Education and Training

Publications

1. 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.
2. 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.
3. 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 OHDSI Network Study.. Ophthalmology. Retina, 2024.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.
40. 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.
41. McBride D, Garushyants S, Franks J, Magee A, Overend S, Huey D, Williams A, Faith S, Kandeil A, Trifkovic S, Miller L, Jeevan T, Patel A, Nolting J, Tonkovich M, Genders JT, Montoney A, Kasnyik K, Linder T, Bevins S, Lenoch J, Chandler J, DeLiberto T, Koonin E, Suchard M, Lemey P, Webby R, Nelson M, Bowman A. Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.. Research square, 2023.
42. Schuemie MJ, Bu F, Nishimura A, Suchard MA. Adjusting for both sequential testing and systematic error in safety surveillance using observational data: Empirical calibration and MaxSPRT.. Statistics in medicine, 2023.
43. 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, 2022.
44. Schuemie MJ, Arshad F, Pratt N, Nyberg F, Alshammari TM, Hripcsak G, Ryan P, Prieto-Alhambra D, Lai LYH, Li X, Fortin S, Minty E, Suchard MA. Corrigendum: Vaccine safety surveillance using routinely collected healthcare data-An empirical evaluation of epidemiological designs.. Frontiers in pharmacology, 2022.
45. Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Bulgarian SARS-CoV-2 sequencing group, Communicable Diseases Genomics Network (Australia and New Zealand), COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveillance Network, GISAID core curation team, Network for Genomic Surveillance in South Africa (NGS-SA), Swiss SARS-CoV-2 Sequencing Consortium, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance.. Nature communications, 2022.
46. Oikonomou EK, Spatz ES, Suchard MA, Khera R. Individualising intensive systolic blood pressure reduction in hypertension using computational trial phenomaps and machine learning: a post-hoc analysis of randomised clinical trials.. The Lancet. Digital health, 2022.
47. 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.
48. Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S. Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades.. Nature communications, 2022.
49. Nahata KD, Bielejec F, Monetta J, Dellicour S, Rambaut A, Suchard MA, Baele G, Lemey P. SPREAD 4: online visualisation of pathogen phylogeographic reconstructions.. Virus evolution, 2022.
50. 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.
51. 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.
52. Parker E, Anderson C, Zeller M, Tibi A, Havens JL, Laroche G, Benlarbi M, Ariana A, Robles-Sikisaka R, Latif AA, Watts A, Awidi A, Jaradat SA, Gangavarapu K, Ramesh K, Kurzban E, Matteson NL, Han AX, Hughes LD, McGraw M, Spencer E, Nicholson L, Khan K, Suchard MA, Wertheim JO, Wohl S, Côté M, Abdelnour A, Andersen KG, Abu-Dayyeh I. Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions.. Nature communications, 2022.
53. 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, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, COVID-19 Genomics UK (COG-UK) Consortium, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant.. Nature, 2022.
54. 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.
55. 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, Park H, Park MS, Ching Zi Yan K, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.. Science (New York, N.Y.), 2022.
56. Schuemie MJ, Arshad F, Pratt N, Nyberg F, Alshammari TM, Hripcsak G, Ryan P, Prieto-Alhambra D, Lai LYH, Li X, Fortin S, Minty E, Suchard MA. Vaccine Safety Surveillance Using Routinely Collected Healthcare Data-An Empirical Evaluation of Epidemiological Designs.. Frontiers in pharmacology, 2022.
57. 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.
58. Hassler GW, Gallone B, Aristide L, Allen WL, Tolkoff MR, Holbrook AJ, Baele G, Lemey P, Suchard MA. Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis.. Methods in ecology and evolution, 2022.
59. 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.
60. 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.
61. 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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63. Quintero I, Suchard MA, Jetz W. Macroevolutionary dynamics of climatic niche space.. Proceedings. Biological sciences, 2022.
64. Dellicour S, Lemey P, Suchard MA, Gilbert M, Baele G. Accommodating sampling location uncertainty in continuous phylogeography.. Virus evolution, 2022.
65. 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.
66. 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.
67. 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.
68. 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.
69. 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.
70. Holbrook AJ, Ji X, Suchard MA. From viral evolution to spatial contagion: a biologically modulated Hawkes model.. Bioinformatics (Oxford, England), 2022.
71. Lai LY, Arshad F, Areia C, Alshammari TM, Alghoul H, Casajust P, Li X, Dawoud D, Nyberg F, Pratt N, Hripcsak G, Suchard MA, Prieto-Alhambra D, Ryan P, Schuemie MJ. Current Approaches to Vaccine Safety Using Observational Data: A Rationale for the EUMAEUS (Evaluating Use of Methods for Adverse Events Under Surveillance-for Vaccines) Study Design.. Frontiers in pharmacology, 2022.
72. Kostka K, Duarte-Salles T, Prats-Uribe A, Sena AG, Pistillo A, Khalid S, Lai LYH, Golozar A, Alshammari TM, Dawoud DM, Nyberg F, Wilcox AB, Andryc A, Williams A, Ostropolets A, Areia C, Jung CY, Harle CA, Reich CG, Blacketer C, Morales DR, Dorr DA, Burn E, Roel E, Tan EH, Minty E, DeFalco F, de Maeztu G, Lipori G, Alghoul H, Zhu H, Thomas JA, Bian J, Park J, Martínez Roldán J, Posada JD, Banda JM, Horcajada JP, Kohler J, Shah K, Natarajan K, Lynch KE, Liu L, Schilling LM, Recalde M, Spotnitz M, Gong M, Matheny ME, Valveny N, Weiskopf NG, Shah N, Alser O, Casajust P, Park RW, Schuff R, Seager S, DuVall SL, You SC, Song S, Fernández-Bertolín S, Fortin S, Magoc T, Falconer T, Subbian V, Huser V, Ahmed WU, Carter W, Guan Y, Galvan Y, He X, Rijnbeek PR, Hripcsak G, Ryan PB, Suchard MA, Prieto-Alhambra D. Unraveling COVID-19: A Large-Scale Characterization of 4.5 Million COVID-19 Cases Using CHARYBDIS.. Clinical epidemiology, 2022.
73. 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.
74. Lu Y, Van Zandt M, Liu Y, Li J, Wang X, Chen Y, Chen Z, Cho J, Dorajoo SR, Feng M, Hsu MH, Hsu JC, Iqbal U, Jonnagaddala J, Li YC, Liaw ST, Lim HS, Ngiam KY, Nguyen PA, Park RW, Pratt N, Reich C, Rhee SY, Sathappan SMK, Shin SJ, Tan HX, You SC, Zhang X, Krumholz HM, Suchard MA, Xu H. Analysis of Dual Combination Therapies Used in Treatment of Hypertension in a Multinational Cohort.. JAMA network open, 2022.
75. 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.
76. 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.
77. 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.
78. 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.
79. Moreno-Martos D, Verhamme K, Ostropolets A, Kostka K, Duarte-Sales T, Prieto-Alhambra D, Alshammari TM, Alghoul H, Ahmed WU, Blacketer C, DuVall S, Lai L, Matheny M, Nyberg F, Posada J, Rijnbeek P, Spotnitz M, Sena A, Shah N, Suchard M, Chan You S, Hripcsak G, Ryan P, Morales D. Characteristics and outcomes of COVID-19 patients with COPD from the United States, South Korea, and Europe.. Wellcome open research, 2022.
80. Reyes C, Pistillo A, Fernández-Bertolín S, Recalde M, Roel E, Puente D, Sena AG, Blacketer C, Lai L, Alshammari TM, Ahmed WU, Alser O, Alghoul H, Areia C, Dawoud D, Prats-Uribe A, Valveny N, de Maeztu G, Sorlí Redó L, Martinez Roldan J, Lopez Montesinos I, Schilling LM, Golozar A, Reich C, Posada JD, Shah N, You SC, Lynch KE, DuVall SL, Matheny ME, Nyberg F, Ostropolets A, Hripcsak G, Rijnbeek PR, Suchard MA, Ryan P, Kostka K, Duarte-Salles T. Characteristics and outcomes of patients with COVID-19 with and without prevalent hypertension: a multinational cohort study.. BMJ open, 2021.
81. 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, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, COVID-19 genomics UK (COG-UK) consortium, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant.. medRxiv : the preprint server for health sciences, 2021.
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84. Schuemie MJ, Chen Y, Madigan D, Suchard MA. Combining cox regressions across a heterogeneous distributed research network facing small and zero counts.. Statistical methods in medical research, 2021.
85. Li X, Lai LY, Ostropolets A, Arshad F, Tan EH, Casajust P, Alshammari TM, Duarte-Salles T, Minty EP, Areia C, Pratt N, Ryan PB, Hripcsak G, Suchard MA, Schuemie MJ, Prieto-Alhambra D. Bias, Precision and Timeliness of Historical (Background) Rate Comparison Methods for Vaccine Safety Monitoring: An Empirical Multi-Database Analysis.. Frontiers in pharmacology, 2021.
86. Tan EH, Sena AG, Prats-Uribe A, You SC, Ahmed WU, Kostka K, Reich C, Duvall SL, Lynch KE, Matheny ME, Duarte-Salles T, Bertolin SF, Hripcsak G, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Blacketer C, Alshammari TM, Alghoul H, Alser O, Lane JCE, Dawoud DM, Shah K, Yang Y, Zhang L, Areia C, Golozar A, Recalde M, Casajust P, Jonnagaddala J, Subbian V, Vizcaya D, Lai LYH, Nyberg F, Morales DR, Posada JD, Shah NH, Gong M, Vivekanantham A, Abend A, Minty EP, Suchard M, Rijnbeek P, Ryan PB, Prieto-Alhambra D. COVID-19 in patients with autoimmune diseases: characteristics and outcomes in a multinational network of cohorts across three countries.. Rheumatology (Oxford, England), 2021.
87. Khalid S, Yang C, Blacketer C, Duarte-Salles T, Fernández-Bertolín S, Kim C, Park RW, Park J, Schuemie MJ, Sena AG, Suchard MA, You SC, Rijnbeek PR, Reps JM. A standardized analytics pipeline for reliable and rapid development and validation of prediction models using observational health data.. Computer methods and programs in biomedicine, 2021.
88. 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.
89. Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States.. Cell, 2021.
90. Chen R, Suchard MA, Krumholz HM, Schuemie MJ, Shea S, Duke J, Pratt N, Reich CG, Madigan D, You SC, Ryan PB, Hripcsak G. Comparative First-Line Effectiveness and Safety of ACE (Angiotensin-Converting Enzyme) Inhibitors and Angiotensin Receptor Blockers: A Multinational Cohort Study.. Hypertension (Dallas, Tex. : 1979), 2021.
91. Roel E, Pistillo A, Recalde M, Sena AG, Fernández-Bertolín S, Aragón M, Puente D, Ahmed WU, Alghoul H, Alser O, Alshammari TM, Areia C, Blacketer C, Carter W, Casajust P, Culhane AC, Dawoud D, DeFalco F, DuVall SL, Falconer T, Golozar A, Gong M, Hester L, Hripcsak G, Tan EH, Jeon H, Jonnagaddala J, Lai LYH, Lynch KE, Matheny ME, Morales DR, Natarajan K, Nyberg F, Ostropolets A, Posada JD, Prats-Uribe A, Reich CG, Rivera DR, Schilling LM, Soerjomataram I, Shah K, Shah NH, Shen Y, Spotniz M, Subbian V, Suchard MA, Trama A, Zhang L, Zhang Y, Ryan PB, Prieto-Alhambra D, Kostka K, Duarte-Salles T. Characteristics and Outcomes of Over 300,000 Patients with COVID-19 and History of Cancer in the United States and Spain.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2021.
92. Meyer M, Gunn BM, Malherbe DC, Gangavarapu K, Yoshida A, Pietzsch C, Kuzmina NA, Saphire EO, Collins PL, Crowe JE, Zhu JJ, Suchard MA, Brining DL, Mire CE, Cross RW, Geisbert JB, Samal SK, Andersen KG, Alter G, Geisbert TW, Bukreyev A. Ebola vaccine-induced protection in nonhuman primates correlates with antibody specificity and Fc-mediated effects.. Science translational medicine, 2021.
93. Oikonomou EK, Van Dijk D, Parise H, Suchard MA, de Lemos J, Antoniades C, Velazquez EJ, Miller EJ, Khera R. A phenomapping-derived tool to personalize the selection of anatomical vs. functional testing in evaluating chest pain (ASSIST).. European heart journal, 2021.
94. Lane JCE, Weaver J, Kostka K, Duarte-Salles T, Abrahao MTF, Alghoul H, Alser O, Alshammari TM, Areia C, Biedermann P, Banda JM, Burn E, Casajust P, Fister K, Hardin J, Hester L, Hripcsak G, Kaas-Hansen BS, Khosla S, Kolovos S, Lynch KE, Makadia R, Mehta PP, Morales DR, Morgan-Stewart H, Mosseveld M, Newby D, Nyberg F, Ostropolets A, Woong Park R, Prats-Uribe A, Rao GA, Reich C, Rijnbeek P, Sena AG, Shoaibi A, Spotnitz M, Subbian V, Suchard MA, Vizcaya D, Wen H, Wilde M, Xie J, You SC, Zhang L, Lovestone S, Ryan P, Prieto-Alhambra D, OHDSI-COVID-19 consortium. Risk of depression, suicide and psychosis with hydroxychloroquine treatment for rheumatoid arthritis: a multinational network cohort study.. Rheumatology (Oxford, England), 2021.
95. 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, Dellicour S. Untangling introductions and persistence in COVID-19 resurgence in Europe.. Nature, 2021.
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97. De Maio N, Alekseyenko AV, Coleman-Smith WJ, Pardi F, Suchard MA, Tamuri AU, Truszkowski J, Goldman N. A phylogenetic approach for weighting genetic sequences.. BMC bioinformatics, 2021.
98. Duarte-Salles T, Vizcaya D, Pistillo A, Casajust P, Sena AG, Lai LYH, Prats-Uribe A, Ahmed WU, Alshammari TM, Alghoul H, Alser O, Burn E, You SC, Areia C, Blacketer C, DuVall S, Falconer T, Fernandez-Bertolin S, Fortin S, Golozar A, Gong M, Tan EH, Huser V, Iveli P, Morales DR, Nyberg F, Posada JD, Recalde M, Roel E, Schilling LM, Shah NH, Shah K, Suchard MA, Zhang L, Zhang Y, Williams AE, Reich CG, Hripcsak G, Rijnbeek P, Ryan P, Kostka K, Prieto-Alhambra D. Thirty-Day Outcomes of Children and Adolescents With COVID-19: An International Experience.. Pediatrics, 2021.
99. Prats-Uribe A, Sena AG, Lai LYH, Ahmed WU, Alghoul H, Alser O, Alshammari TM, Areia C, Carter W, Casajust P, Dawoud D, Golozar A, Jonnagaddala J, Mehta PP, Gong M, Morales DR, Nyberg F, Posada JD, Recalde M, Roel E, Shah K, Shah NH, Schilling LM, Subbian V, Vizcaya D, Zhang L, Zhang Y, Zhu H, Liu L, Cho J, Lynch KE, Matheny ME, You SC, Rijnbeek PR, Hripcsak G, Lane JC, Burn E, Reich C, Suchard MA, Duarte-Salles T, Kostka K, Ryan PB, Prieto-Alhambra D. Use of repurposed and adjuvant drugs in hospital patients with covid-19: multinational network cohort study.. BMJ (Clinical research ed.), 2021.
100. Xu JJ, Chen JT, Belin TR, Brookmeyer RS, Suchard MA, Ramirez CM. Male-Female Disparities in Years of Potential Life Lost Attributable to COVID-19 in the United States: A State-by-State Analysis.. medRxiv : the preprint server for health sciences, 2021.
101. Hripcsak G, Schuemie MJ, Madigan D, Ryan PB, Suchard MA. Drawing Reproducible Conclusions from Observational Clinical Data with OHDSI.. Yearbook of medical informatics, 2021.
102. Li X, Ostropolets A, Makadia R, Shaoibi A, Rao G, Sena AG, Martinez-Hernandez E, Delmestri A, Verhamme K, Rijnbeek PR, Duarte-Salles T, Suchard M, Ryan P, Hripcsak G, Prieto-Alhambra D. Characterizing the incidence of adverse events of special interest for COVID-19 vaccines across eight countries: a multinational network cohort study.. medRxiv : the preprint server for health sciences, 2021.
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105. Hong SL, Lemey P, Suchard MA, Baele G. Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST.. Current protocols, 2021.
106. Mbala-Kingebeni P, Pratt C, Mutafali-Ruffin M, Pauthner MG, Bile F, Nkuba-Ndaye A, Black A, Kinganda-Lusamaki E, Faye M, Aziza A, Diagne MM, Mukadi D, White B, Hadfield J, Gangavarapu K, Bisento N, Kazadi D, Nsunda B, Akonga M, Tshiani O, Misasi J, Ploquin A, Epaso V, Sana-Paka E, N'kasar YTT, Mambu F, Edidi F, Matondo M, Bula Bula J, Diallo B, Keita M, Belizaire MRD, Fall IS, Yam A, Mulangu S, Rimoin AW, Salfati E, Torkamani A, Suchard MA, Crozier I, Hensley L, Rambaut A, Faye O, Sall A, Sullivan NJ, Bedford T, Andersen KG, Wiley MR, Ahuka-Mundeke S, Muyembe Tamfum JJ. Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease.. The New England journal of medicine, 2021.
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108. Chan You S, Krumholz HM, Suchard MA, Schuemie MJ, Hripcsak G, Chen R, Shea S, Duke J, Pratt N, Reich CG, Madigan D, Ryan PB, Woong Park R, Park S. Comprehensive Comparative Effectiveness and Safety of First-Line β-Blocker Monotherapy in Hypertensive Patients: A Large-Scale Multicenter Observational Study.. Hypertension (Dallas, Tex. : 1979), 2021.
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111. Xu JJ, Chen JT, Belin TR, Brookmeyer RS, Suchard MA, Ramirez CM. Racial and Ethnic Disparities in Years of Potential Life Lost Attributable to COVID-19 in the United States: An Analysis of 45 States and the District of Columbia.. International journal of environmental research and public health, 2021.
112. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, de S Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.. medRxiv : the preprint server for health sciences, 2021.
113. Prieto-Alhambra D, Kostka K, Duarte-Salles T, Prats-Uribe A, Sena A, Pistillo A, Khalid S, Lai L, Golozar A, Alshammari TM, Dawoud D, Nyberg F, Wilcox A, Andryc A, Williams A, Ostropolets A, Areia C, Jung CY, Harle C, Reich C, Blacketer C, Morales D, Dorr DA, Burn E, Roel E, Tan EH, Minty E, DeFalco F, de Maeztu G, Lipori G, Alghoul H, Zhu H, Thomas J, Bian J, Park J, Roldán JM, Posada J, Banda JM, Horcajada JP, Kohler J, Shah K, Natarajan K, Lynch K, Liu L, Schilling L, Recalde M, Spotnitz M, Gong M, Matheny M, Valveny N, Weiskopf N, Shah N, Alser O, Casajust P, Park RW, Schuff R, Seager S, DuVall S, You SC, Song S, Fernández-Bertolín S, Fortin S, Magoc T, Falconer T, Subbian V, Huser V, Ahmed WU, Carter W, Guan Y, Galvan Y, He X, Rijnbeek P, Hripcsak G, Ryan P, Suchard M. Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS.. Research square, 2021.
114. Burn E, Sena AG, Prats-Uribe A, Spotnitz M, DuVall S, Lynch KE, Matheny ME, Nyberg F, Ahmed WU, Alser O, Alghoul H, Alshammari T, Zhang L, Casajust P, Areia C, Shah K, Reich C, Blacketer C, Andryc A, Fortin S, Natarajan K, Gong M, Golozar A, Morales D, Rijnbeek P, Subbian V, Roel E, Recalde M, Lane JCE, Vizcaya D, Posada JD, Shah NH, Jonnagaddala J, Lai LYH, Avilés-Jurado FX, Hripcsak G, Suchard MA, Ranzani OT, Ryan P, Prieto-Alhambra D, Kostka K, Duarte-Salles T. Use of dialysis, tracheostomy, and extracorporeal membrane oxygenation among 842,928 patients hospitalized with COVID-19 in the United States.. medRxiv : the preprint server for health sciences, 2021.
115. Fisher AA, Ji X, Zhang Z, Lemey P, Suchard MA. Relaxed Random Walks at Scale.. Systematic biology, 2021.
116. Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Sadilek A, Lai S, Tatem AJ, Baele G, Suchard MA, Dellicour S. SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data.. Research square, 2021.
117. Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh N, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States.. medRxiv : the preprint server for health sciences, 2021.
118. Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Barrett KMS, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu C, Suchard MA, Lu JT, Lee W, Andersen KG. Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.. medRxiv : the preprint server for health sciences, 2021.
119. Schuemie MJ, Ryan PB, Pratt N, Chen R, You SC, Krumholz HM, Madigan D, Hripcsak G, Suchard MA. Erratum to: Large-Scale Evidence Generation and Evaluation across a Network of Databases (LEGEND): Assessing Validity Using Hypertension as a Case Study.. Journal of the American Medical Informatics Association : JAMIA, 2021.
120. Holbrook AJ, Loeffler CE, Flaxman SR, Suchard MA. Scalable Bayesian inference for self-excitatory stochastic processes applied to big American gunfire data.. Statistics and computing, 2021.
121. 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, 2021.
122. Morales DR, Conover MM, You SC, Pratt N, Kostka K, Duarte-Salles T, Fernández-Bertolín S, Aragón M, DuVall SL, Lynch K, Falconer T, van Bochove K, Sung C, Matheny ME, Lambert CG, Nyberg F, Alshammari TM, Williams AE, Park RW, Weaver J, Sena AG, Schuemie MJ, Rijnbeek PR, Williams RD, Lane JCE, Prats-Uribe A, Zhang L, Areia C, Krumholz HM, Prieto-Alhambra D, Ryan PB, Hripcsak G, Suchard MA. Renin-angiotensin system blockers and susceptibility to COVID-19: an international, open science, cohort analysis.. The Lancet. Digital health, 2020.
123. Kawaguchi ES, Shen JI, Suchard MA, Li G. Scalable Algorithms for Large Competing Risks Data.. Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America, 2020.
124. Allicock OM, Sahadeo N, Lemey P, Auguste AJ, Suchard MA, Rambaut A, Carrington CVF. Determinants of dengue virus dispersal in the Americas.. Virus evolution, 2020.
125. Tan EH, Sena AG, Prats-Uribe A, You SC, Ahmed WU, Kostka K, Reich C, Duvall SL, Lynch KE, Matheny ME, Duarte-Salles T, Bertolin SF, Hripcsak G, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Blacketer C, Alshammari TM, Alghoul H, Alser O, Lane JCE, Dawoud DM, Shah K, Yang Y, Zhang L, Areia C, Golozar A, Relcade M, Casajust P, Jonnagaddala J, Subbian V, Vizcaya D, Lai LY, Nyberg F, Morales DR, Posada JD, Shah NH, Gong M, Vivekanantham A, Abend A, Minty EP, Suchard M, Rijnbeek P, Ryan PB, Prieto-Alhambra D. Characteristics, outcomes, and mortality amongst 133,589 patients with prevalent autoimmune diseases diagnosed with, and 48,418 hospitalised for COVID-19: a multinational distributed network cohort analysis.. medRxiv : the preprint server for health sciences, 2020.
126. Xiong D, Zhang L, Watson GL, Sundin P, Bufford T, Zoller JA, Shamshoian J, Suchard MA, Ramirez CM. Pseudo-likelihood based logistic regression for estimating COVID-19 infection and case fatality rates by gender, race, and age in California.. Epidemics, 2020.
127. Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.. Nature communications, 2020.
128. Duarte-Salles T, Vizcaya D, Pistillo A, Casajust P, Sena AG, Lai LYH, Prats-Uribe A, Ahmed WU, Alshammari TM, Alghoul H, Alser O, Burn E, You SC, Areia C, Blacketer C, DuVall S, Falconer T, Fernandez-Bertolin S, Fortin S, Golozar A, Gong M, Tan EH, Huser V, Iveli P, Morales DR, Nyberg F, Posada JD, Recalde M, Roel E, Schilling LM, Shah NH, Shah K, Suchard MA, Zhang L, Zhang Y, Williams AE, Reich CG, Hripcsak G, Rijnbeek P, Ryan P, Kostka K, Prieto-Alhambra D. Baseline characteristics, management, and outcomes of 55,270 children and adolescents diagnosed with COVID-19 and 1,952,693 with influenza in France, Germany, Spain, South Korea and the United States: an international network cohort study.. medRxiv : the preprint server for health sciences, 2020.
129. You SC, Rho Y, Bikdeli B, Kim J, Siapos A, Weaver J, Londhe A, Cho J, Park J, Schuemie M, Suchard MA, Madigan D, Hripcsak G, Gupta A, Reich CG, Ryan PB, Park RW, Krumholz HM. Association of Ticagrelor vs Clopidogrel With Net Adverse Clinical Events in Patients With Acute Coronary Syndrome Undergoing Percutaneous Coronary Intervention.. JAMA, 2020.
130. Golozar A, Lai LY, Sena AG, Vizcaya D, Schilling LM, Huser V, Nyberg F, Duvall SL, Morales DR, Alshammari TM, Abedtash H, Ahmed WU, Alser O, Alghoul H, Zhang Y, Gong M, Guan Y, Areia C, Jonnagaddala J, Shah K, Lane JCE, Prats-Uribe A, Posada JD, Shah NH, Subbian V, Zhang L, Abrahão MTF, Rijnbeek PR, You SC, Casajust P, Roel E, Recalde M, Fernández-Bertolín S, Andryc A, Thomas JA, Wilcox AB, Fortin S, Blacketer C, DeFalco F, Natarajan K, Falconer T, Spotnitz M, Ostropolets A, Hripcsak G, Suchard M, Lynch KE, Matheny ME, Williams A, Reich C, Duarte-Salles T, Kostka K, Ryan PB, Prieto-Alhambra D. Baseline phenotype and 30-day outcomes of people tested for COVID-19: an international network cohort including >3.32 million people tested with real-time PCR and >219,000 tested positive for SARS-CoV-2 in South Korea, Spain and the United States.. medRxiv : the preprint server for health sciences, 2020.
131. Karcher MD, Carvalho LM, Suchard MA, Dudas G, Minin VN. Estimating effective population size changes from preferentially sampled genetic sequences.. PLoS computational biology, 2020.
132. Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2.. Nature communications, 2020.
133. Burn E, You SC, Sena AG, Kostka K, Abedtash H, Abrahão MTF, Alberga A, Alghoul H, Alser O, Alshammari TM, Aragon M, Areia C, Banda JM, Cho J, Culhane AC, Davydov A, DeFalco FJ, Duarte-Salles T, DuVall S, Falconer T, Fernandez-Bertolin S, Gao W, Golozar A, Hardin J, Hripcsak G, Huser V, Jeon H, Jing Y, Jung CY, Kaas-Hansen BS, Kaduk D, Kent S, Kim Y, Kolovos S, Lane JCE, Lee H, Lynch KE, Makadia R, Matheny ME, Mehta PP, Morales DR, Natarajan K, Nyberg F, Ostropolets A, Park RW, Park J, Posada JD, Prats-Uribe A, Rao G, Reich C, Rho Y, Rijnbeek P, Schilling LM, Schuemie M, Shah NH, Shoaibi A, Song S, Spotnitz M, Suchard MA, Swerdel JN, Vizcaya D, Volpe S, Wen H, Williams AE, Yimer BB, Zhang L, Zhuk O, Prieto-Alhambra D, Ryan P. Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study.. Nature communications, 2020.
134. Ji X, Zhang Z, Holbrook A, Nishimura A, Baele G, Rambaut A, Lemey P, Suchard MA. Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics.. Molecular biology and evolution, 2020.
135. 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, 2020.
136. Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America.. Science (New York, N.Y.), 2020.
137. 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, Baele G, Lemey P, Su S. Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus.. Molecular biology and evolution, 2020.
138. Lane JCE, Weaver J, Kostka K, Duarte-Salles T, Abrahao MTF, Alghoul H, Alser O, Alshammari TM, Biedermann P, Banda JM, Burn E, Casajust P, Conover MM, Culhane AC, Davydov A, DuVall SL, Dymshyts D, Fernandez-Bertolin S, Fišter K, Hardin J, Hester L, Hripcsak G, Kaas-Hansen BS, Kent S, Khosla S, Kolovos S, Lambert CG, van der Lei J, Lynch KE, Makadia R, Margulis AV, Matheny ME, Mehta P, Morales DR, Morgan-Stewart H, Mosseveld M, Newby D, Nyberg F, Ostropolets A, Park RW, Prats-Uribe A, Rao GA, Reich C, Reps J, Rijnbeek P, Sathappan SMK, Schuemie M, Seager S, Sena AG, Shoaibi A, Spotnitz M, Suchard MA, Torre CO, Vizcaya D, Wen H, de Wilde M, Xie J, You SC, Zhang L, Zhuk O, Ryan P, Prieto-Alhambra D, OHDSI-COVID-19 consortium. Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study.. The Lancet. Rheumatology, 2020.
139. Schuemie MJ, Ryan PB, Pratt N, Chen R, You SC, Krumholz HM, Madigan D, Hripcsak G, Suchard MA. Large-scale evidence generation and evaluation across a network of databases (LEGEND): assessing validity using hypertension as a case study.. Journal of the American Medical Informatics Association : JAMIA, 2020.
140. 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, 2020.
141. Kim Y, Tian Y, Yang J, Huser V, Jin P, Lambert CG, Park H, You SC, Park RW, Rijnbeek PR, Van Zandt M, Reich C, Vashisht R, Wu Y, Duke J, Hripcsak G, Madigan D, Shah NH, Ryan PB, Schuemie MJ, Suchard MA. Comparative safety and effectiveness of alendronate versus raloxifene in women with osteoporosis.. Scientific reports, 2020.
142. Burn E, You SC, Sena A, Kostka K, Abedtash H, Abrahao MTF, Alberga A, Alghoul H, Alser O, Alshammari TM, Aragon M, Areia C, Banda JM, Cho J, Culhane AC, Davydov A, DeFalco FJ, Duarte-Salles T, DuVall SL, Falconer T, Fernandez-Bertolin S, Gao W, Golozar A, Hardin J, Hripcsak G, Huser V, Jeon H, Jing Y, Jung CY, Kaas-Hansen BS, Kaduk D, Kent S, Kim Y, Kolovos S, Lane J, Lee H, Lynch KE, Makadia R, Matheny ME, Mehta P, Morales DR, Natarajan K, Nyberg F, Ostropolets A, Park RW, Park J, Posada JD, Prats-Uribe A, Rao GA, Reich C, Rho Y, Rijnbeek P, Schilling LM, Schuemie M, Shah NH, Shoaibi A, Song S, Spotnitz M, Suchard MA, Swerdel J, Vizcaya D, Volpe S, Wen H, Williams AE, Yimer BB, Zhang L, Zhuk O, Prieto-Alhambra D, Ryan P. Deep phenotyping of 34,128 patients hospitalised with COVID-19 and a comparison with 81,596 influenza patients in America, Europe and Asia: an international network study.. medRxiv : the preprint server for health sciences, 2020.
143. Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study.. bioRxiv : the preprint server for biology, 2020.
144. 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, Mankertz A, Leendertz FH, Harper K, Schnalke T, Lemey P, Calvignac-Spencer S. Measles virus and rinderpest virus divergence dated to the sixth century BCE.. Science (New York, N.Y.), 2020.
145. Morales DR, Conover MM, You SC, Pratt N, Kostka K, Duarte-Salles T, Fernández-Bertolín S, Aragón M, DuVall SL, Lynch K, Falconer T, van Bochove K, Sung C, Matheny ME, Lambert CG, Nyberg F, Alshammari TM, Williams AE, Park RW, Weaver J, Sena AG, Schuemie MJ, Rijnbeek PR, Williams RD, Lane JCE, Prats-Uribe A, Zhang L, Areia C, Krumholz HM, Prieto-Alhambra D, Ryan PB, Hripcsak G, Suchard MA. Renin-angiotensin system blockers and susceptibility to COVID-19: a multinational open science cohort study.. medRxiv : the preprint server for health sciences, 2020.
146. 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.
147. 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.
148. 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.
149. 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.
150. 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.
151. 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.
152. 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.
153. 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.
154. 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.
155. 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.
156. 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.
157. 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.
158. 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.
159. 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.
160. 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.
161. 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.
162. 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.
163. 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.
164. 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.
165. 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.
166. 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.
167. 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.
168. 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.
169. 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.
170. 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.
171. Tian Y, Schuemie MJ, Suchard MA. Evaluating large-scale propensity score performance through real-world and synthetic data experiments.. International journal of epidemiology, 2018.
172. Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B. Recent advances in computational phylodynamics.. Current opinion in virology, 2018.
173. 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.
174. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.. Systematic biology, 2018.
175. 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.
176. Dinh V, Tung Ho LS, Suchard MA, Matsen FA. Consistency and convergence rate of phylogenetic inference via regularization.. Annals of statistics, 2018.
177. 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.
178. 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.
179. Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis.. Systematic biology, 2018.
180. 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.
181. Crawford FW, Ho LST, Suchard MA. Computational methods for birth-death processes.. Wiley interdisciplinary reviews. Computational statistics, 2018.
182. Vrancken B, Suchard MA, Lemey P. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.. Virus evolution, 2017.
183. 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.
184. 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.
185. 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.
186. Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA. A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution.. Systematic biology, 2017.
187. 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.
188. 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.
189. 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.
190. 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.
191. Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics.. Systematic biology, 2017.
192. 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.
193. Schuemie MJ, Hripcsak G, Ryan PB, Madigan D, Suchard MA. Robust empirical calibration of p-values using observational data.. Statistics in medicine, 2016.
194. 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.
195. Bielejec F, Baele G, Rodrigo AG, Suchard MA, Lemey P. Identifying predictors of time-inhomogeneous viral evolutionary processes.. Virus evolution, 2016.
196. 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.
197. Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA. Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates.. Systematic biology, 2016.
198. Baele G, Suchard MA, Bielejec F, Lemey P. Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation.. Microbial genomics, 2016.
199. 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.
200. 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.
201. 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.
202. 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.
203. 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.
204. Singh S, Suchard MA. Pioglitazone Use and Risk of Bladder Cancer.. JAMA, 2015.
205. Baele G, Lemey P, Suchard MA. Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty.. Systematic biology, 2015.
206. 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.
207. 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.
208. 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.
209. 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.
210. 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.
211. 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.
212. 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.
213. 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.
214. 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.
215. 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.
216. 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.
217. 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.
218. 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.
219. 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.
220. 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.
221. 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.
222. 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.
223. 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.
224. 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.
225. 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.
226. 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.
227. 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.
228. 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.
229. Crawford FW, Minin VN, Suchard MA. Estimation for general birth-death processes.. Journal of the American Statistical Association, 2014.
230. Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.. Systematic biology, 2014.
231. 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.
232. 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.
233. 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.
234. 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.
235. Mittal S, Madigan D, Burd RS, Suchard MA. High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.. Biostatistics (Oxford, England), 2013.
236. 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.
237. 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.
238. 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.
239. 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.
240. 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.
241. 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.
242. Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein.. eLife, 2013.
243. 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.
244. Crawford FW, Suchard MA. Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees.. Systematic biology, 2013.
245. 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.
246. 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.
247. 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.
248. 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.
249. Wu CH, Suchard MA, Drummond AJ. Bayesian selection of nucleotide substitution models and their site assignments.. Molecular biology and evolution, 2012.
250. 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.
251. 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.
252. 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.
253. 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.
254. 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.
255. 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.
256. 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.
257. 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.
258. 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.
259. 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.
260. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7.. Molecular biology and evolution, 2012.
261. 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.
262. 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.
263. 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.
264. Tom JA, Sinsheimer JS, Suchard MA. Does history repeat itself? Wavelets and the phylodynamics of influenza A.. Molecular biology and evolution, 2011.
265. 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.
266. Faria NR, Suchard MA, Rambaut A, Lemey P. Toward a quantitative understanding of viral phylogeography.. Current opinion in virology, 2011.
267. Crawford FW, Suchard MA. Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution.. Journal of mathematical biology, 2011.
268. 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.
269. Bielejec F, Rambaut A, Suchard MA, Lemey P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics.. Bioinformatics (Oxford, England), 2011.
270. Weiss RE, Jia J, Suchard MA. A Bayesian model for the common effects of multiple predictors on mixed outcomes.. Interface focus, 2011.
271. 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.
272. 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.
273. 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.
274. Huelsenbeck JP, Alfaro ME, Suchard MA. Biologically inspired phylogenetic models strongly outperform the no common mechanism model.. Systematic biology, 2011.
275. Telesca D, Müller P, Kornblau SM, Suchard MA, Ji Y. Modeling Protein Expression and Protein Signaling Pathways.. Journal of the American Statistical Association, 2011.
276. 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.
277. 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.
278. 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.
279. 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.
280. Bloomquist EW, Lemey P, Suchard MA. Three roads diverged? Routes to phylogeographic inference.. Trends in ecology & evolution, 2010.
281. Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all.. BMC biology, 2010.
282. 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.
283. 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.
284. 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.
285. 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.
286. 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.
287. 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.
288. Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time.. Molecular biology and evolution, 2010.
289. 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.
290. Bloomquist EW, Suchard MA. Unifying vertical and nonvertical evolution: a stochastic ARG-based framework.. Systematic biology, 2009.
291. Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots.. PLoS computational biology, 2009.
292. 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.
293. Liang LJ, Weiss RE, Redelings B, Suchard MA. Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.. Bioinformatics (Oxford, England), 2009.
294. Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics.. Bioinformatics (Oxford, England), 2009.
295. 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.
296. O'Brien JD, Minin VN, Suchard MA. Learning to count: robust estimates for labeled distances between molecular sequences.. Molecular biology and evolution, 2009.
297. Minin VN, Suchard MA. Fast, accurate and simulation-free stochastic mapping.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2008.
298. 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.
299. Drummond AJ, Suchard MA. Fully Bayesian tests of neutrality using genealogical summary statistics.. BMC genetics, 2008.
300. Alekseyenko AV, Lee CJ, Suchard MA. Wagner and Dollo: a stochastic duet by composing two parsimonious solos.. Systematic biology, 2008.
301. Bloomquist EW, Dorman KS, Suchard MA. StepBrothers: inferring partially shared ancestries among recombinant viral sequences.. Biostatistics (Oxford, England), 2008.
302. O'Brien JD, She ZS, Suchard MA. Dating the time of viral subtype divergence.. BMC evolutionary biology, 2008.
303. 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.
304. Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.. Molecular biology and evolution, 2008.
305. Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis.. Science (New York, N.Y.), 2008.
306. 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.
307. Huelsenbeck JP, Suchard MA. A nonparametric method for accommodating and testing across-site rate variation.. Systematic biology, 2007.
308. 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.
309. 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.
310. Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution.. Journal of mathematical biology, 2007.
311. 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.
312. 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.
313. Redelings BD, Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens.. BMC evolutionary biology, 2007.
314. 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.
315. Fang F, Ding J, Minin VN, Suchard MA, Dorman KS. cBrother: relaxing parental tree assumptions for Bayesian recombination detection.. Bioinformatics (Oxford, England), 2006.
316. 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.
317. Guo H, Weiss RE, Gu X, Suchard MA. Time squared: repeated measures on phylogenies.. Molecular biology and evolution, 2006.
318. 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.
319. 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.
320. Suchard MA, Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.. Bioinformatics (Oxford, England), 2006.
321. 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.
322. Suchard MA, Weiss RE, Sinsheimer JS. Models for estimating bayes factors with applications to phylogeny and tests of monophyly.. Biometrics, 2005.
323. Redelings BD, Suchard MA. Joint Bayesian estimation of alignment and phylogeny.. Systematic biology, 2005.
324. Minin VN, Dorman KS, Fang F, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection.. Bioinformatics (Oxford, England), 2005.
325. Suchard MA. Stochastic models for horizontal gene transfer: taking a random walk through tree space.. Genetics, 2005.
326. Hamilton G, Currat M, Ray N, Heckel G, Beaumont M, Excoffier L. Bayesian estimation of recent migration rates after a spatial expansion.. Genetics, 2005.
327. 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.
328. 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.
329. 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.
330. 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.
331. 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.
332. Suchard MA, Kitchen CM, Sinsheimer JS, Weiss RE. Hierarchical phylogenetic models for analyzing multipartite sequence data.. Systematic biology, 2003.
333. 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.
334. 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.
335. 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.
336. 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.
337. 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.