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Suchard Marc

Title(s)Member, CTSI
SchoolCTSI
Phone(310) 825-7442
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    Other Positions
    Title(s)Professor, Biostatistics

    Title(s)Professor, Biomathematics

    Title(s)Professor, Human Genetics

    Title(s)Member, Bioinformatics GPB Home Area

    Title(s)Member, Genetics & Genomics GPB Home Area


    Collapse Research 
    Collapse Research Activities and Funding
    Bayesian Joint Estimation of Alignment and Phylogeny
    NIH/NIGMS R01GM086887Aug 1, 2008 - Jul 31, 2014
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G. In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography. Viruses. 2020 Feb 05; 12(2). PMID: 32033422.
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    2. Monjane AL, Dellicour S, Hartnady P, Oyeniran KA, Owor BE, Bezeidenhout 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. Symptom evolution following the emergence of maize streak virus. Elife. 2020 Jan 15; 9. PMID: 31939738.
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    3. Kawaguchi ES, Suchard MA, Liu Z, Li G. A surrogate l0 sparse Cox's regression with applications to sparse high-dimensional massive sample size time-to-event data. Stat Med. 2019 Dec 08. PMID: 31814146.
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    4. 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. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog. 2019 Dec; 15(12):e1007976. PMID: 31809523.
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    5. 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. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - application to H5N1 spread in the Mekong region. Bioinformatics. 2019 Dec 02. PMID: 31790143.
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    6. Ho LST, Dinh V, Matsen FA, Suchard MA. On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model. J Math Biol. 2019 Nov 21. PMID: 31754778.
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    7. Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics. Syst Biol. 2019 11 01; 68(6):1052-1061. PMID: 31034053.
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    8. Suchard MA, Schuemie MJ, Krumholz HM, You SC, Chen R, Pratt N, Reich CG, Duke J, Madigan D, Hripcsak G, Ryan PB. Comprehensive comparative effectiveness and safety of first-line antihypertensive drug classes: a systematic, multinational, large-scale analysis. Lancet. 2019 11 16; 394(10211):1816-1826. PMID: 31668726.
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    9. Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P. Divergence dating using mixed effects clock modelling: An application to HIV-1. Virus Evol. 2019 Jul; 5(2):vez036. PMID: 31720009.
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    10. You SC, Jung S, Swerdel JN, Ryan PB, Schuemie MJ, Suchard MA, Lee S, Cho J, Hripcsak G, Park RW, Park S. Comparison of First-Line Dual Combination Treatments in Hypertension: Real-World Evidence from Multinational Heterogeneous Cohorts. Korean Circ J. 2020 Jan; 50(1):52-68. PMID: 31642211.
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    11. Schuemie MJ, Ryan PB, Man KKC, Wong ICK, Suchard MA, Hripcsak G. A plea to stop using the case-control design in retrospective database studies. Stat Med. 2019 Sep 30; 38(22):4199-4208. PMID: 31436848.
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    12. Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates. Mol Biol Evol. 2019 08 01; 36(8):1793-1803. PMID: 31004175.
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    13. Schuemie MJ, Madigan D, Ryan PB, Reich C, Suchard MA, Berlin JA, Hripcsak G. Comment on "How pharmacoepidemiology networks can manage distributed analyses to improve replicability and transparency and minimize bias". Pharmacoepidemiol Drug Saf. 2019 07; 28(7):1032-1033. PMID: 31066478.
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    14. 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. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019 04; 15(4):e1006650. PMID: 30958812.
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    15. Scotch M, Tahsin T, Weissenbacher D, O'Connor K, Magge A, Vaiente M, Suchard MA, Gonzalez-Hernandez G. Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Virus Evol. 2019 Jan; 5(1):vey043. PMID: 30838129.
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    16. Baele G, Ayres DL, Rambaut A, Suchard MA, Lemey P. High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. Methods Mol Biol. 2019; 1910:691-722. PMID: 31278682.
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    17. Tian Y, Schuemie MJ, Suchard MA. Evaluating large-scale propensity score performance through real-world and synthetic data experiments. Int J Epidemiol. 2018 12 01; 47(6):2005-2014. PMID: 29939268.
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    18. Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B. Recent advances in computational phylodynamics. Curr Opin Virol. 2018 08; 31:24-32. PMID: 30248578.
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    19. Schuemie MJ, Ryan PB, Hripcsak G, Madigan D, Suchard MA. Improving reproducibility by using high-throughput observational studies with empirical calibration. Philos Trans A Math Phys Eng Sci. 2018 Sep 13; 376(2128). PMID: 30082302.
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    20. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol. 2018 09 01; 67(5):901-904. PMID: 29718447.
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    21. Reps JM, Schuemie MJ, Suchard MA, Ryan PB, Rijnbeek PR. Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data. J Am Med Inform Assoc. 2018 08 01; 25(8):969-975. PMID: 29718407.
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    22. Dinh V, Tung Ho LS, Suchard MA, Matsen FA. Consistency and convergence rate of phylogenetic inference via regularization. Ann Stat. 2018 Aug; 46(4):1481-1512. PMID: 30344357.
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    23. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018 Jan; 4(1):vey016. PMID: 29942656.
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    24. Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Commun. 2018 06 08; 9(1):2222. PMID: 29884821.
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    25. Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis. Syst Biol. 2018 May 01; 67(3):384-399. PMID: 28950376.
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    26. Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA. Empirical confidence interval calibration for population-level effect estimation studies in observational healthcare data. Proc Natl Acad Sci U S A. 2018 03 13; 115(11):2571-2577. PMID: 29531023.
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    27. Crawford FW, Ho LST, Suchard MA. Computational methods for birth-death processes. Wiley Interdiscip Rev Comput Stat. 2018 Mar-Apr; 10(2). PMID: 29942419.
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    28. Vrancken B, Suchard MA, Lemey P. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling. Virus Evol. 2017 Jul; 3(2):vex028. PMID: 29026650.
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    29. Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA. Birth/birth-death processes and their computable transition probabilities with biological applications. J Math Biol. 2018 03; 76(4):911-944. PMID: 28741177.
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    30. 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. Risk of angioedema associated with levetiracetam compared with phenytoin: Findings of the observational health data sciences and informatics research network. Epilepsia. 2017 08; 58(8):e101-e106. PMID: 28681416.
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    31. Baele G, Lemey P, Rambaut A, Suchard MA. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics. 2017 Jun 15; 33(12):1798-1805. PMID: 28200071.
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    32. Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA. A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution. Syst Biol. 2017 05 01; 66(3):299-319. PMID: 27798403.
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    33. 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. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017 04 20; 544(7650):309-315. PMID: 28405027.
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    34. 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. The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia. Sci Rep. 2017 03 21; 7:44947. PMID: 28322313.
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    35. Magee D, Suchard MA, Scotch M. 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; 13(2):e1005389. PMID: 28170397.
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    36. Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA. Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza. Stat Med. 2018 Jan 30; 37(2):195-206. PMID: 28098392.
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    37. Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics. Syst Biol. 2017 01 01; 66(1):e47-e65. PMID: 28173504.
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    38. Worobey M, Watts TD, McKay RA, Suchard MA, Granade T, Teuwen DE, Koblin BA, Heneine W, Lemey P, Jaffe HW. 1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America. Nature. 2016 11 03; 539(7627):98-101. PMID: 27783600.
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    39. Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA. Robust empirical calibration of p-values using observational data. Stat Med. 2016 09 30; 35(22):3883-8. PMID: 27592566.
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    40. Raghwani J, Rose R, Sheridan I, Lemey P, Suchard MA, Santantonio T, Farci P, Klenerman P, Pybus OG. Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection. PLoS Pathog. 2016 09; 12(9):e1005894. PMID: 27631086.
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    41. Bielejec F, Baele G, Rodrigo AG, Suchard MA, Lemey P. Identifying predictors of time-inhomogeneous viral evolutionary processes. Virus Evol. 2016 Jul; 2(2):vew023. PMID: 27774306.
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    42. Shaddox TR, Ryan PB, Schuemie MJ, Madigan D, Suchard MA. Hierarchical Models for Multiple, Rare Outcomes Using Massive Observational Healthcare Databases. Stat Anal Data Min. 2016 Aug; 9(4):260-268. PMID: 28503249.
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    43. Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA. Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates. Syst Biol. 2016 Nov; 65(6):1041-1056. PMID: 27368344.
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    44. Baele G, Suchard MA, Bielejec F, Lemey P. Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation. Microb Genom. 2016 06; 2(6):e000057. PMID: 28348854.
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    45. 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. Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada. Proc Natl Acad Sci U S A. 2016 07 19; 113(29):8057-63. PMID: 27274051.
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    46. 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. Characterizing treatment pathways at scale using the OHDSI network. Proc Natl Acad Sci U S A. 2016 07 05; 113(27):7329-36. PMID: 27274072.
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    47. Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P. SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. Mol Biol Evol. 2016 08; 33(8):2167-9. PMID: 27189542.
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    48. Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN. Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. PLoS Comput Biol. 2016 Mar; 12(3):e1004789. PMID: 26938243.
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    49. Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P. Host ecology determines the dispersal patterns of a plant virus. Virus Evol. 2015; 1(1):vev016. PMID: 27774287.
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    50. Singh S, Suchard MA. Pioglitazone Use and Risk of Bladder Cancer. JAMA. 2015 Dec 15; 314(23):2567-8. PMID: 26670976.
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    51. Baele G, Lemey P, Suchard MA. Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty. Syst Biol. 2016 Mar; 65(2):250-64. PMID: 26526428.
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    52. Gräf T, Vrancken B, Maletich Junqueira D, de Medeiros RM, Suchard MA, Lemey P, Esteves de Matos Almeida S, Pinto AR. Contribution of Epidemiological Predictors in Unraveling the Phylogeographic History of HIV-1 Subtype C in Brazil. J Virol. 2015 Dec; 89(24):12341-8. PMID: 26423943.
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    53. Winand R, Theys K, Eusébio M, Aerts J, Camacho RJ, Gomes P, Suchard MA, Vandamme AM, Abecasis AB. Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals. AIDS. 2015 Sep 24; 29(15):2045-52. PMID: 26355575.
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    54. Trovão NS, Suchard MA, Baele G, Gilbert M, Lemey P. Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1. Mol Biol Evol. 2015 Dec; 32(12):3264-75. PMID: 26341298.
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    55. Machkovech HM, Bedford T, Suchard MA, Bloom JD. 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; 89(22):11275-83. PMID: 26311880.
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    56. Vrancken B, Baele G, Vandamme AM, van Laethem K, Suchard MA, Lemey P. Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution. AIDS. 2015 Jul 31; 29(12):1549-56. PMID: 26244394.
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    57. 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. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature. 2015 Jul 09; 523(7559):217-20. PMID: 26053121.
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    58. Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA. ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL. Ann Appl Stat. 2015 Jun; 9(2):969-991. PMID: 27053974.
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    59. Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P. Global migration of influenza A viruses in swine. Nat Commun. 2015 Mar 27; 6:6696. PMID: 25813399.
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    60. Scotch M, Suchard MA, Rabinowitz PM. Analysis of Viral Genetics for Estimating Diffusion of Influenza A H6N1. AMIA Jt Summits Transl Sci Proc. 2015; 2015:36-40. PMID: 26306229.
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    61. 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. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Stud Health Technol Inform. 2015; 216:574-8. PMID: 26262116.
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    62. Vrancken B, Lemey P, Rambaut A, Bedford T, Longdon B, Günthard HF, Suchard MA. Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution. Methods Ecol Evol. 2015 Jan 01; 6(1):67-82. PMID: 25780554.
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    63. Crawford FW, Weiss RE, Suchard MA. 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. PMID: 26500711.
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    64. Magee D, Beard R, Suchard MA, Lemey P, Scotch M. Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion. Arch Virol. 2015 Jan; 160(1):215-24. PMID: 25355432.
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    65. Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proc Natl Acad Sci U S A. 2014 Nov 04; 111(44):E4736-42. PMID: 25336755.
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    66. 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. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science. 2014 10 03; 346(6205):56-61. PMID: 25278604.
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    67. 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. Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS. J Gen Virol. 2014 Dec; 95(Pt 12):2784-95. PMID: 25205684.
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    68. Molak M, Suchard MA, Ho SY, Beilman DW, Shapiro B. 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; 15(1):81-6. PMID: 24964386.
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    69. Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA. pBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinformatics. 2014 May 07; 15:133. PMID: 24885610.
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    70. 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. OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics. 2014 Jun; 7:28-34. PMID: 24928667.
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    71. Nunes MR, Palacios G, Faria NR, Sousa EC, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DB, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PF, Lipkin WI. Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil. PLoS Negl Trop Dis. 2014 Apr; 8(4):e2769. PMID: 24743730.
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    72. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014 Apr; 10(4):e1003537. PMID: 24722319.
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    73. Beard R, Magee D, Suchard MA, Lemey P, Scotch M. Generalized linear models for identifying predictors of the evolutionary diffusion of viruses. AMIA Jt Summits Transl Sci Proc. 2014; 2014:23-8. PMID: 25717395.
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    74. Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comput Biol. 2014 Apr; 10(4):e1003505. PMID: 24699231.
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    75. Crawford FW, Minin VN, Suchard MA. Estimation for general birth-death processes. J Am Stat Assoc. 2014 Apr; 109(506):730-747. PMID: 25328261.
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    76. Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography. Syst Biol. 2014 Jul; 63(4):493-504. PMID: 24627184.
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    77. Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, Russell CA, Smith DJ, Pybus OG, Brockmann D, Suchard MA. Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. PLoS Pathog. 2014 Feb; 10(2):e1003932. PMID: 24586153.
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    78. Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A. Integrating influenza antigenic dynamics with molecular evolution. Elife. 2014; 3:e01914. PMID: 24497547.
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    79. Nylinder S, Lemey P, De Bruyn M, Suchard MA, Pfeil BE, Walsh N, Anderberg AA. On the biogeography of Centipeda: a species-tree diffusion approach. Syst Biol. 2014 Mar; 63(2):178-91. PMID: 24335493.
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    80. Simpson SE, Madigan D, Zorych I, Schuemie MJ, Ryan PB, Suchard MA. Multiple self-controlled case series for large-scale longitudinal observational databases. Biometrics. 2013 Dec; 69(4):893-902. PMID: 24117144.
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    81. Mittal S, Madigan D, Burd RS, Suchard MA. High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis. Biostatistics. 2014 Apr; 15(2):207-21. PMID: 24096388.
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    82. Suchard MA, Zorych I, Simpson SE, Schuemie MJ, Ryan PB, Madigan D. 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. PMID: 24166226.
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    83. Ryan PB, Stang PE, Overhage JM, Suchard MA, Hartzema AG, DuMouchel W, Reich CG, Schuemie MJ, Madigan D. A comparison of the empirical performance of methods for a risk identification system. Drug Saf. 2013 Oct; 36 Suppl 1:S143-58. PMID: 24166231.
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    84. Reich CG, Ryan PB, Suchard MA. 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. PMID: 24166235.
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    88. Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein. Elife. 2013 May 14; 2:e00631. PMID: 23682315.
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    90. Crawford FW, Suchard MA. Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees. Syst Biol. 2013 May 01; 62(3):439-55. PMID: 23417679.
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    93. Suchard MA, Simpson SE, Zorych I, Ryan P, Madigan D. Massive parallelization of serial inference algorithms for a complex generalized linear model. ACM Trans Model Comput Simul. 2013 Jan; 23(1). PMID: 25328363.
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    94. Doss CR, Suchard MA, Holmes I, Kato-Maeda M, Minin VN. Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting. Ann Appl Stat. 2013; 7(4):2315-2335. PMID: 26702330.
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    95. Wu CH, Suchard MA, Drummond AJ. Bayesian selection of nucleotide substitution models and their site assignments. Mol Biol Evol. 2013 Mar; 30(3):669-88. PMID: 23233462.
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    97. Nunes MR, Faria NR, Vasconcelos HB, Medeiros DB, Silva de Lima CP, Carvalho VL, Pinto da Silva EV, Cardoso JF, Sousa EC, Nunes KN, Rodrigues SG, Abecasis AB, Suchard MA, Lemey P, Vasconcelos PF. Phylogeography of dengue virus serotype 4, Brazil, 2010-2011. Emerg Infect Dis. 2012 Nov; 18(11):1858-64. PMID: 23092706.
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    99. Lemey P, Minin VN, Bielejec F, Kosakovsky Pond SL, Suchard MA. A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinformatics. 2012 Dec 15; 28(24):3248-56. PMID: 23064000.
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    101. Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, Gray RD, Suchard MA, Atkinson QD. Mapping the origins and expansion of the Indo-European language family. Science. 2012 Aug 24; 337(6097):957-60. PMID: 22923579.
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    102. Gong YN, Chen GW, Suchard MA. A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. Comput Biol Chem. 2012 Aug; 39:20-8. PMID: 22858722.
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    103. Weinert LA, Welch JJ, Suchard MA, Lemey P, Rambaut A, Fitzgerald JR. Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication. Biol Lett. 2012 Oct 23; 8(5):829-32. PMID: 22628096.
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    104. Kemal KS, Ramirez CM, Burger H, Foley B, Mayers D, Klimkait T, Hamy F, Anastos K, Petrovic K, Minin VN, Suchard MA, Weiser B. Recombination between variants from genital tract and plasma: evolution of multidrug-resistant HIV type 1. AIDS Res Hum Retroviruses. 2012 Dec; 28(12):1766-74. PMID: 22364185.
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    105. Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol. 2012 Sep; 29(9):2157-67. PMID: 22403239.
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    107. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012 May; 61(3):539-42. PMID: 22357727.
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    108. Allicock OM, Lemey P, Tatem AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A, Carrington CV. Phylogeography and population dynamics of dengue viruses in the Americas. Mol Biol Evol. 2012 Jun; 29(6):1533-43. PMID: 22319149.
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    109. Faria NR, Hodges-Mameletzis I, Silva JC, Rodés B, Erasmus S, Paolucci S, Ruelle J, Pieniazek D, Taveira N, Treviño A, Gonçalves MF, Jallow S, Xu L, Camacho RJ, Soriano V, Goubau P, de Sousa JD, Vandamme AM, Suchard MA, Lemey P. Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A. J Gen Virol. 2012 Apr; 93(Pt 4):889-99. PMID: 22190015.
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    113. Crawford FW, Suchard MA. Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution. J Math Biol. 2012 Sep; 65(3):553-80. PMID: 21984359.
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    114. Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol. 2012 Jan; 61(1):170-3. PMID: 21963610.
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    115. Bielejec F, Rambaut A, Suchard MA, Lemey P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics. 2011 Oct 15; 27(20):2910-2. PMID: 21911333.
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    116. Weiss RE, Jia J, Suchard MA. A Bayesian model for the common effects of multiple predictors on mixed outcomes. Interface Focus. 2011 Dec 06; 1(6):886-94. PMID: 22419987.
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    118. Nelson MI, Lemey P, Tan Y, Vincent A, Lam TT, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC, Gramer M. Spatial dynamics of human-origin H1 influenza A virus in North American swine. PLoS Pathog. 2011 Jun; 7(6):e1002077. PMID: 21695237.
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    119. Faria NR, Suchard MA, Abecasis A, Sousa JD, Ndembi N, Bonfim I, Camacho RJ, Vandamme AM, Lemey P. Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. Infect Genet Evol. 2012 Mar; 12(2):453-60. PMID: 21565285.
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    120. Huelsenbeck JP, Alfaro ME, Suchard MA. Biologically inspired phylogenetic models strongly outperform the no common mechanism model. Syst Biol. 2011 Mar; 60(2):225-32. PMID: 21252385.
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    121. Telesca D, Müller P, Kornblau SM, Suchard MA, Ji Y. Modeling Protein Expression and Protein Signaling Pathways. J Am Stat Assoc. 2011; 107(500):1372-1384. PMID: 26246646.
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    123. Gray RR, Tatem AJ, Johnson JA, Alekseyenko AV, Pybus OG, Suchard MA, Salemi M. Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework. Mol Biol Evol. 2011 May; 28(5):1593-603. PMID: 21112962.
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    124. Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Nourlil J, Jalal N, Faouzi A, Echevarría JE, Vazquez Morón S, Rambaut A, Campiz N, Tatem AJ, Holmes EC, Bourhy H. Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS Pathog. 2010 Oct 28; 6(10):e1001166. PMID: 21060816.
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    125. Shapiro B, Ho SY, Drummond AJ, Suchard MA, Pybus OG, Rambaut A. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol. 2011 Feb; 28(2):879-87. PMID: 20889726.
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    128. Zhou H, Lange K, Suchard MA. Graphics Processing Units and High-Dimensional Optimization. Stat Sci. 2010 Aug 01; 25(3):311-324. PMID: 21847315.
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    130. Suchard MA, Wang Q, Chan C, Frelinger J, Cron A, West M. Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures. J Comput Graph Stat. 2010 Jun 01; 19(2):419-438. PMID: 20877443.
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    131. Shi B, Kitchen C, Weiser B, Mayers D, Foley B, Kemal K, Anastos K, Suchard M, Parker M, Brunner C, Burger H. Evolution and recombination of genes encoding HIV-1 drug resistance and tropism during antiretroviral therapy. Virology. 2010 Aug 15; 404(1):5-20. PMID: 20451945.
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    132. Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol. 2010 Sep; 27(9):2038-51. PMID: 20363828.
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    133. Campos PF, Willerslev E, Sher A, Orlando L, Axelsson E, Tikhonov A, Aaris-Sørensen K, Greenwood AD, Kahlke RD, Kosintsev P, Krakhmalnaya T, Kuznetsova T, Lemey P, MacPhee R, Norris CA, Shepherd K, Suchard MA, Zazula GD, Shapiro B, Gilbert MT. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc Natl Acad Sci U S A. 2010 Mar 23; 107(12):5675-80. PMID: 20212118.
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    135. Tom JA, Sinsheimer JS, Suchard MA. Reuse, Recycle, Reweigh: Combating Influenza through Efficient Sequential Bayesian Computation for Massive Data. Ann Appl Stat. 2010; 4(4):1722-1748. PMID: 26681992.
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    136. Bloomquist EW, Suchard MA. Unifying vertical and nonvertical evolution: a stochastic ARG-based framework. Syst Biol. 2010 Jan; 59(1):27-41. PMID: 20525618.
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    139. Liang LJ, Weiss RE, Redelings B, Suchard MA. Improving phylogenetic analyses by incorporating additional information from genetic sequence databases. Bioinformatics. 2009 Oct 01; 25(19):2530-6. PMID: 19661240.
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    141. Kitchen CM, Kroll J, Kuritzkes DR, Bloomquist E, Deeks SG, Suchard MA. Two-way Bayesian hierarchical phylogenetic models: An application to the co-evolution of gp120 and gp41 during and after enfuvirtide treatment. Comput Stat Data Anal. 2009 Jan 15; 53(3):766-775. PMID: 20442796.
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    142. O'Brien JD, Minin VN, Suchard MA. Learning to count: robust estimates for labeled distances between molecular sequences. Mol Biol Evol. 2009 Apr; 26(4):801-14. PMID: 19131426.
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    143. Minin VN, Suchard MA. Fast, accurate and simulation-free stochastic mapping. Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27; 363(1512):3985-95. PMID: 18852111.
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    144. McBride AJ, Cerqueira GM, Suchard MA, Moreira AN, Zuerner RL, Reis MG, Haake DA, Ko AI, Dellagostin OA. Genetic diversity of the Leptospiral immunoglobulin-like (Lig) genes in pathogenic Leptospira spp. Infect Genet Evol. 2009 Mar; 9(2):196-205. PMID: 19028604.
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    145. Drummond AJ, Suchard MA. Fully Bayesian tests of neutrality using genealogical summary statistics. BMC Genet. 2008 Oct 31; 9:68. PMID: 18976476.
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    146. Alekseyenko AV, Lee CJ, Suchard MA. Wagner and Dollo: a stochastic duet by composing two parsimonious solos. Syst Biol. 2008 Oct; 57(5):772-84. PMID: 18853363.
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    147. Bloomquist EW, Dorman KS, Suchard MA. StepBrothers: inferring partially shared ancestries among recombinant viral sequences. Biostatistics. 2009 Jan; 10(1):106-20. PMID: 18562348.
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    149. Seeram NP, Zhang Y, McKeever R, Henning SM, Lee RP, Suchard MA, Li Z, Chen S, Thames G, Zerlin A, Nguyen M, Wang D, Dreher M, Heber D. Pomegranate juice and extracts provide similar levels of plasma and urinary ellagitannin metabolites in human subjects. J Med Food. 2008 Jun; 11(2):390-4. PMID: 18598186.
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    150. Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 2008 Jul; 25(7):1459-71. PMID: 18408232.
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    151. Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis. Science. 2008 Jan 25; 319(5862):473-6. PMID: 18218900.
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    152. Stanczak CM, Chen Z, Nelson SF, Suchard M, McCabe ER, McGhee S. Representational oligonucleotide microarray analysis (ROMA) and comparison of binning and change-point methods of analysis: application to detection of del22q11.2 (DiGeorge) syndrome. Hum Mutat. 2008 Jan; 29(1):176-81. PMID: 17694540.
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    153. Huelsenbeck JP, Suchard MA. A nonparametric method for accommodating and testing across-site rate variation. Syst Biol. 2007 Dec; 56(6):975-87. PMID: 18075934.
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    154. Stevenson B, Choy HA, Pinne M, Rotondi ML, Miller MC, Demoll E, Kraiczy P, Cooley AE, Creamer TP, Suchard MA, Brissette CA, Verma A, Haake DA. Leptospira interrogans endostatin-like outer membrane proteins bind host fibronectin, laminin and regulators of complement. PLoS One. 2007 Nov 14; 2(11):e1188. PMID: 18000555.
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    155. Su F, Lang J, Kumar A, Ng C, Hsieh B, Suchard MA, Reddy ST, Farias-Eisner R. Validation of candidate serum ovarian cancer biomarkers for early detection. Biomark Insights. 2007 Oct 16; 2:369-75. PMID: 19662218.
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    156. Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol. 2008 Mar; 56(3):391-412. PMID: 17874105.
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    157. Seeram NP, Aronson WJ, Zhang Y, Henning SM, Moro A, Lee RP, Sartippour M, Harris DM, Rettig M, Suchard MA, Pantuck AJ, Belldegrun A, Heber D. Pomegranate ellagitannin-derived metabolites inhibit prostate cancer growth and localize to the mouse prostate gland. J Agric Food Chem. 2007 Sep 19; 55(19):7732-7. PMID: 17722872.
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    158. Liao JC, Mastali M, Li Y, Gau V, Suchard MA, Babbitt J, Gornbein J, Landaw EM, McCabe ER, Churchill BM, Haake DA. Development of an advanced electrochemical DNA biosensor for bacterial pathogen detection. J Mol Diagn. 2007 Apr; 9(2):158-68. PMID: 17384207.
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    159. Redelings BD, Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evol Biol. 2007 Mar 14; 7:40. PMID: 17359539.
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    160. Minin VN, Dorman KS, Fang F, Suchard MA. Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes. Genetics. 2007 Apr; 175(4):1773-85. PMID: 17194781.
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    161. Fang F, Ding J, Minin VN, Suchard MA, Dorman KS. cBrother: relaxing parental tree assumptions for Bayesian recombination detection. Bioinformatics. 2007 Feb 15; 23(4):507-8. PMID: 17145740.
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    162. Kitchen CM, Lu J, Suchard MA, Hoh R, Martin JN, Kuritzkes DR, Deeks SG. Continued evolution in gp41 after interruption of enfuvirtide in subjects with advanced HIV type 1 disease. AIDS Res Hum Retroviruses. 2006 Dec; 22(12):1260-6. PMID: 17209769.
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    163. Guo H, Weiss RE, Gu X, Suchard MA. Time squared: repeated measures on phylogenies. Mol Biol Evol. 2007 Feb; 24(2):352-62. PMID: 17079699.
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    164. Seeram NP, Henning SM, Zhang Y, Suchard M, Li Z, Heber D. Pomegranate juice ellagitannin metabolites are present in human plasma and some persist in urine for up to 48 hours. J Nutr. 2006 Oct; 136(10):2481-5. PMID: 16988113.
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    165. Milane MS, Suchard MA, Wong ML, Licinio J. Modeling of the temporal patterns of fluoxetine prescriptions and suicide rates in the United States. PLoS Med. 2006 Jun; 3(6):e190. PMID: 16768544.
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    166. Suchard MA, Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics. 2006 Aug 15; 22(16):2047-8. PMID: 16679334.
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    167. Liao JC, Mastali M, Gau V, Suchard MA, Møller AK, Bruckner DA, Babbitt JT, Li Y, Gornbein J, Landaw EM, McCabe ER, Churchill BM, Haake DA. Use of electrochemical DNA biosensors for rapid molecular identification of uropathogens in clinical urine specimens. J Clin Microbiol. 2006 Feb; 44(2):561-70. PMID: 16455913.
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    170. Minin VN, Dorman KS, Fang F, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics. 2005 Jul 01; 21(13):3034-42. PMID: 15914546.
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    171. Suchard MA. Stochastic models for horizontal gene transfer: taking a random walk through tree space. Genetics. 2005 May; 170(1):419-31. PMID: 15781714.
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    172. Hamilton G, Currat M, Ray N, Heckel G, Beaumont M, Excoffier L. Bayesian estimation of recent migration rates after a spatial expansion. Genetics. 2005 May; 170(1):409-17. PMID: 15716508.
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    173. Vongtama R, Lee M, Kim B, Sercarz J, Lin K, Suchard MA, Lee SP, Juillard G. Early nodal response as a predictor for necessity of functional neck dissection after chemoradiation. Cancer J. 2004 Nov-Dec; 10(6):339-42. PMID: 15701264.
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    174. Kitchen CM, Philpott S, Burger H, Weiser B, Anastos K, Suchard MA. Evolution of human immunodeficiency virus type 1 coreceptor usage during antiretroviral Therapy: a Bayesian approach. J Virol. 2004 Oct; 78(20):11296-302. PMID: 15452249.
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    175. Suchard JR, Suchard MA, Steinfeldt JL. Physician knowledge of herbal toxicities and adverse herb-drug interactions. Eur J Emerg Med. 2004 Aug; 11(4):193-7. PMID: 15249804.
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    176. Yildiz BO, Suchard MA, Wong ML, McCann SM, Licinio J. Alterations in the dynamics of circulating ghrelin, adiponectin, and leptin in human obesity. Proc Natl Acad Sci U S A. 2004 Jul 13; 101(28):10434-9. PMID: 15231997.
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    177. Haake DA, Suchard MA, Kelley MM, Dundoo M, Alt DP, Zuerner RL. Molecular evolution and mosaicism of leptospiral outer membrane proteins involves horizontal DNA transfer. J Bacteriol. 2004 May; 186(9):2818-28. PMID: 15090524.
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    178. Suchard MA, Kitchen CM, Sinsheimer JS, Weiss RE. Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst Biol. 2003 Oct; 52(5):649-64. PMID: 14530132.
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    179. D'Orsogna MR, Suchard MA, Chou T. Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Aug; 68(2 Pt 1):021925. PMID: 14525024.
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    180. Suchard MA, Weiss RE, Sinsheimer JS. Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian framework. Syst Biol. 2003 Feb; 52(1):48-54. PMID: 12554439.
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    181. Sinsheimer JS, Suchard MA, Dorman KS, Fang F, Weiss RE. Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains. Appl Bioinformatics. 2003; 2(3):131-44. PMID: 15130798.
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    182. Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst Biol. 2002 Oct; 51(5):715-28. PMID: 12396586.
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    183. Chan JL, Blüher S, Yiannakouris N, Suchard MA, Kratzsch J, Mantzoros CS. Regulation of circulating soluble leptin receptor levels by gender, adiposity, sex steroids, and leptin: observational and interventional studies in humans. Diabetes. 2002 Jul; 51(7):2105-12. PMID: 12086939.
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    184. Suchard MA, Yudkin P, Sinsheimer JS, Fowler GH. General practitioners' views on genetic screening for common diseases. Br J Gen Pract. 1999 Jan; 49(438):45-6. PMID: 10622017.
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