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Items: 1 to 50 of 166

1.

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.

2.

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.

3.

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.

PMID:
28950376
4.

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.

5.

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.

PMID:
28681416
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

PMID:
28200071
11.

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.

12.

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.

13.

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.

PMID:
28098392
14.

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.

15.

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.

PMID:
27798403
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

Characterizing treatment pathways at scale using the OHDSI network.

Hripcsak G, Ryan PB, Duke JD, Shah NH, Park RW, Huser V, Suchard MA, Schuemie MJ, DeFalco FJ, Perotte A, Banda JM, Reich CG, Schilling LM, Matheny ME, Meeker D, Pratt N, Madigan D.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7329-36. doi: 10.1073/pnas.1510502113. Epub 2016 Jun 6.

22.

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

Heintzman PD, Froese D, Ives JW, Soares AE, Zazula GD, Letts B, Andrews TD, Driver JC, Hall E, Hare PG, Jass CN, MacKay G, Southon JR, Stiller M, Woywitka R, Suchard MA, Shapiro B.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8057-63. doi: 10.1073/pnas.1601077113. Epub 2016 Jun 6.

23.

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

Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P.

Mol Biol Evol. 2016 Aug;33(8):2167-9. doi: 10.1093/molbev/msw082. Epub 2016 Apr 23.

PMID:
27189542
24.

ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.

Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA.

Ann Appl Stat. 2015 Jun;9(2):969-991.

25.

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

Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN.

PLoS Comput Biol. 2016 Mar 3;12(3):e1004789. doi: 10.1371/journal.pcbi.1004789. eCollection 2016 Mar.

26.

Pioglitazone Use and Risk of Bladder Cancer.

Singh S, Suchard MA.

JAMA. 2015 Dec 15;314(23):2567-8. doi: 10.1001/jama.2015.13912. No abstract available.

PMID:
26670976
27.

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty.

Baele G, Lemey P, Suchard MA.

Syst Biol. 2016 Mar;65(2):250-64. doi: 10.1093/sysbio/syv083. Epub 2015 Nov 1.

28.
29.

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

Gräf T, Vrancken B, Maletich Junqueira D, de Medeiros RM, Suchard MA, Lemey P, Esteves de Matos Almeida S, Pinto AR.

J Virol. 2015 Dec;89(24):12341-8. doi: 10.1128/JVI.01681-15. Epub 2015 Sep 30.

30.

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

Winand R, Theys K, Eusébio M, Aerts J, Camacho RJ, Gomes P, Suchard MA, Vandamme AM, Abecasis AB; Portuguese HIV-1 Resistance Study Group.

AIDS. 2015 Sep 24;29(15):2045-52. doi: 10.1097/QAD.0000000000000811. Erratum in: AIDS. 2016 Feb 20;30(4):679.

31.

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

Trovão NS, Suchard MA, Baele G, Gilbert M, Lemey P.

Mol Biol Evol. 2015 Dec;32(12):3264-75. doi: 10.1093/molbev/msv185. Epub 2015 Sep 3.

32.

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

Machkovech HM, Bedford T, Suchard MA, Bloom JD.

J Virol. 2015 Nov;89(22):11275-83. doi: 10.1128/JVI.01571-15. Epub 2015 Aug 26.

33.

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

Scotch M, Suchard MA, Rabinowitz PM.

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

34.

Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.

Hripcsak G, Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, Suchard MA, Park RW, Wong IC, Rijnbeek PR, van der Lei J, Pratt N, Norén GN, Li YC, Stang PE, Madigan D, Ryan PB.

Stud Health Technol Inform. 2015;216:574-8.

35.

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

Vrancken B, Baele G, Vandamme AM, van Laethem K, Suchard MA, Lemey P.

AIDS. 2015 Jul 31;29(12):1549-56. doi: 10.1097/QAD.0000000000000731.

36.

Global circulation patterns of seasonal influenza viruses vary with antigenic drift.

Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox NJ, Daniels RS, Gunasekaran CP, Hurt AC, Kelso A, Klimov A, Lewis NS, Li X, McCauley JW, Odagiri T, Potdar V, Rambaut A, Shu Y, Skepner E, Smith DJ, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P, Russell CA.

Nature. 2015 Jul 9;523(7559):217-20. doi: 10.1038/nature14460. Epub 2015 Jun 8.

37.

Global migration of influenza A viruses in swine.

Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P.

Nat Commun. 2015 Mar 27;6:6696. doi: 10.1038/ncomms7696.

38.

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

Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF, Suchard MA.

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

39.

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

Beard R, Magee D, Suchard MA, Lemey P, Scotch M.

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

40.

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

Magee D, Beard R, Suchard MA, Lemey P, Scotch M.

Arch Virol. 2015 Jan;160(1):215-24. doi: 10.1007/s00705-014-2262-5. Epub 2014 Oct 30.

41.

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

Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4736-42. doi: 10.1073/pnas.1416574111. Epub 2014 Oct 21.

42.

Estimation for general birth-death processes.

Crawford FW, Minin VN, Suchard MA.

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

43.

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

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P.

Science. 2014 Oct 3;346(6205):56-61. doi: 10.1126/science.1256739. Epub 2014 Oct 2.

44.

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

Strickland SL, Rife BD, Lamers SL, Nolan DJ, Veras NM, Prosperi MC, Burdo TH, Autissier P, Nowlin B, Goodenow MM, Suchard MA, Williams KC, Salemi M.

J Gen Virol. 2014 Dec;95(Pt 12):2784-95. doi: 10.1099/vir.0.070318-0. Epub 2014 Sep 9.

45.

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

Molak M, Suchard MA, Ho SY, Beilman DW, Shapiro B.

Mol Ecol Resour. 2015 Jan;15(1):81-6. doi: 10.1111/1755-0998.12295. Epub 2014 Jul 4.

46.

OutbreakTools: a new platform for disease outbreak analysis using the R software.

Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N.

Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.

47.

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

Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA.

BMC Bioinformatics. 2014 May 7;15:133. doi: 10.1186/1471-2105-15-133.

48.

Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil.

Nunes MR, Palacios G, Faria NR, Sousa EC Jr, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DB, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PF, Lipkin WI.

PLoS Negl Trop Dis. 2014 Apr 17;8(4):e2769. doi: 10.1371/journal.pntd.0002769. eCollection 2014 Apr.

49.

BEAST 2: a software platform for Bayesian evolutionary analysis.

Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ.

PLoS Comput Biol. 2014 Apr 10;10(4):e1003537. doi: 10.1371/journal.pcbi.1003537. eCollection 2014 Apr.

50.

The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.

Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P.

PLoS Comput Biol. 2014 Apr 3;10(4):e1003505. doi: 10.1371/journal.pcbi.1003505. eCollection 2014 Apr.

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