Marc Adam Suchard
Professor, Human Genetics, University of California Los Angeles
Professor, Computational Medicine, University of California Los Angeles
Education and Training
University of California, Los Angeles | MD | 2004 | |
University of California, Los Angeles | PhD | 2002 | Biomathematics |
Publications
- Collienne L, Barker M, Suchard MA, Matsen Iv FA. Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference.. Systematic biology, 2024.
- Holtz A, Van Weyenbergh J, Hong SL, Cuypers L, O'Toole Á, Dudas G, Gerdol M, Potter BI, Ntoumi F, Mapanguy CCM, Vanmechelen B, Wawina-Bokalanga T, Van Holm B, Menezes SM, Soubotko K, Van Pottelbergh G, Wollants E, Vermeersch P, Jacob AS, Maes B, Obbels D, Matheeussen V, Martens G, Gras J, Verhasselt B, Laffut W, Vael C, Goegebuer T, van der Kant R, Rousseau F, Schymkowitz J, Serrano L, Delgado J, Wenseleers T, Bours V, André E, Suchard MA, Rambaut A, Dellicour S, Maes P, Durkin K, Baele G. Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature.. BMC infectious diseases, 2024.
- Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.. Cell, 2024.
- Zhao J, Wan W, Yu K, Lemey P, Pettersson JH, Bi Y, Lu M, Li X, Chen Z, Zheng M, Yan G, Dai J, Li Y, Haerheng A, He N, Tu C, Suchard MA, Holmes EC, He WT, Su S. Farmed fur animals harbour viruses with zoonotic spillover potential.. Nature, 2024.
- Khera R, Aminorroaya A, Dhingra LS, Thangaraj PM, Pedroso Camargos A, Bu F, Ding X, Nishimura A, Anand TV, Arshad F, Blacketer C, Chai Y, Chattopadhyay S, Cook M, Dorr DA, Duarte-Salles T, DuVall SL, Falconer T, French TE, Hanchrow EE, Kaur G, Lau WCY, Li J, Li K, Liu Y, Lu Y, Man KKC, Matheny ME, Mathioudakis N, McLeggon JA, McLemore MF, Minty E, Morales DR, Nagy P, Ostropolets A, Pistillo A, Phan TP, Pratt N, Reyes C, Richter L, Ross JS, Ruan E, Seager SL, Simon KR, Viernes B, Yang J, Yin C, You SC, Zhou JJ, Ryan PB, Schuemie MJ, Krumholz HM, Hripcsak G, Suchard MA. Comparative Effectiveness of Second-Line Antihyperglycemic Agents for Cardiovascular Outcomes: A Multinational, Federated Analysis of LEGEND-T2DM.. Journal of the American College of Cardiology, 2024.
- Brusselmans M, Carvalho LM, Hong SL, Gao J, Matsen FA, Rambaut A, Lemey P, Suchard MA, Dudas G, Baele G. On the importance of assessing topological convergence in Bayesian phylogenetic inference.. ArXiv, 2024.
- Pekar JE, Wang Y, Wang JC, Shao Y, Taki F, Forgione LA, Amin H, Clabby T, Johnson K, Torian LV, Braunstein SL, Pathela P, Omoregie E, Hughes S, Suchard MA, Vasylyeva TI, Lemey P, Wertheim JO. Genomic epidemiology reveals 2022 mpox epidemic in New York City governed by heavy-tailed sexual contact networks.. medRxiv : the preprint server for health sciences, 2024.
- Gallego-García P, Estévez-Gómez N, De Chiara L, Alvariño P, Juiz-González PM, Torres-Beceiro I, Poza M, Vallejo JA, Rumbo-Feal S, Conde-Pérez K, Aja-Macaya P, Ladra S, Moreno-Flores A, Gude-González MJ, Coira A, Aguilera A, Costa-Alcalde JJ, Trastoy R, Barbeito-Castiñeiras G, García-Souto D, Tubio JMC, Trigo-Daporta M, Camacho-Zamora P, Costa JG, González-Domínguez M, Canoura-Fernández L, Glez-Peña D, Pérez-Castro S, Cabrera JJ, Daviña-Núñez C, Godoy-Diz M, Treinta-Álvarez AB, Veiga MI, Sousa JC, Osório NS, Comas I, González-Candelas F, Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Agulla A, Bou G, Alonso-García P, Pérez-Del-Molino ML, García-Campello M, Paz-Vidal I, Regueiro B, Posada D. Dispersal history of SARS-CoV-2 in Galicia, Spain.. Journal of medical virology, 2024.
- Gallego-García P, Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Posada D. Dispersal history of SARS-CoV-2 variants Alpha, Delta, and Omicron (BA.1) in Spain.. medRxiv : the preprint server for health sciences, 2024.
- Fridgeirsson EA, Williams R, Rijnbeek P, Suchard MA, Reps JM. Comparing penalization methods for linear models on large observational health data.. Journal of the American Medical Informatics Association : JAMIA, 2024.
- Parker E, Omah IF, Varilly P, Magee A, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-Ewe OO, Ogunsanya OA, Olono A, Eromon P, Tomkins-Tinch CH, Otieno JR, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, Djuicy DD, Essengue LLM, Yifomnjou MHM, Zeller M, Gangavarapu K, O'Toole Á, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Njoum R, Ihekweazu C, Jide I, Adetifa I, Happi CT. Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans.. medRxiv : the preprint server for health sciences, 2024.
- Djuicy DD, Omah IF, Parker E, Tomkins-Tinch CH, Otieno JR, Yifomnjou MHM, Essengue LLM, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-Ewe OO, Ogunsanya OA, Olono A, Eromon P, Yonga MGW, Essima GD, Touoyem IP, Mounchili LJM, Eyangoh SI, Esso L, Nguidjol IME, Metomb SF, Chebo C, Agwe SM, Mossi HM, Bilounga CN, Etoundi AGM, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, O'Toole Á, Magee A, Zeller M, Gangavarapu K, Varilly P, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Ihekweazu C, Jide I, Adetifa I, Njoum R, Happi CT. Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa.. medRxiv : the preprint server for health sciences, 2024.
- Kang M, Wang LF, Sun BW, Wan WB, Ji X, Baele G, Bi YH, Suchard MA, Lai A, Zhang M, Wang L, Zhu YH, Ma L, Li HP, Haerheng A, Qi YR, Wang RL, He N, Su S. Zoonotic infections by avian influenza virus: changing global epidemiology, investigation, and control.. The Lancet. Infectious diseases, 2024.
- Bastide P, Rocu P, Wirtz J, Hassler GW, Chevenet F, Fargette D, Suchard MA, Dellicour S, Lemey P, Guindon S. Modeling the velocity of evolving lineages and predicting dispersal patterns.. bioRxiv : the preprint server for biology, 2024.
- Li Y, Bollen N, Hong SL, Brusselmans M, Gámbaro F, Suchard MA, Rambaut A, Lemey P, Dellicour S, Baele G. spread.gl: visualising pathogen dispersal in a high-performance browser application.. medRxiv : the preprint server for health sciences, 2024.
- Dellicour S, Bastide P, Rocu P, Fargette D, Hardy OJ, Suchard MA, Guindon S, Lemey P. How fast are viruses spreading in the wild?. bioRxiv : the preprint server for biology, 2024.
- Thangaraj PM, Oikonomou EK, Dhingra LS, Aminorroaya A, Jayaram R, Suchard MA, Khera R. Computational Phenomapping of Randomized Clinical Trials to Enable Assessment of their Real-world Representativeness and Personalized Inference.. medRxiv : the preprint server for health sciences, 2024.
- Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Matsen Iv FA, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. Random-effects substitution models for phylogenetics via scalable gradient approximations.. Systematic biology, 2024.
- Hripcsak G, Zhang L, Li K, Suchard MA, Ryan PB, Schuemie MJ. Assessing Covariate Balance with Small Sample Sizes.. medRxiv : the preprint server for health sciences, 2024.
- Langedijk AC, Vrancken B, Lebbink RJ, Wilkins D, Kelly EJ, Baraldi E, Mascareñas de Los Santos AH, Danilenko DM, Choi EH, Palomino MA, Chi H, Keller C, Cohen R, Papenburg J, Pernica J, Greenough A, Richmond P, Martinón-Torres F, Heikkinen T, Stein RT, Hosoya M, Nunes MC, Verwey C, Evers A, Kragten-Tabatabaie L, Suchard MA, Kosakovsky Pond SL, Poletto C, Colizza V, Lemey P, Bont LJ, INFORM-RSV Study Group. The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus.. Nature communications, 2024.
- Shao Y, Magee AF, Vasylyeva TI, Suchard MA. Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.. PLoS computational biology, 2024.
- Cai CX, Nishimura A, Bowring MG, Westlund E, Tran D, Ng JH, Nagy P, Cook M, McLeggon JA, DuVall SL, Matheny ME, Golozar A, Ostropolets A, Minty E, Desai P, Bu F, Toy B, Hribar M, Falconer T, Zhang L, Lawrence-Archer L, Boland MV, Goetz K, Hall N, Shoaibi A, Reps J, Sena AG, Blacketer C, Swerdel J, Jhaveri KD, Lee E, Gilbert Z, Zeger SL, Crews DC, Suchard MA, Hripcsak G, Ryan PB. Similar Risk of Kidney Failure among Patients with Blinding Diseases Who Receive Ranibizumab, Aflibercept, and Bevacizumab: An Observational Health Data Sciences and Informatics Network Study.. Ophthalmology. Retina, 2024.
- Anand TV, Bu F, Schuemie MJ, Suchard MA, Hripcsak G. Comparative safety and effectiveness of angiotensin converting enzyme inhibitors and thiazides and thiazide-like diuretics under strict monotherapy.. Journal of clinical hypertension (Greenwich, Conn.), 2024.
- Parino F, Gustani-Buss E, Bedford T, Suchard MA, Trovão NS, Rambaut A, Colizza V, Poletto C, Lemey P. Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation.. medRxiv : the preprint server for health sciences, 2024.
- Bu F, Arshad F, Hripcsak G, Ryan PB, Schuemie MJ, Suchard MA. Authors' Response to Huang et al.'s Comment on "Serially Combining Epidemiological Designs Does Not Improve Overall Signal Detection in Vaccine Safety Surveillance".. Drug safety, 2024.
- Gallego-García P, Estévez-Gómez N, De Chiara L, Alvariño P, Juiz-González PM, Torres-Beceiro I, Poza M, Vallejo JA, Rumbo-Feal S, Conde-Pérez K, Aja-Macaya P, Ladra S, Moreno-Flores A, Gude-González MJ, Coira A, Aguilera A, Costa-Alcalde JJ, Trastoy R, Barbeito-Castiñeiras G, García-Souto D, Tubio JMC, Trigo-Daporta M, Camacho-Zamora P, Costa JG, González-Domínguez M, Canoura-Fernández L, Glez-Peña D, Pérez-Castro S, Cabrera JJ, Daviña-Núñez C, Godoy-Diz M, Treinta-Álvarez AB, Veiga MI, Sousa JC, Osório NS, Comas I, González-Candelas F, Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Agulla A, Bou G, Alonso-García P, Pérez-Del-Molino ML, García-Campello M, Paz-Vidal I, Regueiro B, Posada D. Dispersal history of SARS-CoV-2 in Galicia, Spain.. medRxiv : the preprint server for health sciences, 2024.
- Khera R, Aminorroaya A, Dhingra LS, Thangaraj PM, Camargos AP, Bu F, Ding X, Nishimura A, Anand TV, Arshad F, Blacketer C, Chai Y, Chattopadhyay S, Cook M, Dorr DA, Duarte-Salles T, DuVall SL, Falconer T, French TE, Hanchrow EE, Kaur G, Lau WC, Li J, Li K, Liu Y, Lu Y, Man KK, Matheny ME, Mathioudakis N, McLeggon JA, McLemore MF, Minty E, Morales DR, Nagy P, Ostropolets A, Pistillo A, Phan TP, Pratt N, Reyes C, Richter L, Ross J, Ruan E, Seager SL, Simon KR, Viernes B, Yang J, Yin C, You SC, Zhou JJ, Ryan PB, Schuemie MJ, Krumholz HM, Hripcsak G, Suchard MA. Comparative Effectiveness of Second-line Antihyperglycemic Agents for Cardiovascular Outcomes: A Large-scale, Multinational, Federated Analysis of the LEGEND-T2DM Study.. medRxiv : the preprint server for health sciences, 2024.
- Gangavarapu K, Ji X, Baele G, Fourment M, Lemey P, Matsen FA, Suchard MA. Many-core algorithms for high-dimensional gradients on phylogenetic trees.. Bioinformatics (Oxford, England), 2024.
- Schuemie M, Reps J, Black A, Defalco F, Evans L, Fridgeirsson E, Gilbert JP, Knoll C, Lavallee M, Rao GA, Rijnbeek P, Sadowski K, Sena A, Swerdel J, Williams RD, Suchard M. Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research.. Studies in health technology and informatics, 2024.
- Didier G, Glatt-Holtz NE, Holbrook AJ, Magee AF, Suchard MA. On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2.. Proceedings of the National Academy of Sciences of the United States of America, 2024.
- Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics.. Cell, 2023.
- Bu F, Schuemie MJ, Nishimura A, Smith LH, Kostka K, Falconer T, McLeggon JA, Ryan PB, Hripcsak G, Suchard MA. Bayesian safety surveillance with adaptive bias correction.. Statistics in medicine, 2023.
- Oikonomou EK, Thangaraj PM, Bhatt DL, Ross JS, Young LH, Krumholz HM, Suchard MA, Khera R. An explainable machine learning-based phenomapping strategy for adaptive predictive enrichment in randomized clinical trials.. NPJ digital medicine, 2023.
- Makadia R, Shoaibi A, Rao GA, Ostropolets A, Rijnbeek PR, Voss EA, Duarte-Salles T, Ramírez-Anguita JM, Mayer MA, Maljkovic F, Denaxas S, Nyberg F, Papez V, Sena AG, Alshammari TM, Lai LYH, Haynes K, Suchard MA, Hripcsak G, Ryan PB. Evaluating the impact of alternative phenotype definitions on incidence rates across a global data network.. JAMIA open, 2023.
- Fisher AA, Ji X, Nishimura A, Baele G, Lemey P, Suchard MA. Shrinkage-based Random Local Clocks with Scalable Inference.. Molecular biology and evolution, 2023.
- O'Toole Á, Neher RA, Ndodo N, Borges V, Gannon B, Gomes JP, Groves N, King DJ, Maloney D, Lemey P, Lewandowski K, Loman N, Myers R, Omah IF, Suchard MA, Worobey M, Chand M, Ihekweazu C, Ulaeto D, Adetifa I, Rambaut A. APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016.. Science (New York, N.Y.), 2023.
- Shao Y, Magee AF, Vasylyeva TI, Suchard MA. Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.. bioRxiv : the preprint server for biology, 2023.
- Oikonomou EK, Thangaraj PM, Bhatt DL, Ross JS, Young LH, Krumholz HM, Suchard MA, Khera R. An explainable machine learning-based phenomapping strategy for adaptive predictive enrichment in randomized controlled trials.. medRxiv : the preprint server for health sciences, 2023.
- Ji X, Fisher AA, Su S, Thorne JL, Potter B, Lemey P, Baele G, Suchard MA. Scalable Bayesian Divergence Time Estimation With Ratio Transformations.. Systematic biology, 2023.
- Schar D, Zhang Z, Pires J, Vrancken B, Suchard MA, Lemey P, Ip M, Gilbert M, Van Boeckel T, Dellicour S. Dispersal history and bidirectional human-fish host switching of invasive, hypervirulent Streptococcus agalactiae sequence type 283.. PLOS global public health, 2023.
- Khera R, Dhingra LS, Aminorroaya A, Li K, Zhou JJ, Arshad F, Blacketer C, Bowring MG, Bu F, Cook M, Dorr DA, Duarte-Salles T, DuVall SL, Falconer T, French TE, Hanchrow EE, Horban S, Lau WC, Li J, Liu Y, Lu Y, Man KK, Matheny ME, Mathioudakis N, McLemore MF, Minty E, Morales DR, Nagy P, Nishimura A, Ostropolets A, Pistillo A, Posada JD, Pratt N, Reyes C, Ross JS, Seager S, Shah N, Simon K, Wan EY, Yang J, Yin C, You SC, Schuemie MJ, Ryan PB, Hripcsak G, Krumholz H, Suchard MA. Multinational patterns of second line antihyperglycaemic drug initiation across cardiovascular risk groups: federated pharmacoepidemiological evaluation in LEGEND-T2DM.. BMJ medicine, 2023.
- Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Iv FAM, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. Random-effects substitution models for phylogenetics via scalable gradient approximations.. ArXiv, 2023.
- Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.. bioRxiv : the preprint server for biology, 2023.
- You SC, Seo SI, Falconer T, Yanover C, Duarte-Salles T, Seager S, Posada JD, Shah NH, Nguyen PA, Kim Y, Hsu JC, Van Zandt M, Hsu MH, Lee HL, Ko H, Shin WG, Pratt N, Park RW, Reich CG, Suchard MA, Hripcsak G, Park CH, Prieto-Alhambra D. Ranitidine Use and Incident Cancer in a Multinational Cohort.. JAMA network open, 2023.
- McBride DS, Garushyants SK, Franks J, Magee AF, Overend SH, Huey D, Williams AM, Faith SA, Kandeil A, Trifkovic S, Miller L, Jeevan T, Patel A, Nolting JM, Tonkovich MJ, Genders JT, Montoney AJ, Kasnyik K, Linder TJ, Bevins SN, Lenoch JB, Chandler JC, DeLiberto TJ, Koonin EV, Suchard MA, Lemey P, Webby RJ, Nelson MI, Bowman AS. Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.. Nature communications, 2023.
- Zhang Z, Nishimura A, Trovão NS, Cherry JL, Holbrook AJ, Ji X, Lemey P, Suchard MA. Accelerating Bayesian inference of dependency between mixed-type biological traits.. PLoS computational biology, 2023.
- Wu Q, Schuemie MJ, Suchard MA, Ryan P, Hripcsak GM, Rohde CA, Chen Y. Padé approximant meets federated learning: A nearly lossless, one-shot algorithm for evidence synthesis in distributed research networks with rare outcomes.. Journal of biomedical informatics, 2023.
- He WT, Li D, Baele G, Zhao J, Jiang Z, Ji X, Veit M, Suchard MA, Holmes EC, Lemey P, Boni MF, Su S. Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype.. Virus evolution, 2023.
- Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals.. Trends in microbiology, 2023.
- Jun SH, Nasif H, Jennings-Shaffer C, Rich DH, Kooperberg A, Fourment M, Zhang C, Suchard MA, Matsen FA. A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm.. Algorithms for molecular biology : AMB, 2023.
- Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, COVID-19 Genomics UK (COG-UK) consortium¶, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.. Science (New York, N.Y.), 2023.
- Pekar JE, Lytras S, Ghafari M, Magee AF, Parker E, Havens JL, Katzourakis A, Vasylyeva TI, Suchard MA, Hughes AC, Hughes J, Robertson DL, Dellicour S, Worobey M, Wertheim JO, Lemey P. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.. bioRxiv : the preprint server for biology, 2023.
- Yang J, Schuemie MJ, Ji X, Suchard MA. Massive Parallelization of Massive Sample-size Survival Analysis.. Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America, 2023.
- Arshad F, Schuemie MJ, Bu F, Minty EP, Alshammari TM, Lai LYH, Duarte-Salles T, Fortin S, Nyberg F, Ryan PB, Hripcsak G, Prieto-Alhambra D, Suchard MA. Serially Combining Epidemiological Designs Does Not Improve Overall Signal Detection in Vaccine Safety Surveillance.. Drug safety, 2023.
- Fourment M, Swanepoel CJ, Galloway JG, Ji X, Gangavarapu K, Suchard MA, Matsen Iv FA. Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation.. Genome biology and evolution, 2023.
- Ostropolets A, Albogami Y, Conover M, Banda JM, Baumgartner WA, Blacketer C, Desai P, DuVall SL, Fortin S, Gilbert JP, Golozar A, Ide J, Kanter AS, Kern DM, Kim C, Lai LYH, Li C, Liu F, Lynch KE, Minty E, Neves MI, Ng DQ, Obene T, Pera V, Pratt N, Rao G, Rappoport N, Reinecke I, Saroufim P, Shoaibi A, Simon K, Suchard MA, Swerdel JN, Voss EA, Weaver J, Zhang L, Hripcsak G, Ryan PB. Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study.. Journal of the American Medical Informatics Association : JAMIA, 2023.
- Voss EA, Shoaibi A, Yin Hui Lai L, Blacketer C, Alshammari T, Makadia R, Haynes K, Sena AG, Rao G, van Sandijk S, Fraboulet C, Boyer L, Le Carrour T, Horban S, Morales DR, Martínez Roldán J, Ramírez-Anguita JM, Mayer MA, de Wilde M, John LH, Duarte-Salles T, Roel E, Pistillo A, Kolde R, Maljkovic F, Denaxas S, Papez V, Kahn MG, Natarajan K, Reich C, Secora A, Minty EP, Shah NH, Posada JD, Garcia Morales MT, Bosca D, Cadenas Juanino H, Diaz Holgado A, Pedrera Jiménez M, Serrano Balazote P, García Barrio N, Sen S, Üresin AY, Erdogan B, Belmans L, Byttebier G, Malbrain MLNG, Dedman DJ, Cuccu Z, Vashisht R, Butte AJ, Patel A, Dahm L, Han C, Bu F, Arshad F, Ostropolets A, Nyberg F, Hripcsak G, Suchard MA, Prieto-Alhambra D, Rijnbeek PR, Schuemie MJ, Ryan PB. Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study.. EClinicalMedicine, 2023.
- Nargesi AA, Clark C, Aminorroaya A, Chen L, Liu M, Reddy A, Amodeo S, Oikonomou EK, Suchard MA, McGuire DK, Lin Z, Inzucchi S, Khera R. Persistence on Novel Cardioprotective Antihyperglycemic Therapies in the United States.. The American journal of cardiology, 2023.
- Gangavarapu K, Ji X, Baele G, Fourment M, Lemey P, Iv FAM, Suchard MA. Many-core algorithms for high-dimensional gradients on phylogenetic trees.. ArXiv, 2023.
- Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S, GISAID Core and Curation Team, Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.. Nature methods, 2023.
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- Li X, Burn E, Duarte-Salles T, Yin C, Reich C, Delmestri A, Verhamme K, Rijnbeek P, Suchard MA, Li K, Mosseveld M, John LH, Mayer MA, Ramirez-Anguita JM, Cohet C, Strauss V, Prieto-Alhambra D. Comparative risk of thrombosis with thrombocytopenia syndrome or thromboembolic events associated with different covid-19 vaccines: international network cohort study from five European countries and the US.. BMJ (Clinical research ed.), 2022.
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- Nishimura A, Xie J, Kostka K, Duarte-Salles T, Fernández Bertolín S, Aragón M, Blacketer C, Shoaibi A, DuVall SL, Lynch K, Matheny ME, Falconer T, Morales DR, Conover MM, Chan You S, Pratt N, Weaver J, Sena AG, Schuemie MJ, Reps J, Reich C, Rijnbeek PR, Ryan PB, Hripcsak G, Prieto-Alhambra D, Suchard MA. International cohort study indicates no association between alpha-1 blockers and susceptibility to COVID-19 in benign prostatic hyperplasia patients.. Frontiers in pharmacology, 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, 2022.
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- Worobey M, Levy JI, Malpica Serrano L, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, Suchard MA, Wertheim JO, Lemey P, Robertson DL, Garry RF, Holmes EC, Rambaut A, Andersen KG. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic.. Science (New York, N.Y.), 2022.
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- Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou J, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RT, Freitas L, Maurer-Stroh S, GISAID core and curation team, Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.. Research square, 2022.
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- Truong Nguyen P, Kant R, Van den Broeck F, Suvanto MT, Alburkat H, Virtanen J, Ahvenainen E, Castren R, Hong SL, Baele G, Ahava MJ, Jarva H, Jokiranta ST, Kallio-Kokko H, Kekäläinen E, Kirjavainen V, Kortela E, Kurkela S, Lappalainen M, Liimatainen H, Suchard MA, Hannula S, Ellonen P, Sironen T, Lemey P, Vapalahti O, Smura T. The phylodynamics of SARS-CoV-2 during 2020 in Finland.. Communications medicine, 2022.
- Khera R, Schuemie MJ, Lu Y, Ostropolets A, Chen R, Hripcsak G, Ryan PB, Krumholz HM, Suchard MA. Large-scale evidence generation and evaluation across a network of databases for type 2 diabetes mellitus (LEGEND-T2DM): a protocol for a series of multinational, real-world comparative cardiovascular effectiveness and safety studies.. BMJ open, 2022.
- Shoaibi A, Rao GA, Voss EA, Ostropolets A, Mayer MA, Ramírez-Anguita JM, Maljkovic F, Carevic B, Horban S, Morales DR, Duarte-Salles T, Fraboulet C, Le Carrour T, Denaxas S, Papez V, John LH, Rijneek PR, Minty E, Alshammari TM, Makadia R, Blacketer C, DeFalco F, Sena AG, Suchard MA, Prieto-Alhambra D, Ryan PB. Phenotype Algorithms for the Identification and Characterization of Vaccine-Induced Thrombotic Thrombocytopenia in Real World Data: A Multinational Network Cohort Study.. Drug safety, 2022.
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- Quintero I, Suchard MA, Jetz W. Macroevolutionary dynamics of climatic niche space.. Proceedings. Biological sciences, 2022.
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- Patrono LV, Vrancken B, Budt M, Düx A, Lequime S, Boral S, Gilbert MTP, Gogarten JF, Hoffmann L, Horst D, Merkel K, Morens D, Prepoint B, Schlotterbeck J, Schuenemann VJ, Suchard MA, Taubenberger JK, Tenkhoff L, Urban C, Widulin N, Winter E, Worobey M, Schnalke T, Wolff T, Lemey P, Calvignac-Spencer S. Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic.. Nature communications, 2022.
- Nishimura A, Suchard MA. Prior-Preconditioned Conjugate Gradient Method for Accelerated Gibbs Sampling in "Large n, Large p" Bayesian Sparse Regression.. Journal of the American Statistical Association, 2022.
- Ostropolets A, Li X, Makadia R, Rao G, Rijnbeek PR, Duarte-Salles T, Sena AG, Shaoibi A, Suchard MA, Ryan PB, Prieto-Alhambra D, Hripcsak G. Factors Influencing Background Incidence Rate Calculation: Systematic Empirical Evaluation Across an International Network of Observational Databases.. Frontiers in pharmacology, 2022.
- Nishimura A, Suchard MA. Shrinkage with shrunken shoulders: Gibbs sampling shrinkage model posteriors with guaranteed convergence rates.. Bayesian analysis, 2022.
- Oikonomou EK, Suchard MA, McGuire DK, Khera R. Phenomapping-Derived Tool to Individualize the Effect of Canagliflozin on Cardiovascular Risk in Type 2 Diabetes.. Diabetes care, 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, 2022.
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- Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJR, Baliga NS, Stoeger T, Ruffin F, Richardson RAK, Gao CA, Horvath TD, Haag AM, Wu Q, Savidge T, Yeaman MR. Mathematical models to study the biology of pathogens and the infectious diseases they cause.. iScience, 2022.
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- 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, Li J, Lemey P, Guo D, Tu C, Holmes EC, Shi M, Su S. Virome characterization of game animals in China reveals a spectrum of emerging pathogens.. Cell, 2022.
- Morales DR, Ostropolets A, Lai L, Sena A, Duvall S, Suchard M, Verhamme K, Rjinbeek P, Posada J, Ahmed W, Alshammary T, Alghoul H, Alser O, Areia C, Blacketer C, Burn E, Casajust P, You SC, Dawoud D, Golozar A, Gong M, Jonnagaddala J, Lynch K, Matheny M, Minty E, Nyberg F, Uribe A, Recalde M, Reich C, Scheumie M, Shah K, Shah N, Schilling L, Vizcaya D, Zhang L, Hripcsak G, Ryan P, Prieto-Alhambra D, Durate-Salles T, Kostka K. Characteristics and outcomes of COVID-19 patients with and without asthma from the United States, South Korea, and Europe.. The Journal of asthma : official journal of the Association for the Care of Asthma, 2022.
- 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, Baele G, Su S. Phylogeography Reveals Association between Swine Trade and the Spread of Porcine Epidemic Diarrhea Virus in China and across the World.. Molecular biology and evolution, 2022.
- Williams RD, Markus AF, Yang C, Duarte-Salles T, DuVall SL, Falconer T, Jonnagaddala J, Kim C, Rho Y, Williams AE, Machado AA, An MH, Aragón M, Areia C, Burn E, Choi YH, Drakos I, Abrahão MTF, Fernández-Bertolín S, Hripcsak G, Kaas-Hansen BS, Kandukuri PL, Kors JA, Kostka K, Liaw ST, Lynch KE, Machnicki G, Matheny ME, Morales D, Nyberg F, Park RW, Prats-Uribe A, Pratt N, Rao G, Reich CG, Rivera M, Seinen T, Shoaibi A, Spotnitz ME, Steyerberg EW, Suchard MA, You SC, Zhang L, Zhou L, Ryan PB, Prieto-Alhambra D, Reps JM, Rijnbeek PR. Seek COVER: using a disease proxy to rapidly develop and validate a personalized risk calculator for COVID-19 outcomes in an international network.. BMC medical research methodology, 2022.
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- Dellicour S, Gill MS, Faria NR, Rambaut A, Pybus OG, Suchard MA, Lemey P. Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST.. Molecular biology and evolution, 2021.
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- 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 : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America, 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, 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, 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, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. 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, 2020.
- Hripcsak G, Suchard MA, Shea S, Chen R, You SC, Pratt N, Madigan D, Krumholz HM, Ryan PB, Schuemie MJ. Comparison of Cardiovascular and Safety Outcomes of Chlorthalidone vs Hydrochlorothiazide to Treat Hypertension.. JAMA internal medicine, 2020.
- Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D, Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz S, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region.. Bioinformatics (Oxford, England), 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, 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, 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, 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, 2020.
- Schuemie MJ, Cepeda MS, Suchard MA, Yang J, Tian Y, Schuler A, Ryan PB, Madigan D, Hripcsak G. How Confident Are We about Observational Findings in Healthcare: A Benchmark Study.. Harvard data science review, 2020.
- Monjane AL, Dellicour S, Hartnady P, Oyeniran KA, Owor BE, Bezuidenhout M, Linderme D, Syed RA, Donaldson L, Murray S, Rybicki EP, Kvarnheden A, Yazdkhasti E, Lefeuvre P, Froissart R, Roumagnac P, Shepherd DN, Harkins GW, Suchard MA, Lemey P, Varsani A, Martin DP. Symptom evolution following the emergence of maize streak virus.. eLife, 2020.
- Kawaguchi ES, Suchard MA, Liu Z, Li G. A surrogate ℓ0 sparse Cox's regression with applications to sparse high-dimensional massive sample size time-to-event data.. Statistics in medicine, 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, Hamers RL, Ndembi N, Baele G, Peeters M, Pybus OG, Lemey P, Dellicour S. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa.. PLoS pathogens, 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, 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, 2019.
- Suchard MA, Schuemie MJ, Krumholz HM, You SC, Chen R, Pratt N, Reich CG, Duke J, Madigan D, Hripcsak G, Ryan PB. Comprehensive comparative effectiveness and safety of first-line antihypertensive drug classes: a systematic, multinational, large-scale analysis.. Lancet (London, England), 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, 2019.
- You SC, Jung S, Swerdel JN, Ryan PB, Schuemie MJ, Suchard MA, Lee S, Cho J, Hripcsak G, Park RW, Park S. Comparison of First-Line Dual Combination Treatments in Hypertension: Real-World Evidence from Multinational Heterogeneous Cohorts.. Korean circulation journal, 2019.
- Schuemie MJ, Ryan PB, Man KKC, Wong ICK, Suchard MA, Hripcsak G. A plea to stop using the case-control design in retrospective database studies.. Statistics in medicine, 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, 2019.
- Schuemie MJ, Madigan D, Ryan PB, Reich C, Suchard MA, Berlin JA, Hripcsak G. Comment on "How pharmacoepidemiology networks can manage distributed analyses to improve replicability and transparency and minimize bias".. Pharmacoepidemiology and drug safety, 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, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.. PLoS computational biology, 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, 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.), 2019.
- Tian Y, Schuemie MJ, Suchard MA. Evaluating large-scale propensity score performance through real-world and synthetic data experiments.. International journal of epidemiology, 2018.
- Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B. Recent advances in computational phylodynamics.. Current opinion in virology, 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, 2018.
- Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.. Systematic biology, 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, 2018.
- Dinh V, Tung Ho LS, Suchard MA, Matsen FA. Consistency and convergence rate of phylogenetic inference via regularization.. Annals of statistics, 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, 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, 2018.
- Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis.. Systematic biology, 2018.
- Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA. Empirical confidence interval calibration for population-level effect estimation studies in observational healthcare data.. Proceedings of the National Academy of Sciences of the United States of America, 2018.
- Crawford FW, Ho LST, Suchard MA. Computational methods for birth-death processes.. Wiley interdisciplinary reviews. Computational statistics, 2018.
- Vrancken B, Suchard MA, Lemey P. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.. Virus evolution, 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, 2017.
- Duke JD, Ryan PB, Suchard MA, Hripcsak G, Jin P, Reich C, Schwalm MS, Khoma Y, Wu Y, Xu H, Shah NH, Banda JM, Schuemie MJ. Risk of angioedema associated with levetiracetam compared with phenytoin: Findings of the observational health data sciences and informatics research network.. Epilepsia, 2017.
- Baele G, Lemey P, Rambaut A, Suchard MA. Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.. Bioinformatics (Oxford, England), 2017.
- Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA. A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution.. Systematic biology, 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, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A. Virus genomes reveal factors that spread and sustained the Ebola epidemic.. Nature, 2017.
- 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, 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, 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, 2017.
- Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics.. Systematic biology, 2017.
- Worobey M, Watts TD, McKay RA, Suchard MA, Granade T, Teuwen DE, Koblin BA, Heneine W, Lemey P, Jaffe HW. 1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America.. Nature, 2016.
- Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA. Robust empirical calibration of p-values using observational data.. Statistics in medicine, 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, 2016.
- Bielejec F, Baele G, Rodrigo AG, Suchard MA, Lemey P. Identifying predictors of time-inhomogeneous viral evolutionary processes.. Virus evolution, 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, 2016.
- Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA. Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates.. Systematic biology, 2016.
- Baele G, Suchard MA, Bielejec F, Lemey P. Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation.. Microbial genomics, 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, Shapiro B. 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, 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, Pratt N, Madigan D. Characterizing treatment pathways at scale using the OHDSI network.. Proceedings of the National Academy of Sciences of the United States of America, 2016.
- Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P. SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.. Molecular biology and evolution, 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, 2016.
- 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, 2015.
- Singh S, Suchard MA. Pioglitazone Use and Risk of Bladder Cancer.. JAMA, 2015.
- Baele G, Lemey P, Suchard MA. Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty.. Systematic biology, 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, 2015.
- Winand R, Theys K, Eusébio M, Aerts J, Camacho RJ, Gomes P, Suchard MA, Vandamme AM, Abecasis AB, Portuguese HIV-1 Resistance Study Group. Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals.. AIDS (London, England), 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, 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, 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), 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, Potdar V, Rambaut A, Shu Y, Skepner E, Smith DJ, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P, Russell CA. Global circulation patterns of seasonal influenza viruses vary with antigenic drift.. Nature, 2015.
- 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, 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, 2015.
- Scotch M, Suchard MA, Rabinowitz PM. Analysis of Viral Genetics for Estimating Diffusion of Influenza A H6N1.. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 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, Madigan D, Ryan PB. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.. Studies in health technology and informatics, 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, 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, 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, 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, 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.), 2014.
- Strickland SL, Rife BD, Lamers SL, Nolan DJ, Veras NMC, Prosperi MCF, 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, 2014.
- 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, 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, 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, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N. OutbreakTools: a new platform for disease outbreak analysis using the R software.. Epidemics, 2014.
- 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, 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, 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 Joint Summits on Translational Science, 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, 2014.
- Crawford FW, Minin VN, Suchard MA. Estimation for general birth-death processes.. Journal of the American Statistical Association, 2014.
- Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.. Systematic biology, 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, 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, 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, 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, 2013.
- Mittal S, Madigan D, Burd RS, Suchard MA. High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.. Biostatistics (Oxford, England), 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, 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, 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, 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, 2013.
- 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), 2013.
- 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, 2013.
- Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein.. eLife, 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, 2013.
- Crawford FW, Suchard MA. Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees.. Systematic biology, 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, 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, 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, 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, 2013.
- Wu CH, Suchard MA, Drummond AJ. Bayesian selection of nucleotide substitution models and their site assignments.. Molecular biology and evolution, 2012.
- 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, 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, 2012.
- Baele G, Li WL, Drummond AJ, Suchard MA, Lemey P. Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.. Molecular biology and evolution, 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), 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, 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.), 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, 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, 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, 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, 2012.
- Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7.. Molecular biology and evolution, 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, 2012.
- Allicock OM, Lemey P, Tatem AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A, Carrington CV. Phylogeography and population dynamics of dengue viruses in the Americas.. Molecular biology and evolution, 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, Goubau P, de Sousa JD, Vandamme AM, Suchard MA, Lemey P. Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A.. The Journal of general virology, 2011.
- Tom JA, Sinsheimer JS, Suchard MA. Does history repeat itself? Wavelets and the phylodynamics of influenza A.. Molecular biology and evolution, 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, Rasmussen M, Campos PF, Leonard JA, Koepfli KP, Froese D, Zazula G, Stafford TW, Aaris-Sørensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. Species-specific responses of Late Quaternary megafauna to climate and humans.. Nature, 2011.
- Faria NR, Suchard MA, Rambaut A, Lemey P. Toward a quantitative understanding of viral phylogeography.. Current opinion in virology, 2011.
- Crawford FW, Suchard MA. Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution.. Journal of mathematical biology, 2011.
- 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, 2011.
- Bielejec F, Rambaut A, Suchard MA, Lemey P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics.. Bioinformatics (Oxford, England), 2011.
- Weiss RE, Jia J, Suchard MA. A Bayesian model for the common effects of multiple predictors on mixed outcomes.. Interface focus, 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, Thomas MG, Bradley DG, Shapiro B. Ancient hybridization and an Irish origin for the modern polar bear matriline.. Current biology : CB, 2011.
- Nelson MI, Lemey P, Tan Y, Vincent A, Lam TT, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC, Gramer M. Spatial dynamics of human-origin H1 influenza A virus in North American swine.. PLoS pathogens, 2011.
- 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, 2011.
- Huelsenbeck JP, Alfaro ME, Suchard MA. Biologically inspired phylogenetic models strongly outperform the no common mechanism model.. Systematic biology, 2011.
- Telesca D, Müller P, Kornblau SM, Suchard MA, Ji Y. Modeling Protein Expression and Protein Signaling Pathways.. Journal of the American Statistical Association, 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, 2010.
- 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, 2010.
- Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Nourlil J, Jalal N, Faouzi A, Echevarría JE, Vazquez Morón S, Rambaut A, Campiz N, Tatem AJ, Holmes EC, Bourhy H. Phylodynamics and human-mediated dispersal of a zoonotic virus.. PLoS pathogens, 2010.
- Shapiro B, Ho SY, Drummond AJ, Suchard MA, Pybus OG, Rambaut A. A Bayesian phylogenetic method to estimate unknown sequence ages.. Molecular biology and evolution, 2010.
- Bloomquist EW, Lemey P, Suchard MA. Three roads diverged? Routes to phylogeographic inference.. Trends in ecology & evolution, 2010.
- Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all.. BMC biology, 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, 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, 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, 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, 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, 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, Shepherd K, Suchard MA, Zazula GD, Shapiro B, Gilbert MT. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics.. Proceedings of the National Academy of Sciences of the United States of America, 2010.
- Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time.. Molecular biology and evolution, 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, 2010.
- Bloomquist EW, Suchard MA. Unifying vertical and nonvertical evolution: a stochastic ARG-based framework.. Systematic biology, 2009.
- Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots.. PLoS computational biology, 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, 2009.
- Liang LJ, Weiss RE, Redelings B, Suchard MA. Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.. Bioinformatics (Oxford, England), 2009.
- Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics.. Bioinformatics (Oxford, England), 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, 2009.
- O'Brien JD, Minin VN, Suchard MA. Learning to count: robust estimates for labeled distances between molecular sequences.. Molecular biology and evolution, 2009.
- Minin VN, Suchard MA. Fast, accurate and simulation-free stochastic mapping.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2008.
- 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, 2008.
- Drummond AJ, Suchard MA. Fully Bayesian tests of neutrality using genealogical summary statistics.. BMC genetics, 2008.
- Alekseyenko AV, Lee CJ, Suchard MA. Wagner and Dollo: a stochastic duet by composing two parsimonious solos.. Systematic biology, 2008.
- Bloomquist EW, Dorman KS, Suchard MA. StepBrothers: inferring partially shared ancestries among recombinant viral sequences.. Biostatistics (Oxford, England), 2008.
- O'Brien JD, She ZS, Suchard MA. Dating the time of viral subtype divergence.. BMC evolutionary biology, 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, 2008.
- Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.. Molecular biology and evolution, 2008.
- Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis.. Science (New York, N.Y.), 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, 2008.
- Huelsenbeck JP, Suchard MA. A nonparametric method for accommodating and testing across-site rate variation.. Systematic biology, 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, 2007.
- Su F, Lang J, Kumar A, Ng C, Hsieh B, Suchard MA, Reddy ST, Farias-Eisner R. Validation of candidate serum ovarian cancer biomarkers for early detection.. Biomarker insights, 2007.
- Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution.. Journal of mathematical biology, 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, 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, 2007.
- Redelings BD, Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens.. BMC evolutionary biology, 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, 2006.
- Fang F, Ding J, Minin VN, Suchard MA, Dorman KS. cBrother: relaxing parental tree assumptions for Bayesian recombination detection.. Bioinformatics (Oxford, England), 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, 2006.
- Guo H, Weiss RE, Gu X, Suchard MA. Time squared: repeated measures on phylogenies.. Molecular biology and evolution, 2006.
- Seeram NP, Henning SM, Zhang Y, Suchard M, Li Z, Heber D. Pomegranate juice ellagitannin metabolites are present in human plasma and some persist in urine for up to 48 hours.. The Journal of nutrition, 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, 2006.
- Suchard MA, Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.. Bioinformatics (Oxford, England), 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, 2006.
- Suchard MA, Weiss RE, Sinsheimer JS. Models for estimating bayes factors with applications to phylogeny and tests of monophyly.. Biometrics, 2005.
- Redelings BD, Suchard MA. Joint Bayesian estimation of alignment and phylogeny.. Systematic biology, 2005.
- Minin VN, Dorman KS, Fang F, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection.. Bioinformatics (Oxford, England), 2005.
- Suchard MA. Stochastic models for horizontal gene transfer: taking a random walk through tree space.. Genetics, 2005.
- Hamilton G, Currat M, Ray N, Heckel G, Beaumont M, Excoffier L. Bayesian estimation of recent migration rates after a spatial expansion.. Genetics, 2005.
- 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.), 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, 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, 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, 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, 2004.
- Suchard MA, Kitchen CM, Sinsheimer JS, Weiss RE. Hierarchical phylogenetic models for analyzing multipartite sequence data.. Systematic biology, 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, 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, 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, 2003.
- Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage.. Systematic biology, 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, 2002.
- Suchard MA, Yudkin P, Sinsheimer JS, Fowler GH. General practitioners' views on genetic screening for common diseases.. The British journal of general practice : the journal of the Royal College of General Practitioners, 1999.