Marc A. Suchard, Ph.D. - Publications

2002 University of California, Los Angeles, Los Angeles, CA 
Biostatistics Biology

198 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, et al. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nature Communications. 11: 5620. PMID 33159066 DOI: 10.1038/s41467-020-19122-z  0.64
2020 Karcher MD, Carvalho LM, Suchard MA, Dudas G, Minin VN. Estimating effective population size changes from preferentially sampled genetic sequences. Plos Computational Biology. 16: e1007774. PMID 33044955 DOI: 10.1371/journal.pcbi.1007774  1
2020 Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature Communications. 11: 5110. PMID 33037213 DOI: 10.1038/s41467-020-18877-9  0.64
2020 Baele G, Gill MS, Lemey P, Suchard MA. Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework. Wellcome Open Research. 5: 53. PMID 32923688 DOI: 10.12688/wellcomeopenres.15770.1  0.64
2020 Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America. Science (New York, N.Y.). PMID 32912998 DOI: 10.1126/science.abc8169  0.64
2020 Fisher AA, Ji X, Zhang Z, Lemey P, Suchard MA. Relaxed Random Walks at Scale. Systematic Biology. PMID 32687171 DOI: 10.1093/sysbio/syaa056  0.64
2020 Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O'Toole A, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. Biorxiv : the Preprint Server For Biology. PMID 32596695 DOI: 10.1101/2020.06.22.165464  0.64
2020 Düx A, Lequime S, Patrono LV, Vrancken B, Boral S, Gogarten JF, Hilbig A, Horst D, Merkel K, Prepoint B, Santibanez S, Schlotterbeck J, Suchard MA, Ulrich M, Widulin N, et al. Measles virus and rinderpest virus divergence dated to the sixth century BCE. Science (New York, N.Y.). 368: 1367-1370. PMID 32554594 DOI: 10.1126/science.aba9411  0.64
2020 Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and the US. Biorxiv : the Preprint Server For Biology. PMID 32511416 DOI: 10.1101/2020.05.21.109322  0.64
2020 Ji X, Zhang Z, Holbrook A, Nishimura A, Baele G, Rambaut A, Lemey P, Suchard MA. Gradients do grow on trees: a linear-time Molecular Biology and Evolution. PMID 32458974 DOI: 10.1093/molbev/msaa130  0.64
2020 Baele G, Gill MS, Bastide P, Lemey P, Suchard MA. Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST. Systematic Biology. PMID 32415977 DOI: 10.1093/sysbio/syaa037  0.64
2020 He WT, Ji X, He W, Dellicour S, Wang S, Li G, Zhang L, Gilbert M, Zhu H, Xing G, Veit M, Huang Z, Han GZ, Huang Y, Suchard MA, et al. Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus. Molecular Biology and Evolution. PMID 32407507 DOI: 10.1093/molbev/msaa117  0.64
2020 Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, ... ... Suchard MA, et al. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences of the United States of America. PMID 32381734 DOI: 10.1073/pnas.2007295117  0.64
2020 Sun J, He WT, Wang L, Lai A, Ji X, Zhai X, Li G, Suchard MA, Tian J, Zhou J, Veit M, Su S. COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives. Trends in Molecular Medicine. 26: 483-495. PMID 32359479 DOI: 10.1016/j.molmed.2020.02.008  0.32
2020 Yang Q, Zhao X, Lemey P, Suchard MA, Bi Y, Shi W, Liu D, Qi W, Zhang G, Stenseth NC, Pybus OG, Tian H. Assessing the role of live poultry trade in community-structured transmission of avian influenza in China. Proceedings of the National Academy of Sciences of the United States of America. PMID 32123088 DOI: 10.1073/pnas.1906954117  0.64
2020 Gill MS, Lemey P, Suchard MA, Rambaut A, Baele G. Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction. Molecular Biology and Evolution. PMID 32101295 DOI: 10.1093/molbev/msaa047  0.64
2020 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. 12. PMID 32033422 DOI: 10.3390/v12020182  0.64
2020 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, ... ... Suchard MA, et al. Symptom evolution following the emergence of maize streak virus. Elife. 9. PMID 31939738 DOI: 10.7554/eLife.51984  0.64
2019 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, et al. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. Plos Pathogens. 15: e1007976. PMID 31809523 DOI: 10.1371/journal.ppat.1007976  0.64
2019 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, et al. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - application to H5N1 spread in the Mekong region. Bioinformatics (Oxford, England). PMID 31790143 DOI: 10.1093/bioinformatics/btz882  0.64
2019 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. Journal of Mathematical Biology. PMID 31754778 DOI: 10.1007/s00285-019-01453-1  0.8
2019 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 Evolution. 5: vez036. PMID 31720009 DOI: 10.1093/ve/vez036  0.64
2019 Baele G, Ayres DL, Rambaut A, Suchard MA, Lemey P. High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. Methods in Molecular Biology (Clifton, N.J.). 1910: 691-722. PMID 31278682 DOI: 10.1007/978-1-4939-9074-0_23  0.64
2019 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. Systematic Biology. PMID 31034053 DOI: 10.1093/sysbio/syz020  0.64
2019 Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian inference of evolutionary histories under time-dependent substitution rates. Molecular Biology and Evolution. PMID 31004175 DOI: 10.1093/molbev/msz094  0.64
2018 Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B. Recent advances in computational phylodynamics. Current Opinion in Virology. 31: 24-32. PMID 30248578 DOI: 10.1016/j.coviro.2018.08.009  0.64
2018 Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution. 4: vey016. PMID 29942656 DOI: 10.1093/ve/vey016  0.64
2018 Crawford FW, Ho LST, Suchard MA. Computational methods for birth-death processes. Wiley Interdisciplinary Reviews. Computational Statistics. 10. PMID 29942419 DOI: 10.1002/wics.1423  1
2018 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. Nature Communications. 9: 2222. PMID 29884821 DOI: 10.1038/s41467-018-03763-2  0.64
2017 Vrancken B, Suchard MA, Lemey P. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling. Virus Evolution. 3: vex028. PMID 29026650 DOI: 10.1093/ve/vex028  0.64
2017 Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis. Systematic Biology. PMID 28950376 DOI: 10.1093/sysbio/syx066  0.64
2017 Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA. Birth/birth-death processes and their computable transition probabilities with biological applications. Journal of Mathematical Biology. PMID 28741177 DOI: 10.1007/s00285-017-1160-3  1
2017 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, ... ... Suchard MA, et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. PMID 28405027 DOI: 10.1038/nature22040  0.64
2017 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. Scientific Reports. 7: 44947. PMID 28322313 DOI: 10.1038/srep44947  0.64
2017 Baele G, Lemey P, Rambaut A, Suchard MA. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics (Oxford, England). PMID 28200071 DOI: 10.1093/bioinformatics/btx088  0.64
2017 Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics. Systematic Biology. 66: e47-e65. PMID 28173504 DOI: 10.1093/sysbio/syw054  0.64
2017 Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA. Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza. Statistics in Medicine. PMID 28098392 DOI: 10.1002/sim.7196  0.68
2016 Baele G, Suchard MA, Bielejec F, Lemey P. Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation. Microbial Genomics. 2: e000057. PMID 28348854 DOI: 10.1099/mgen.0.000057  0.64
2016 Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA. A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution. Systematic Biology. PMID 27798403 DOI: 10.1093/sysbio/syw093  0.64
2016 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. PMID 27783600 DOI: 10.1038/nature19827  0.64
2016 Bielejec F, Baele G, Rodrigo AG, Suchard MA, Lemey P. Identifying predictors of time-inhomogeneous viral evolutionary processes. Virus Evolution. 2: vew023. PMID 27774306 DOI: 10.1093/ve/vew023  0.64
2016 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 Pathogens. 12: e1005894. PMID 27631086 DOI: 10.1371/journal.ppat.1005894  1
2016 Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA. Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates. Systematic Biology. PMID 27368344 DOI: 10.1093/sysbio/syw050  0.64
2016 Baele G, Suchard MA, Rambaut A, Lemey P. Emerging concepts of data integration in pathogen phylodynamics. Systematic Biology. PMID 27288481 DOI: 10.1093/sysbio/syw054  0.64
2016 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, et al. Characterizing treatment pathways at scale using the OHDSI network. Proceedings of the National Academy of Sciences of the United States of America. PMID 27274072 DOI: 10.1073/pnas.1510502113  1
2016 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, et al. Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada. Proceedings of the National Academy of Sciences of the United States of America. PMID 27274051 DOI: 10.1073/pnas.1601077113  1
2016 Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P. SpreaD3: interactive visualisation of spatiotemporal history and trait evolutionary processes. Molecular Biology and Evolution. PMID 27189542 DOI: 10.1093/molbev/msw082  0.64
2016 Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN. Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. Plos Computational Biology. 12: e1004789. PMID 26938243 DOI: 10.1371/journal.pcbi.1004789  1
2015 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 Evolution. 1: vev016. PMID 27774287 DOI: 10.1093/ve/vev016  0.64
2015 Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA. ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL. The Annals of Applied Statistics. 9: 969-991. PMID 27053974 DOI: 10.1214/15-AOAS821  1
2015 Singh S, Suchard MA. Pioglitazone Use and Risk of Bladder Cancer. Jama. 314: 2567-8. PMID 26670976 DOI: 10.1001/jama.2015.13912  1
2015 Baele G, Lemey P, Suchard MA. Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty. Systematic Biology. PMID 26526428 DOI: 10.1093/sysbio/syv083  1
2015 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. Journal of Virology. 89: 12341-8. PMID 26423943 DOI: 10.1128/JVI.01681-15  1
2015 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 (London, England). 29: 2045-52. PMID 26355575 DOI: 10.1097/QAD.0000000000000811  1
2015 Trovão NS, Suchard MA, Baele G, Gilbert M, Lemey P. Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1. Molecular Biology and Evolution. PMID 26341298 DOI: 10.1093/molbev/msv185  0.64
2015 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. Journal of Virology. 89: 11275-83. PMID 26311880 DOI: 10.1128/JVI.01571-15  1
2015 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, et al. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Studies in Health Technology and Informatics. 216: 574-8. PMID 26262116 DOI: 10.3233/978-1-61499-564-7-574  1
2015 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 (London, England). 29: 1549-56. PMID 26244394 DOI: 10.1097/QAD.0000000000000731  1
2015 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, ... ... Suchard MA, et al. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature. 523: 217-20. PMID 26053121 DOI: 10.1038/nature14460  1
2015 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. Nature Communications. 6: 6696. PMID 25813399 DOI: 10.1038/ncomms7696  1
2015 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 in Ecology and Evolution / British Ecological Society. 6: 67-82. PMID 25780554 DOI: 10.1111/2041-210X.12293  0.64
2015 Magee D, Beard R, Suchard MA, Lemey P, Scotch M. Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion. Archives of Virology. 160: 215-24. PMID 25355432 DOI: 10.1007/s00705-014-2262-5  1
2015 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. Molecular Ecology Resources. 15: 81-6. PMID 24964386 DOI: 10.1111/1755-0998.12295  1
2015 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 in Ecology and Evolution. 6: 67-82. DOI: 10.1111/2041-210X.12293  1
2014 Beard R, Magee D, Suchard MA, Lemey P, Scotch M. Generalized linear models for identifying predictors of the evolutionary diffusion of viruses. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2014: 23-8. PMID 25717395  0.64
2014 Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proceedings of the National Academy of Sciences of the United States of America. 111: E4736-42. PMID 25336755 DOI: 10.1073/pnas.1416574111  1
2014 Crawford FW, Minin VN, Suchard MA. Estimation for general birth-death processes. Journal of the American Statistical Association. 109: 730-747. PMID 25328261 DOI: 10.1080/01621459.2013.866565  1
2014 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 (New York, N.Y.). 346: 56-61. PMID 25278604 DOI: 10.1126/science.1256739  1
2014 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. The Journal of General Virology. 95: 2784-95. PMID 25205684 DOI: 10.1099/vir.0.070318-0  1
2014 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, ... ... Suchard MA, et al. OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics. 7: 28-34. PMID 24928667 DOI: 10.1016/j.epidem.2014.04.003  1
2014 Bielejec F, Lemey P, Carvalho LM, Baele G, Rambaut A, Suchard MA. πBUSS: A parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios Bmc Bioinformatics. 15. PMID 24885610 DOI: 10.1186/1471-2105-15-133  1
2014 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 Neglected Tropical Diseases. 8: e2769. PMID 24743730 DOI: 10.1371/journal.pntd.0002769  1
2014 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 Computational Biology. 10. PMID 24722319 DOI: 10.1371/journal.pcbi.1003537  1
2014 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 Computational Biology. 10. PMID 24699231 DOI: 10.1371/journal.pcbi.1003505  1
2014 Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: From sequence substitution to phylogeography Systematic Biology. 63: 493-504. PMID 24627184 DOI: 10.1093/sysbio/syu015  1
2014 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 Pathogens. 10: e1003932. PMID 24586153 DOI: 10.1371/journal.ppat.1003932  1
2014 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. 3: e01914. PMID 24497547 DOI: 10.7554/eLife.01914  1
2014 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. Systematic Biology. 63: 178-91. PMID 24335493 DOI: 10.1093/sysbio/syt102  1
2014 Mittal S, Madigan D, Burd RS, Suchard MA. High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis. Biostatistics (Oxford, England). 15: 207-21. PMID 24096388 DOI: 10.1093/biostatistics/kxt043  1
2014 Schuemie MJ, Ryan PB, Suchard MA, Shahn Z, Madigan D. Discussion: An estimate of the science-wise false discovery rate and application to the top medical literature. Biostatistics (Oxford, England). 15: 36-9; discussion 39-. PMID 24068252 DOI: 10.1093/biostatistics/kxt037  1
2014 Schuemie MJ, Ryan PB, DuMouchel W, Suchard MA, Madigan D. Interpreting observational studies: why empirical calibration is needed to correct p-values. Statistics in Medicine. 33: 209-18. PMID 23900808 DOI: 10.1002/sim.5925  1
2014 Weiss RE, Suchard MA. Comment on article by rubio and steel Bayesian Analysis. 9: 29-38. DOI: 10.1214/14-BA870  1
2014 Madigan D, Stang PE, Berlin JA, Schuemie M, Overhage JM, Suchard MA, Dumouchel B, Hartzema AG, Ryan PB. A systematic statistical approach to evaluating evidence from observational studies Annual Review of Statistics and Its Application. 1: 11-39. DOI: 10.1146/annurev-statistics-022513-115645  1
2013 Doss CR, Suchard MA, Holmes I, Kato-Maeda M, Minin VN. Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting. The Annals of Applied Statistics. 7: 2315-2335. PMID 26702330 DOI: 10.1214/13-AOAS673  1
2013 Suchard MA, Simpson SE, Zorych I, Ryan P, Madigan D. Massive parallelization of serial inference algorithms for a complex generalized linear model. Acm Transactions On Modeling and Computer Simulation : a Publication of the Association For Computing Machinery. 23. PMID 25328363 DOI: 10.1145/2414416.2414791  1
2013 Shi M, Lemey P, Singh Brar M, Suchard MA, Murtaugh MP, Carman S, D'Allaire S, Delisle B, Lambert MÈ, Gagnon CA, Ge L, Qu Y, Yoo D, Holmes EC, Chi-Ching Leung F. The spread of type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: a phylogeographic approach. Virology. 447: 146-54. PMID 24210109 DOI: 10.1016/j.virol.2013.08.028  1
2013 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 Safety. 36: S195-204. PMID 24166235 DOI: 10.1007/s40264-013-0112-0  1
2013 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 Safety. 36: S143-58. PMID 24166231 DOI: 10.1007/s40264-013-0108-9  1
2013 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 Safety. 36: S83-93. PMID 24166226 DOI: 10.1007/s40264-013-0100-4  1
2013 Simpson SE, Madigan D, Zorych I, Schuemie MJ, Ryan PB, Suchard MA. Multiple self-controlled case series for large-scale longitudinal observational databases. Biometrics. 69: 893-902. PMID 24117144 DOI: 10.1111/biom.12078  1
2013 Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, ... ... Suchard MA, et al. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science (New York, N.Y.). 341: 1514-7. PMID 24030491 DOI: 10.1126/science.1240578  1
2013 Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein. Elife. 2: e00631. PMID 23682315 DOI: 10.7554/eLife.00631  1
2013 Madigan D, Ryan PB, Schuemie M, Stang PE, Overhage JM, Hartzema AG, Suchard MA, DuMouchel W, Berlin JA. Evaluating the impact of database heterogeneity on observational study results. American Journal of Epidemiology. 178: 645-51. PMID 23648805 DOI: 10.1093/aje/kwt010  1
2013 Crawford FW, Suchard MA. Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees. Systematic Biology. 62: 439-55. PMID 23417679 DOI: 10.1093/sysbio/syt010  1
2013 Cybis GB, Sinsheimer JS, Lemey P, Suchard MA. Graph hierarchies for phylogeography. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120206. PMID 23382428 DOI: 10.1098/rstb.2012.0206  1
2013 Faria NR, Suchard MA, Rambaut A, Streicker DG, Lemey P. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120196. PMID 23382420 DOI: 10.1098/rstb.2012.0196  1
2013 Wu CH, Suchard MA, Drummond AJ. Bayesian selection of nucleotide substitution models and their site assignments. Molecular Biology and Evolution. 30: 669-88. PMID 23233462 DOI: 10.1093/molbev/mss258  1
2013 Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Molecular Biology and Evolution. 30: 713-24. PMID 23180580 DOI: 10.1093/molbev/mss265  1
2013 Baele G, Li WL, Drummond AJ, Suchard MA, Lemey P. Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Molecular Biology and Evolution. 30: 239-43. PMID 23090976 DOI: 10.1093/molbev/mss243  1
2013 Ryan P, Suchard MA, Schuemie M, Madigan D. Learning From Epidemiology: Interpreting Observational Database Studies for the Effects of Medical Products Statistics in Biopharmaceutical Research. 5: 170-179. DOI: 10.1080/19466315.2013.791638  1
2012 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. Emerging Infectious Diseases. 18: 1858-64. PMID 23092706 DOI: 10.3201/eid1811.120217  1
2012 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 (Oxford, England). 28: 3248-56. PMID 23064000 DOI: 10.1093/bioinformatics/bts580  1
2012 Pybus OG, Suchard MA, Lemey P, Bernardin FJ, Rambaut A, Crawford FW, Gray RR, Arinaminpathy N, Stramer SL, Busch MP, Delwart EL. Unifying the spatial epidemiology and molecular evolution of emerging epidemics. Proceedings of the National Academy of Sciences of the United States of America. 109: 15066-71. PMID 22927414 DOI: 10.1073/pnas.1206598109  1
2012 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 (New York, N.Y.). 337: 957-60. PMID 22923579 DOI: 10.1126/science.1219669  1
2012 Gong YN, Chen GW, Suchard MA. A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. Computational Biology and Chemistry. 39: 20-8. PMID 22858722 DOI: 10.1016/j.compbiolchem.2012.06.004  1
2012 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 Biology Letters. 8: 829-832. PMID 22628096 DOI: 10.1098/rsbl.2012.0290  1
2012 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. Molecular Biology and Evolution. 29: 2157-67. PMID 22403239 DOI: 10.1093/molbev/mss084  1
2012 Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7 Molecular Biology and Evolution. 29: 1969-1973. PMID 22367748 DOI: 10.1093/molbev/mss075  1
2012 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 Research and Human Retroviruses. 28: 1766-74. PMID 22364185 DOI: 10.1089/AID.2011.0383  1
2012 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. Systematic Biology. 61: 539-42. PMID 22357727 DOI: 10.1093/sysbio/sys029  1
2012 Allicock OM, Lemey P, Tatem AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A, Carrington CVF. Phylogeography and population dynamics of dengue viruses in the Americas Molecular Biology and Evolution. 29: 1533-1543. PMID 22319149 DOI: 10.1093/molbev/msr320  1
2012 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, ... ... Suchard MA, et al. Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A. The Journal of General Virology. 93: 889-99. PMID 22190015 DOI: 10.1099/vir.0.038638-0  1
2012 Tom JA, Sinsheimer JS, Suchard MA. Does history repeat itself? Wavelets and the phylodynamics of influenza A. Molecular Biology and Evolution. 29: 1367-77. PMID 22160768 DOI: 10.1093/molbev/msr305  1
2012 Crawford FW, Suchard MA. Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution. Journal of Mathematical Biology. 65: 553-80. PMID 21984359 DOI: 10.1007/s00285-011-0471-z  1
2012 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. Systematic Biology. 61: 170-3. PMID 21963610 DOI: 10.1093/sysbio/syr100  1
2012 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. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 12: 453-60. PMID 21565285 DOI: 10.1016/j.meegid.2011.04.028  1
2011 Telesca D, Müller P, Kornblau SM, Suchard MA, Ji Y. Modeling Protein Expression and Protein Signaling Pathways. Journal of the American Statistical Association. 107: 1372-1384. PMID 26246646 DOI: 10.1080/01621459.2012.706121  1
2011 Faria NR, Suchard MA, Rambaut A, Lemey P. Toward a quantitative understanding of viral phylogeography Current Opinion in Virology. 1: 423-429. PMID 22440846 DOI: 10.1016/j.coviro.2011.10.003  1
2011 Weiss RE, Jia J, Suchard MA. A Bayesian model for the common effects of multiple predictors on mixed outcomes. Interface Focus. 1: 886-94. PMID 22419987 DOI: 10.1098/rsfs.2011.0041  1
2011 Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MT, Nielsen R, Ho SY, Goebel T, Graf KE, Byers D, Stenderup JT, ... ... Suchard MA, et al. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature. 479: 359-64. PMID 22048313 DOI: 10.1038/nature10574  1
2011 Bielejec F, Rambaut A, Suchard MA, Lemey P. SPREAD: Spatial phylogenetic reconstruction of evolutionary dynamics Bioinformatics. 27: 2910-2912. PMID 21911333 DOI: 10.1093/bioinformatics/btr481  1
2011 Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, et al. Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology : Cb. 21: 1251-8. PMID 21737280 DOI: 10.1016/j.cub.2011.05.058  1
2011 Nelson MI, Lemey P, Tan Y, Vincent A, LamTommy TTY, 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 Pathogens. 7. PMID 21695237 DOI: 10.1371/journal.ppat.1002077  1
2011 Huelsenbeck JP, Alfaro ME, Suchard MA. Biologically inspired phylogenetic models strongly outperform the no common mechanism model. Systematic Biology. 60: 225-32. PMID 21252385 DOI: 10.1093/sysbio/syq089  1
2011 Edo-Matas D, Lemey P, Tom JA, Serna-Bolea C, van den Blink AE, van 't Wout AB, Schuitemaker H, Suchard MA. Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models. Molecular Biology and Evolution. 28: 1605-16. PMID 21135151 DOI: 10.1093/molbev/msq326  1
2011 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. Molecular Biology and Evolution. 28: 1593-603. PMID 21112962 DOI: 10.1093/molbev/msq319  1
2011 Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG, Rambaut A. A bayesian phylogenetic method to estimate unknown sequence ages Molecular Biology and Evolution. 28: 879-887. PMID 20889726 DOI: 10.1093/molbev/msq262  1
2010 Tom JA, Sinsheimer JS, Suchard MA. Reuse, Recycle, Reweigh: Combating Influenza through Efficient Sequential Bayesian Computation for Massive Data. The Annals of Applied Statistics. 4: 1722-1748. PMID 26681992 DOI: 10.1214/10-AOAS349  1
2010 Zhou H, Lange K, Suchard MA. Graphics Processing Units and High-Dimensional Optimization. Statistical Science : a Review Journal of the Institute of Mathematical Statistics. 25: 311-324. PMID 21847315 DOI: 10.1214/10-STS336  1
2010 Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Jalal N, Faouzi A, Echevarría JE, Morón SV, Rambaut A, Campiz N, Tatem AJ, Holmes EC, Bourhy H. Phylodynamics and Human-mediated dispersal of a zoonotic virus Plos Pathogens. 6. PMID 21060816 DOI: 10.1371/journal.ppat.1001166  1
2010 Suchard MA, Wang Q, Chan C, Frelinger J, Cron A, West M. Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures. Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. 19: 419-438. PMID 20877443 DOI: 10.1198/jcgs.2010.10016  1
2010 Bloomquist EW, Lemey P, Suchard MA. Three roads diverged? Routes to phylogeographic inference. Trends in Ecology & Evolution. 25: 626-32. PMID 20863591 DOI: 10.1016/j.tree.2010.08.010  1
2010 Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all. Bmc Biology. 8: 114. PMID 20807414 DOI: 10.1186/1741-7007-8-114  1
2010 Auguste AJ, Lemey P, Pybus OG, Suchard MA, Salas RA, Adesiyun AA, Barrett AD, Tesh RB, Weaver SC, Carrington CV. Yellow fever virus maintenance in Trinidad and its dispersal throughout the Americas. Journal of Virology. 84: 9967-77. PMID 20631128 DOI: 10.1128/JVI.00588-10  1
2010 Bloomquist EW, Suchard MA. Unifying vertical and nonvertical evolution: a stochastic ARG-based framework. Systematic Biology. 59: 27-41. PMID 20525618 DOI: 10.1093/sysbio/syp076  1
2010 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 Molecular Biology and Evolution. 27: 2038-2051. PMID 20363828 DOI: 10.1093/molbev/msq088  1
2010 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, ... ... Suchard MA, et al. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proceedings of the National Academy of Sciences of the United States of America. 107: 5675-80. PMID 20212118 DOI: 10.1073/pnas.0907189107  1
2010 Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time Molecular Biology and Evolution. 27: 1877-1885. PMID 20203288 DOI: 10.1093/molbev/msq067  1
2010 Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Muñoz-Jordán JL, Pybus OG, Holmes EC, Gubler DJ. Epidemic dynamics revealed in dengue evolution. Molecular Biology and Evolution. 27: 811-8. PMID 19965886 DOI: 10.1093/molbev/msp285  1
2009 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. Computational Statistics & Data Analysis. 53: 766-775. PMID 20442796 DOI: 10.1016/j.csda.2008.06.007  1
2009 Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots Plos Computational Biology. 5. PMID 19779555 DOI: 10.1371/journal.pcbi.1000520  1
2009 Liang LJ, Weiss RE, Redelings B, Suchard MA. Improving phylogenetic analyses by incorporating additional information from genetic sequence databases. Bioinformatics (Oxford, England). 25: 2530-6. PMID 19661240 DOI: 10.1093/bioinformatics/btp473  1
2009 Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics Bioinformatics. 25: 1370-1376. PMID 19369496 DOI: 10.1093/bioinformatics/btp244  1
2009 O'Brien JD, Minin VN, Suchard MA. Learning to count: robust estimates for labeled distances between molecular sequences. Molecular Biology and Evolution. 26: 801-14. PMID 19131426 DOI: 10.1093/molbev/msp003  1
2009 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. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 9: 196-205. PMID 19028604 DOI: 10.1016/j.meegid.2008.10.012  1
2009 Bloomquist EW, Dorman KS, Suchard MA. StepBrothers: inferring partially shared ancestries among recombinant viral sequences. Biostatistics (Oxford, England). 10: 106-20. PMID 18562348 DOI: 10.1093/biostatistics/kxn019  1
2009 Redelings BD, Suchard MA. Robust inferences from ambiguous alignments Sequence Alignment: Methods, Models, Concepts, and Strategies. 209-270.  1
2008 Drummond AJ, Suchard MA. Fully Bayesian tests of neutrality using genealogical summary statistics. Bmc Genetics. 9: 68. PMID 18976476 DOI: 10.1186/1471-2156-9-68  1
2008 Alekseyenko AV, Lee CJ, Suchard MA. Wagner and Dollo: a stochastic duet by composing two parsimonious solos. Systematic Biology. 57: 772-84. PMID 18853363 DOI: 10.1080/10635150802434394  1
2008 Minin VN, Suchard MA. Fast, accurate and simulation-free stochastic mapping. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3985-95. PMID 18852111 DOI: 10.1098/rstb.2008.0176  1
2008 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. Journal of Medicinal Food. 11: 390-4. PMID 18598186 DOI: 10.1089/jmf.2007.650  1
2008 O'Brien JD, She ZS, Suchard MA. Dating the time of viral subtype divergence. Bmc Evolutionary Biology. 8: 172. PMID 18541033 DOI: 10.1186/1471-2148-8-172  1
2008 Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology and Evolution. 25: 1459-71. PMID 18408232 DOI: 10.1093/molbev/msn090  1
2008 Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis. Science (New York, N.Y.). 319: 473-6. PMID 18218900 DOI: 10.1126/science.1151532  1
2008 Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. Journal of Mathematical Biology. 56: 391-412. PMID 17874105 DOI: 10.1007/s00285-007-0120-8  1
2008 Ferreira MAR, Suchard MA. Bayesian analysis of elapsed times in continuous-time Markov chains Canadian Journal of Statistics. 36: 355-368.  1
2007 Huelsenbeck JP, Suchard MA. A nonparametric method for accommodating and testing across-site rate variation. Systematic Biology. 56: 975-87. PMID 18075934 DOI: 10.1080/10635150701670569  1
2007 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. 2: e1188. PMID 18000555 DOI: 10.1371/journal.pone.0001188  1
2007 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. Journal of Agricultural and Food Chemistry. 55: 7732-7. PMID 17722872 DOI: 10.1021/jf071303g  1
2007 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. The Journal of Molecular Diagnostics : Jmd. 9: 158-68. PMID 17384207 DOI: 10.2353/jmoldx.2007.060052  1
2007 Redelings BD, Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. Bmc Evolutionary Biology. 7: 40. PMID 17359539 DOI: 10.1186/1471-2148-7-40  1
2007 Minin VN, Dorman KS, Fang F, Suchard MA. Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes. Genetics. 175: 1773-85. PMID 17194781 DOI: 10.1534/genetics.106.066258  1
2007 Fang F, Ding J, Minin VN, Suchard MA, Dorman KS. cBrother: relaxing parental tree assumptions for Bayesian recombination detection. Bioinformatics (Oxford, England). 23: 507-8. PMID 17145740 DOI: 10.1093/bioinformatics/btl613  1
2007 Guo H, Weiss RE, Gu X, Suchard MA. Time squared: repeated measures on phylogenies. Molecular Biology and Evolution. 24: 352-62. PMID 17079699 DOI: 10.1093/molbev/msl165  1
2007 Rajaram ML, Minin VN, Suchard MA, Dorman KS. Hot and cold: Spatial fluctuation in HIV-1 recombination rates Proceedings of the 7th Ieee International Conference On Bioinformatics and Bioengineering, Bibe. 707-714. DOI: 10.1109/BIBE.2007.4375638  1
2006 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 Research and Human Retroviruses. 22: 1260-6. PMID 17209769 DOI: 10.1089/aid.2006.22.1260  1
2006 Milane MS, Suchard MA, Wong ML, Licinio J. Modeling of the temporal patterns of fluoxetine prescriptions and suicide rates in the United States. Plos Medicine. 3: e190. PMID 16768544 DOI: 10.1371/journal.pmed.0030190  1
2006 Suchard MA, Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics (Oxford, England). 22: 2047-8. PMID 16679334 DOI: 10.1093/bioinformatics/btl175  1
2006 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. Journal of Clinical Microbiology. 44: 561-70. PMID 16455913 DOI: 10.1128/JCM.44.2.561-570.2006  1
2005 Suchard MA, Weiss RE, Sinsheimer JS. Models for estimating bayes factors with applications to phylogeny and tests of monophyly. Biometrics. 61: 665-73. PMID 16135017 DOI: 10.1111/j.1541-0420.2005.00352.x  1
2005 Redelings BD, Suchard MA. Joint Bayesian estimation of alignment and phylogeny. Systematic Biology. 54: 401-18. PMID 16012107 DOI: 10.1080/10635150590947041  1
2005 Minin VN, Dorman KS, Fang F, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics (Oxford, England). 21: 3034-42. PMID 15914546 DOI: 10.1093/bioinformatics/bti459  1
2005 Suchard MA. Stochastic models for horizontal gene transfer: taking a random walk through tree space. Genetics. 170: 419-31. PMID 15781714 DOI: 10.1534/genetics.103.025692  1
2004 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 Journal (Sudbury, Mass.). 10: 339-42. PMID 15701264 DOI: 10.1097/00130404-200411000-00002  1
2004 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. Journal of Virology. 78: 11296-302. PMID 15452249 DOI: 10.1128/JVI.78.20.11296-11302.2004  1
2004 Suchard JR, Suchard MA, Steinfeldt JL. Physician knowledge of herbal toxicities and adverse herb-drug interactions. European Journal of Emergency Medicine : Official Journal of the European Society For Emergency Medicine. 11: 193-7. PMID 15249804  1
2004 Yildiz BO, Suchard MA, Wong ML, McCann SM, Licinio J. Alterations in the dynamics of circulating ghrelin, adiponectin, and leptin in human obesity. Proceedings of the National Academy of Sciences of the United States of America. 101: 10434-9. PMID 15231997 DOI: 10.1073/pnas.0403465101  1
2004 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. Journal of Bacteriology. 186: 2818-28. PMID 15090524 DOI: 10.1128/JB.186.9.2818-2828.2004  1
2003 Sinsheimer JS, Suchard MA, Dorman KS, Fang F, Weiss RE. Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains. Applied Bioinformatics. 2: 131-44. PMID 15130798  1
2003 Suchard MA, Kitchen CM, Sinsheimer JS, Weiss RE. Hierarchical phylogenetic models for analyzing multipartite sequence data. Systematic Biology. 52: 649-64. PMID 14530132 DOI: 10.1080/10635150390238879  1
2003 D'Orsogna MR, Suchard MA, Chou T. Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 68: 021925. PMID 14525024 DOI: 10.1103/PhysRevE.68.021925  1
2003 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. Systematic Biology. 52: 48-54. PMID 12554439  1
2003 Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS. Inferring spatial phylogenetic variation along nucleotide sequences: A multiple changepoint model Journal of the American Statistical Association. 98: 427-437. DOI: 10.1198/016214503000215  1
2003 Suchard MA, Weiss RE, Sinsheimer JS, Dorman KS, Patel M, McCabe ERB. Evolutionary Similarity Among Genes Journal of the American Statistical Association. 98: 653-662. DOI: 10.1198/016214503000000558  1
2002 Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Systematic Biology. 51: 715-28. PMID 12396586 DOI: 10.1080/10635150290102384  1
2002 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. 51: 2105-12. PMID 12086939  1
2001 Suchard MA, Bailey JN, Elashoff DA, Sinsheimer JS. SNPing away at candidate genes Genetic Epidemiology. 21: S643-S648. PMID 11793754  1
2001 Mantzoros CS, Ozata M, Negrao AB, Suchard MA, Ziotopoulou M, Caglayan S, Elashoff RM, Cogswell RJ, Negro P, Liberty V, Wong ML, Veldhuis J, Ozdemir IC, Gold PW, Flier JS, et al. Synchronicity of frequently sampled thyrotropin (TSH) and leptin concentrations in healthy adults and leptin-deficient subjects: Evidence for possible partial TSH regulation by leptin in humans Journal of Clinical Endocrinology and Metabolism. 86: 3284-3291. PMID 11443202 DOI: 10.1210/jc.86.7.3284  1
2001 Suchard MA, Weiss RE, Sinsheimer JS. Bayesian selection of continuous-time Markov chain evolutionary models. Molecular Biology and Evolution. 18: 1001-13. PMID 11371589  1
2000 Chitnavis J, Sinsheimer JS, Suchard MA, Clipsham K, Carr AJ. End-stage coxarthrosis and gonarthrosis. Aetiology, clinical patterns and radiological features of idiopathic osteoarthritis Rheumatology. 39: 612-619. PMID 10888705  1
1999 Suchard MA, Yudkin P, Sinsheimer JS, Fowler GH. General practitioners' views on genetic screening for common diseases British Journal of General Practice. 49: 45-46. PMID 10622017  1
1999 Bailey JN, Suchard MA, Smalley SL, Sinsheimer JS. Search for a gene x environment interaction: G x E hunt Genetic Epidemiology. 17: S491-S496. PMID 10597481 DOI: 10.1002/gepi.1370170779  1
1999 Suchard MA, Yudkin P, Sinsheimer JS. Are general practitioners willing and able to provide genetic services for common diseases? Journal of Genetic Counseling. 8: 301-311. DOI: 10.1023/A:1022934316284  1
1998 Deloukas P, Schuler GD, Gyapay G, Beasley EM, Soderlund C, Rodriguez-Tomé P, Hui L, Matise TC, McKusick KB, Beckmann JS, Bentolila S, Bihoreau M, Birren BB, Browne J, Butler A, ... ... Suchard MA, et al. A physical map of 30,000 human genes. Science (New York, N.Y.). 282: 744-6. PMID 9784132 DOI: 10.1126/science.282.5389.744  1
1998 Suchard MA, Hadfield R, Elliott T, Kennedy S. Beyond providing information: The Internet as a research tool in reproductive medicine Human Reproduction. 13: 6-7. PMID 9512219  1
1997 Rose PW, Suchard MA. Screening people with a family history of cancer. Taking a family history in primary care is important Bmj (Clinical Research Ed.). 315: 1306. PMID 9390066  1
1997 Bell R, Petticrew M, Rose PW, Suchard MA. Screening people with a family history of cancer (multiple letters) [3] British Medical Journal. 315: 1306.  1
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