN, Harkins GW, Suchard MA, Lemey P, Varsani A, Martin DP.

Elife. 2020 Jan 15;9. pii: e51984. doi: 10.7554/eLife.51984.

6.

A surrogate ℓ0 sparse Cox's regression with applications to sparse high-dimensional massive sample size time-to-event data.

Kawaguchi ES, Suchard MA, Liu Z, Li G.

Stat Med. 2020 Mar 15;39(6):675-686. doi: 10.1002/sim.8438. Epub 2019 Dec 8.

PMID:
31814146
7.

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa.

Faria NR, Vidal N, Lourenco J, Raghwani J, Sigaloff KCE, Tatem AJ, van de Vijver DAM, Pineda-Peña AC, Rose R, Wallis CL, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Muwonga J, Suchard MA, Rinke de Wit TF, Hamers RL, Ndembi N, Baele G, Peeters M, Pybus OG, Lemey P, Dellicour S.

PLoS Pathog. 2019 Dec 6;15(12):e1007976. doi: 10.1371/journal.ppat.1007976. eCollection 2019 Dec.

8.

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - application to H5N1 spread in the Mekong region.

Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D, Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz S, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M.

Bioinformatics. 2019 Dec 2. pii: btz882. doi: 10.1093/bioinformatics/btz882. [Epub ahead of print]

PMID:
31790143
9.

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

Ho LST, Dinh V, Matsen FA 4th, Suchard MA.

J Math Biol. 2020 Mar;80(4):1119-1138. doi: 10.1007/s00285-019-01453-1. Epub 2019 Nov 21.

PMID:
31754778
10.

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

Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P.

Virus Evol. 2019 Sep 5;5(2):vez036. doi: 10.1093/ve/vez036. eCollection 2019 Jul.

11.

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

Suchard MA, Schuemie MJ, Krumholz HM, You SC, Chen R, Pratt N, Reich CG, Duke J, Madigan D, Hripcsak G, Ryan PB.

Lancet. 2019 Nov 16;394(10211):1816-1826. doi: 10.1016/S0140-6736(19)32317-7. Epub 2019 Oct 24.

PMID:
31668726
12.

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

You SC, Jung S, Swerdel JN, Ryan PB, Schuemie MJ, Suchard MA, Lee S, Cho J, Hripcsak G, Park RW, Park S.

Korean Circ J. 2020 Jan;50(1):52-68. doi: 10.4070/kcj.2019.0173. Epub 2019 Aug 28.

13.

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

Schuemie MJ, Ryan PB, Man KKC, Wong ICK, Suchard MA, Hripcsak G.

Stat Med. 2019 Sep 30;38(22):4199-4208. doi: 10.1002/sim.8215. Epub 2019 Aug 22.

14.

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

Baele G, Ayres DL, Rambaut A, Suchard MA, Lemey P.

Methods Mol Biol. 2019;1910:691-722. doi: 10.1007/978-1-4939-9074-0_23.

PMID:
31278682
15.

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

Schuemie MJ, Madigan D, Ryan PB, Reich C, Suchard MA, Berlin JA, Hripcsak G.

Pharmacoepidemiol Drug Saf. 2019 Jul;28(7):1032-1033. doi: 10.1002/pds.4798. Epub 2019 May 8. No abstract available.

PMID:
31066478
16.

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.

Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.

17.

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

Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P.

Mol Biol Evol. 2019 Aug 1;36(8):1793-1803. doi: 10.1093/molbev/msz094.

18.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ.

PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650. eCollection 2019 Apr.

19.

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

Scotch M, Tahsin T, Weissenbacher D, O'Connor K, Magge A, Vaiente M, Suchard MA, Gonzalez-Hernandez G.

Virus Evol. 2019 Feb 28;5(1):vey043. doi: 10.1093/ve/vey043. eCollection 2019 Jan.

20.

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.

Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, Lumley S, Ighodalo Y, Adomeh DI, Olokor T, Omomoh E, Omiunu R, Agbukor J, Ebo B, Aiyepada J, Ebhodaghe P, Osiemi B, Ehikhametalor S, Akhilomen P, Airende M, Esumeh R, Muoebonam E, Giwa R, Ekanem A, Igenegbale G, Odigie G, Okonofua G, Enigbe R, Oyakhilome J, Yerumoh EO, Odia I, Aire C, Okonofua M, Atafo R, Tobin E, Asogun D, Akpede N, Okokhere PO, Rafiu MO, Iraoyah KO, Iruolagbe CO, Akhideno P, Erameh C, Akpede G, Isibor E, Naidoo D, Hewson R, Hiscox JA, Vipond R, Carroll MW, Ihekweazu C, Formenty P, Okogbenin S, Ogbaini-Emovon E, Günther S, Duraffour S.

Science. 2019 Jan 4;363(6422):74-77. doi: 10.1126/science.aau9343.

21.

Consistency and convergence rate of phylogenetic inference via regularization.

Dinh V, Tung Ho LS, Suchard MA, Matsen FA 4th.

Ann Stat. 2018 Aug;46(4):1481-1512. doi: 10.1214/17-AOS1592. Epub 2018 Jun 27.

22.

Recent advances in computational phylodynamics.

Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B.

Curr Opin Virol. 2018 Aug;31:24-32. doi: 10.1016/j.coviro.2018.08.009. Epub 2018 Sep 22. Review.

PMID:
30248578
23.

Genomic and epidemiological monitoring of yellow fever virus transmission potential.

Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG.

Science. 2018 Aug 31;361(6405):894-899. doi: 10.1126/science.aat7115. Epub 2018 Aug 23.

24.

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

Schuemie MJ, Ryan PB, Hripcsak G, Madigan D, Suchard MA.

Philos Trans A Math Phys Eng Sci. 2018 Sep 13;376(2128). pii: 20170356. doi: 10.1098/rsta.2017.0356.

25.

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A.

Virus Evol. 2018 Jun 8;4(1):vey016. doi: 10.1093/ve/vey016. eCollection 2018 Jan.

26.

Computational methods for birth-death processes.

Crawford FW, Ho LST, Suchard MA.

Wiley Interdiscip Rev Comput Stat. 2018 Mar-Apr;10(2). pii: e1423. doi: 10.1002/wics.1423. Epub 2018 Jan 2.

27.

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

Tian Y, Schuemie MJ, Suchard MA.

Int J Epidemiol. 2018 Dec 1;47(6):2005-2014. doi: 10.1093/ije/dyy120.

28.

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

Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P.

Nat Commun. 2018 Jun 8;9(1):2222. doi: 10.1038/s41467-018-03763-2.

29.

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.

Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA.

Syst Biol. 2018 Sep 1;67(5):901-904. doi: 10.1093/sysbio/syy032.

30.

Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data.

Reps JM, Schuemie MJ, Suchard MA, Ryan PB, Rijnbeek PR.

J Am Med Inform Assoc. 2018 Aug 1;25(8):969-975. doi: 10.1093/jamia/ocy032.

31.

Empirical confidence interval calibration for population-level effect estimation studies in observational healthcare data.

Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2571-2577. doi: 10.1073/pnas.1708282114.

32.

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

Vrancken B, Suchard MA, Lemey P.

Virus Evol. 2017 Oct 6;3(2):vex028. doi: 10.1093/ve/vex028. eCollection 2017 Jul.

33.

Phylogenetic Factor Analysis.

Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA.

Syst Biol. 2018 May 1;67(3):384-399. doi: 10.1093/sysbio/syx066.

34.

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

Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA.

J Math Biol. 2018 Mar;76(4):911-944. doi: 10.1007/s00285-017-1160-3. Epub 2017 Jul 24.

35.

Risk of angioedema associated with levetiracetam compared with phenytoin: Findings of the observational health data sciences and informatics research network.

Duke JD, Ryan PB, Suchard MA, Hripcsak G, Jin P, Reich C, Schwalm MS, Khoma Y, Wu Y, Xu H, Shah NH, Banda JM, Schuemie MJ.

Epilepsia. 2017 Aug;58(8):e101-e106. doi: 10.1111/epi.13828. Epub 2017 Jul 6.

36.

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

Shaddox TR, Ryan PB, Schuemie MJ, Madigan D, Suchard MA.

Stat Anal Data Min. 2016 Aug;9(4):260-268. doi: 10.1002/sam.11324. Epub 2016 Jul 17.

37.

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

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

38.

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

Baele G, Suchard MA, Bielejec F, Lemey P.

Microb Genom. 2016 Jun 24;2(6):e000057. doi: 10.1099/mgen.0.000057. eCollection 2016 Jun.

39.

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

Al-Qahtani AA, Baele G, Khalaf N, Suchard MA, Al-Anazi MR, Abdo AA, Sanai FM, Al-Ashgar HI, Khan MQ, Al-Ahdal MN, Lemey P, Vrancken B.

Sci Rep. 2017 Mar 21;7:44947. doi: 10.1038/srep44947.

40.

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

Baele G, Lemey P, Rambaut A, Suchard MA.

Bioinformatics. 2017 Jun 15;33(12):1798-1805. doi: 10.1093/bioinformatics/btx088.

41.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

Baele G, Suchard MA, Rambaut A, Lemey P.

Syst Biol. 2017 Jan 1;66(1):e47-e65. doi: 10.1093/sysbio/syw054. Review.

42.

Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.

Magee D, Suchard MA, Scotch M.

PLoS Comput Biol. 2017 Feb 7;13(2):e1005389. doi: 10.1371/journal.pcbi.1005389. eCollection 2017 Feb.

43.

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

Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA.

Stat Med. 2018 Jan 30;37(2):195-206. doi: 10.1002/sim.7196. Epub 2017 Jan 18.

44.

1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America.

Worobey M, Watts TD, McKay RA, Suchard MA, Granade T, Teuwen DE, Koblin BA, Heneine W, Lemey P, Jaffe HW.

Nature. 2016 Nov 3;539(7627):98-101. doi: 10.1038/nature19827. Epub 2016 Oct 26.

45.

A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution.

Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA.

Syst Biol. 2017 May 1;66(3):299-319. doi: 10.1093/sysbio/syw093.

46.

Identifying predictors of time-inhomogeneous viral evolutionary processes.

Bielejec F, Baele G, Rodrigo AG, Suchard MA, Lemey P.

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

47.

Host ecology determines the dispersal patterns of a plant virus.

Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P.

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

48.

Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection.

Raghwani J, Rose R, Sheridan I, Lemey P, Suchard MA, Santantonio T, Farci P, Klenerman P, Pybus OG.

PLoS Pathog. 2016 Sep 15;12(9):e1005894. doi: 10.1371/journal.ppat.1005894. eCollection 2016 Sep.

49.

Robust empirical calibration of p-values using observational data.

Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA.

Stat Med. 2016 Sep 30;35(22):3883-8. doi: 10.1002/sim.6977. No abstract available.

50.

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

Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA.

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

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