Marc A. Suchard, Ph.D. - Publications

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

193 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
2022 Zhao J, Dellicour S, Yan Z, Veit M, Gill MS, He WT, Zhai X, Ji X, Suchard MA, Lemey P, Su S. Early Genomic Surveillance and Phylogeographic Analysis of Getah Virus, a Reemerging Arbovirus, in Livestock in China. Journal of Virology. e0109122. PMID 36475767 DOI: 10.1128/jvi.01091-22  0.511
2022 Holbrook AJ, Ji X, Suchard MA. BAYESIAN MITIGATION OF SPATIAL COARSENING FOR A HAWKES MODEL APPLIED TO GUNFIRE, WILDFIRE AND VIRAL CONTAGION. The Annals of Applied Statistics. 16: 573-595. PMID 36211254 DOI: 10.1214/21-aoas1517  0.495
2022 Fisher AA, Hassler GW, Ji X, Baele G, Suchard MA, Lemey P. Scalable Bayesian phylogenetics. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210242. PMID 35989603 DOI: 10.1098/rstb.2021.0242  0.497
2022 McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, ... ... Suchard MA, et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature. PMID 35952712 DOI: 10.1038/s41586-022-05200-3  0.449
2022 Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, ... ... Suchard MA, et al. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science (New York, N.Y.). eabp8337. PMID 35881005 DOI: 10.1126/science.abp8337  0.756
2022 Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats. Cell Reports. 39: 110969. PMID 35679864 DOI: 10.1016/j.celrep.2022.110969  0.435
2022 He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, et al. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell. PMID 35298912 DOI: 10.1016/j.cell.2022.02.014  0.421
2022 Holbrook AJ, Ji X, Suchard MA. From viral evolution to spatial contagion: a biologically modulated Hawkes model. Bioinformatics (Oxford, England). PMID 35040956 DOI: 10.1093/bioinformatics/btac027  0.549
2021 McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, ... ... Suchard MA, et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Medrxiv : the Preprint Server For Health Sciences. PMID 34981069 DOI: 10.1101/2021.12.14.21267606  0.451
2021 Kraemer M, McCrone J, Hill V, Bajaj S, Evans-Pena R, Lambert B, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski A, Sadilek A, Wu N, ... ... Suchard M, et al. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Research Square. PMID 34981043 DOI: 10.21203/  0.452
2021 He WT, Bollen N, Xu Y, Zhao J, Dellicour S, Yan Z, Gong W, Zhang C, Zhang L, Lu M, Lai A, Suchard MA, Ji X, Tu C, Lemey P, et al. Phylogeography reveals association between swine trade and the spread of porcine epidemic diarrhea virus in China and across the world. Molecular Biology and Evolution. PMID 34951645 DOI: 10.1093/molbev/msab364  0.477
2021 Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Oude Munnink BB, Koopmans M, Sadilek A, Lai S, Tatem AJ, Baele G, ... Suchard MA, et al. Untangling introductions and persistence in COVID-19 resurgence in Europe. Nature. PMID 34192736 DOI: 10.1038/s41586-021-03754-2  0.461
2021 Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Oude Munnink BB, Koopmans M, Sadilek A, Lai S, Tatem AJ, Baele G, ... Suchard MA, et al. Untangling introductions and persistence in COVID-19 resurgence in Europe. Nature. PMID 34192736 DOI: 10.1038/s41586-021-03754-2  0.461
2021 Lemey P, Ruktanonchai N, Hong S, Colizza V, Poletto C, den Broeck FV, Gill M, Ji X, Levasseur A, Sadilek A, Lai S, Tatem A, Baele G, Suchard M, Dellicour S. SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data. Research Square. PMID 33594355 DOI: 10.21203/  0.463
2020 Hassler G, Tolkoff MR, Allen WL, Ho LST, Lemey P, Suchard MA. Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements. Journal of the American Statistical Association. 117: 678-692. PMID 36060555 DOI: 10.1080/01621459.2020.1799812  0.304
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  0.606
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  0.315
2020 Schuemie MJ, Ryan PB, Pratt N, Chen R, You SC, Krumholz HM, Madigan D, Hripcsak G, Suchard MA. Principles of Large-scale Evidence Generation and Evaluation across a Network of Databases (LEGEND). Journal of the American Medical Informatics Association : Jamia. 27: 1331-1337. PMID 32909033 DOI: 10.1093/Jamia/Ocaa103  0.313
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  0.581
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  0.306
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  0.357
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  0.473
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  0.443
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  0.565
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  0.335
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  0.48
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  0.329
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  0.464
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  0.338
2020 Holbrook AJ, Lemey P, Baele G, Dellicour S, Brockmann D, Rambaut A, Suchard MA. Massive Parallelization Boosts Big Bayesian Multidimensional Scaling Journal of Computational and Graphical Statistics. 1-14. DOI: 10.1080/10618600.2020.1754226  0.319
2020 Hassler G, Tolkoff MR, Allen WL, Ho LST, Lemey P, Suchard MA. Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements Journal of the American Statistical Association. 1-39. DOI: 10.1080/01621459.2020.1799812  0.336
2019 Kawaguchi ES, Suchard MA, Liu Z, Li G. A surrogate ℓ sparse Cox's regression with applications to sparse high-dimensional massive sample size time-to-event data. Statistics in Medicine. PMID 31814146 DOI: 10.1002/Sim.8438  0.401
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  0.308
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  0.374
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  0.388
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  0.582
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  0.388
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  0.35
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  0.436
2019 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, ... ... Suchard MA, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. Plos Computational Biology. 15: e1006650. PMID 30958812 DOI: 10.1371/Journal.Pcbi.1006650  0.383
2019 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 Evolution. 5: vey043. PMID 30838129 DOI: 10.1093/Ve/Vey043  0.377
2019 Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, et al. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science (New York, N.Y.). 363: 74-77. PMID 30606844 DOI: 10.1126/Science.Aau9343  0.355
2018 Dinh V, Tung Ho LS, Suchard MA, Matsen FA. Consistency and convergence rate of phylogenetic inference via regularization. Annals of Statistics. 46: 1481-1512. PMID 30344357 DOI: 10.1214/17-Aos1592  0.388
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  0.407
2018 Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, ... ... Suchard MA, et al. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science (New York, N.Y.). PMID 30139911 DOI: 10.1126/Science.Aat7115  0.351
2018 Schuemie MJ, Ryan PB, Hripcsak G, Madigan D, Suchard MA. Improving reproducibility by using high-throughput observational studies with empirical calibration. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 376. PMID 30082302 DOI: 10.1098/Rsta.2017.0356  0.361
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  0.405
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  0.622
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  0.328
2018 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. Journal of the American Medical Informatics Association : Jamia. PMID 29718407 DOI: 10.1093/Jamia/Ocy032  0.332
2018 Ho LST, Crawford FW, Suchard MA. Direct likelihood-based inference for discretely observed stochastic compartmental models of infectious disease The Annals of Applied Statistics. 12: 1993-2021. DOI: 10.1214/18-Aoas1141  0.589
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  0.407
2017 Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis. Systematic Biology. PMID 28950376 DOI: 10.1093/Sysbio/Syx066  0.411
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  0.726
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  0.371
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  0.361
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  0.442
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  0.455
2017 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 Computational Biology. 13: e1005389. PMID 28170397 DOI: 10.1371/Journal.Pcbi.1005389  0.395
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  0.687
2016 Shaddox TR, Ryan PB, Schuemie MJ, Madigan D, Suchard MA. Hierarchical Models for Multiple, Rare Outcomes Using Massive Observational Healthcare Databases. Statistical Analysis and Data Mining. 9: 260-268. PMID 28503249 DOI: 10.1002/Sam.11324  0.345
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  0.32
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  0.473
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  0.359
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  0.443
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  0.391
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  0.333
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  0.306
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  0.39
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  0.642
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  0.417
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  0.727
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  0.456
2015 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. The Annals of Applied Statistics. 9: 572-596. PMID 26500711 DOI: 10.1214/15-Aoas809  0.675
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  0.311
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  0.358
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  0.308
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  0.326
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  0.36
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  0.46
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  0.363
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  0.346
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  0.323
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  0.576
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  0.716
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  0.333
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  0.344
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  0.37
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  0.392
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  0.305
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  0.384
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  0.48
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  0.386
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  0.339
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  0.327
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  0.314
2014 Weiss RE, Suchard MA. Comment on article by rubio and steel Bayesian Analysis. 9: 29-38. DOI: 10.1214/13-Ba870  0.49
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  0.621
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  0.342
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  0.351
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  0.311
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  0.302
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  0.631
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  0.722
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  0.368
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  0.439
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  0.443
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  0.418
2013 Silverman N, Suchard M. Predicting Horse Race Winners Through A Regularized Conditional Logistic Regression With Frailty The Journal of Prediction Markets. 7: 43-52. DOI: 10.5750/Jpm.V7I1.595  0.357
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  0.336
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  0.37
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  0.634
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  0.62
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  0.367
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  0.339
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  0.456
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  0.414
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  0.59
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  0.423
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  0.4
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  0.366
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  0.811
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  0.57
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  0.362
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  0.395
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  0.329
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  0.363
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  0.642
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  0.309
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  0.318
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  0.346
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  0.375
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  0.807
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  0.391
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  0.398
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  0.801
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  0.363
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  0.372
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  0.746
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  0.361
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  0.389
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  0.77
2010 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. 404: 5-20. PMID 20451945 DOI: 10.1016/J.Virol.2010.04.008  0.331
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  0.402
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  0.339
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  0.434
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  0.453
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  0.744
2009 Lemey P, Suchard M, Rambaut A. Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatial-temporal model for the global spread of H1N1pdm. Plos Currents. 1: RRN1031. PMID 20029613 DOI: 10.1371/Currents.Rrn1031  0.439
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  0.444
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  0.695
2009 Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics Bioinformatics. 25: 1370-1376. PMID 19369496 DOI: 10.1093/Bioinformatics/Btp244  0.409
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  0.667
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  0.317
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  0.806
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  0.399
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  0.46
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  0.611
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  0.413
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  0.807
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  0.372
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  0.607
2008 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. Human Mutation. 29: 176-81. PMID 17694540 DOI: 10.1002/Humu.20593  0.316
2008 Suchard MA, Lange K, Sinsheimer JS. Efficiency of Protein Production from mRNA Journal of Statistical Theory and Practice. 2: 173-182. DOI: 10.1080/15598608.2008.10411869  0.65
2008 Ferreira MAR, Suchard MA. Bayesian analysis of elapsed times in continuous-time Markov chains Canadian Journal of Statistics. 36: 355-368. DOI: 10.1002/Cjs.5550360302  0.358
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  0.359
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  0.411
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  0.749
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  0.729
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  0.62
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  0.71
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  0.367
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  0.42
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  0.744
2005 Redelings BD, Suchard MA. Joint Bayesian estimation of alignment and phylogeny. Systematic Biology. 54: 401-18. PMID 16012107 DOI: 10.1080/10635150590947041  0.42
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  0.749
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  0.399
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  0.376
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  0.343
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  0.788
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  0.784
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  0.321
2003 Paraskevis D, Lemey P, Salemi M, Suchard M, Van De Peer Y, Vandamme AM. Analysis of the Evolutionary Relationships of HIV-1 and SIVcpz Sequences Using Bayesian Inference: Implications for the Origin of HIV-1 Molecular Biology and Evolution. 20: 1986-1996. PMID 12949143 DOI: 10.1093/Molbev/Msg207  0.345
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 DOI: 10.1080/10635150390132713  0.767
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  0.819
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  0.779
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  0.799
2001 Suchard MA, Bailey JN, Elashoff DA, Sinsheimer JS. SNPing away at candidate genes Genetic Epidemiology. 21: S643-S648. PMID 11793754 DOI: 10.1002/Gepi.2001.21.S1.S643  0.67
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 DOI: 10.1093/Oxfordjournals.Molbev.A003872  0.766
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 DOI: 10.1093/Rheumatology/39.6.612  0.635
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  0.614
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  0.638
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  0.64
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