Marc A. Suchard

61 papers C 1Misc 2Journal 55Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
PDA in Action: Ten Principles for High-Quality Multi-Site Clinical Evidence Generation.
CoRR
Yong Chen, Jiayi Tong, Yiwen Lu, Rui Duan, Chongliang Luo, Marc A. Suchard, Patrick B. Ryan, Andrew E. Williams, John H. Holmes, Jason H. Moore, Hua Xu, Yun Lu, Raymond J. Carroll, Scott L. Zeger, George Hripcsak, Martijn J. Schuemie
2026 J jnl
Transfer-learning on federated observational healthcare data for prediction models using Bayesian sparse logistic regression with informed priors.
J. Am. Medical Informatics Assoc.
Kelly Mohe Li, Jenna Marie Reps, Akihiko Nishimura, Martijn J. Schuemie, Marc A. Suchard
2025 J jnl
Artificial intelligence for modelling infectious disease epidemics.
Nat.
Moritz U. G. Kraemer, Joseph L.-H. Tsui, Serina Chang, Spyros Lytras, Mark P. Khurana, Samantha Vanderslott, Sumali Bajaj, Neil Scheidwasser, Jacob Liam Curran-Sebastian, Elizaveta Semenova, Mengyan Zhang, H. Juliette T. Unwin, Oliver J. Watson, Cathal Mills, Abhishek Dasgupta, Luca Ferretti, Samuel V. Scarpino, Etien Koua, Oliver Morgan, Houriiyah Tegally, Ulrich Paquet, Loukas Moutsianas, Christophe Fraser, Neil M. Ferguson, Eric J. Topol, David A. Duchêne, Tanja Stadler, Patricia Kingori, Michael J. Parker, Francesca Dominici, Nigel Shadbolt, Marc A. Suchard, Oliver Ratmann, Seth R. Flaxman, Edward C. Holmes, Manuel Gomez-Rodriguez, Bernhard Schölkopf, Christl A. Donnelly, Oliver G. Pybus, Simon Cauchemez, Samir Bhatt
2025 J jnl
Finding high posterior density phylogenies by systematically extending a directed acyclic graph.
Algorithms Mol. Biol.
Chris Jennings-Shaffer, David H. Rich, Matthew Macaulay, Michael D. Karcher, Tanvi Ganapathy, Shosuke Kiami, Anna Kooperberg, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV
2025 J jnl
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.
Bioinform.
Guy Baele, Luiz Max Carvalho, Marius Brusselmans, Gytis Dudas, Xiang Ji, John T. McCrone, Philippe Lemey, Marc A. Suchard, Andrew Rambaut
2025 J jnl
Objective study validity diagnostics: a framework requiring pre-specified, empirical verification to increase trust in the reliability of real-world evidence.
J. Am. Medical Informatics Assoc.
Mitchell Conover, Patrick B. Ryan, Yong Chen, Marc A. Suchard, George Hripcsak, Martijn J. Schuemie
2025 J jnl
Standardized patient profile review using large language models for case adjudication in observational research.
npj Digit. Medicine
Martijn J. Schuemie, Anna Ostropolets, Aleh Zhuk, Uladzislau Korsik, Seung In Seo, Marc A. Suchard, George Hripcsak, Patrick B. Ryan
2025 J jnl
The Structure of Deviations From Maximum Parsimony for Densely-Sampled Data and Applications for Clade Support Estimation.
IEEE Trans. Comput. Biol. Bioinform.
William Howard-Snyder, Will Dumm, Mary Barker, Ognian Milanov, Claris Winston, David H. Rich, Marc A. Suchard, Frederick A. Matsen IV
2025 J jnl
Unlocking efficiency in real-world collaborative studies: a multi-site international study with one-shot lossless GLMM algorithm.
npj Digit. Medicine
Jiayi Tong, Jenna Marie Reps, Chongliang Luo, Yiwen Lu, Lu Li, Juan Manuel Ramírez-Anguita, Milou T. Brand, Scott L. DuVall, Thomas Falconer, Alex Mayer Fuentes, Xing He, Michael E. Matheny, Miguel A. Mayer, Bhavnisha K. Patel, Katherine Simon, Marc A. Suchard, Guojun Tang, Benjamin Viernes, Ross D. Williams, Mui Van Zandt, Fei Wang, Jiang Bian, Jiayu Zhou, David A. Asch, Yong Chen
2024 J jnl
Comparing penalization methods for linear models on large observational health data.
J. Am. Medical Informatics Assoc.
Egill A. Fridgeirsson, Ross D. Williams, Peter R. Rijnbeek, Marc A. Suchard, Jenna Marie Reps
2024 J jnl
Many-core algorithms for high-dimensional gradients on phylogenetic trees.
Bioinform.
Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard
2024 J jnl
Massive Parallelization of Massive Sample-Size Survival Analysis.
J. Comput. Graph. Stat.
Jianxiao Yang, Martijn J. Schuemie, Xiang Ji, Marc A. Suchard
2024 J jnl
Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.
PLoS Comput. Biol.
Yucai Shao, Andrew F. Magee, Tetyana I. Vasylyeva, Marc A. Suchard
2024 J jnl
Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions.
CoRR
Tianyu Xie, Frederick A. Matsen IV, Marc A. Suchard, Cheng Zhang
2024 J jnl
spread.gl: visualizing pathogen dispersal in a high-performance browser application.
Bioinform.
Yimin Li, Nena Bollen, Samuel L. Hong, Marius Brusselmans, Fabiana Gambaro, Joon Klaps, Marc A. Suchard, Andrew Rambaut, Philippe Lemey, Simon Dellicour, Guy Baele
2023 J jnl
A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm.
Algorithms Mol. Biol.
Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H. Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV
2023 J jnl
Accelerating Bayesian inference of dependency between mixed-type biological traits.
PLoS Comput. Biol.
Zhenyu Zhang, Akihiko Nishimura, Nídia S. Trovão, Joshua L. Cherry, Andrew J. Holbrook, Xiang Ji, Philippe Lemey, Marc A. Suchard
2023 J jnl
An explainable machine learning-based phenomapping strategy for adaptive predictive enrichment in randomized clinical trials.
npj Digit. Medicine
Evangelos K. Oikonomou, Phyllis M. Thangaraj, Deepak L. Bhatt, Joseph S. Ross, Lawrence H. Young, Harlan M. Krumholz, Marc A. Suchard, Rohan Khera
2023 — conf
Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research.
MedInfo
Martijn J. Schuemie, Jenna Reps, Adam Black, Frank J. DeFalco, Lee Evans, Egill A. Fridgeirsson, James P. Gilbert, Chris Knoll, Martin Lavallee, Gowtham A. Rao, Peter R. Rijnbeek, Katy Sadowski, Anthony G. Sena, Joel N. Swerdel, Ross D. Williams, Marc A. Suchard
2023 J jnl
Padé approximant meets federated learning: A nearly lossless, one-shot algorithm for evidence synthesis in distributed research networks with rare outcomes.
J. Biomed. Informatics
Qiong Wu, Martijn J. Schuemie, Marc A. Suchard, Patrick B. Ryan, George Hripcsak, Charles A. Rohde, Yong Chen
2023 J jnl
Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study.
J. Am. Medical Informatics Assoc.
Anna Ostropolets, Yasser Albogami, Mitchell Conover, Juan M. Banda, William A. Baumgartner Jr., Clair Blacketer, Priyamvada Desai, Scott L. DuVall, Stephen P. Fortin, James P. Gilbert, Asieh Golozar, Joshua Ide, Andrew S. Kanter, David M. Kern, Chungsoo Kim, Lana Y. H. Lai, Chenyu Li, Feifan Liu, Kristine E. Lynch, Evan Minty, Maria Inês Neves, Ding Quan Ng, Tontel Obene, Victor Pera, Nicole Pratt, Gowtham Rao, Nadav Rappoport, Ines Reinecke, Paola Saroufim, Azza Shoaibi, Katherine Simon, Marc A. Suchard, Joel N. Swerdel, Erica A. Voss, James Weaver, Linying Zhang, George Hripcsak, Patrick B. Ryan
2022 J jnl
From viral evolution to spatial contagion: a biologically modulated Hawkes model.
Bioinform.
Andrew J. Holbrook, Xiang Ji, Marc A. Suchard
2022 Misc conf
Reproducibility in comparative effectiveness and safety of ACE inhibitors and thiazides for modified monotherapy treatment criteria.
AMIA
Tara V. Anand, Marc A. Suchard, George Hripcsak
2021 J jnl
A phylogenetic approach for weighting genetic sequences.
BMC Bioinform.
Nicola De Maio, Alexander V. Alekseyenko, William J. Coleman-Smith, Fabio Pardi, Marc A. Suchard, Asif U. Tamuri, Jakub Truszkowski, Nick Goldman
2021 J jnl
A standardized analytics pipeline for reliable and rapid development and validation of prediction models using observational health data.
Comput. Methods Programs Biomed.
Sara Khalid, Cynthia Yang, Clair Blacketer, Talita Duarte-Salles, Sergio Fernández-Bertolín, Chungsoo Kim, Rae Woong Park, Jimyung Park, Martijn J. Schuemie, Anthony G. Sena, Marc A. Suchard, Seng Chan You, Peter R. Rijnbeek, Jenna Marie Reps
2021 J jnl
Erratum to: Large-Scale Evidence Generation and Evaluation across a Network of Databases (LEGEND): Assessing Validity Using Hypertension as a Case Study.
J. Am. Medical Informatics Assoc.
Martijn J. Schuemie, Patrick B. Ryan, Nicole Pratt, Ruijun Chen, Seng Chan You, Harlan M. Krumholz, David Madigan, George Hripcsak, Marc A. Suchard
2021 J jnl
Massive Parallelization Boosts Big Bayesian Multidimensional Scaling.
J. Comput. Graph. Stat.
Andrew J. Holbrook, Philippe Lemey, Guy Baele, Simon Dellicour, Dirk Brockmann, Andrew Rambaut, Marc A. Suchard
2021 J jnl
Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model.
PLoS Comput. Biol.
Gregory L. Watson, Di Xiong, Lu Zhang, Joseph A. Zoller, John Shamshoian, Phillip Sundin, Teresa Bufford, Anne W. Rimoin, Marc A. Suchard, Christina M. Ramirez
2021 J jnl
Scalable Algorithms for Large Competing Risks Data.
J. Comput. Graph. Stat.
Eric S. Kawaguchi, Jenny I. Shen, Marc A. Suchard, Gang Li
2021 J jnl
Scalable Bayesian inference for self-excitatory stochastic processes applied to big American gunfire data.
Stat. Comput.
Andrew J. Holbrook, Charles E. Loeffler, Seth R. Flaxman, Marc A. Suchard
2020 J jnl
A Fast and Scalable Implementation Method for Competing Risks Data with the R Package fastcmprsk.
R J.
Eric S. Kawaguchi, Jenny I. Shen, Gang Li, Marc A. Suchard
2020 J jnl
Estimating effective population size changes from preferentially sampled genetic sequences.
PLoS Comput. Biol.
Michael D. Karcher, Luiz Max Carvalho, Marc A. Suchard, Gytis Dudas, Vladimir N. Minin
2020 Misc conf
Evaluation of Large-scale Propensity Score Modeling and Covariate Balance on Potential Unmeasured Confounding in Observational Research.
AMIA
Ruijun Chen, Martijn J. Schuemie, Marc A. Suchard, Anna Ostropolets, Linying Zhang, Patrick B. Ryan, George Hripcsak
2020 J jnl
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region.
Bioinform.
Simon Dellicour, Philippe Lemey, Jean Artois, Tommy T. Lam, Alice Fusaro, Isabella Monne, Giovanni Cattoli, Dmitry Kuznetsov, Ioannis Xenarios, Gwenaelle Dauphin, Wantanee Kalpravidh, Sophie von Dobschütz, Filip Claes, Scott H. Newman, Marc A. Suchard, Guy Baele, Marius Gilbert
2020 J jnl
Large-scale evidence generation and evaluation across a network of databases (LEGEND): assessing validity using hypertension as a case study.
J. Am. Medical Informatics Assoc.
Martijn J. Schuemie, Patrick B. Ryan, Nicole Pratt, Ruijun Chen, Seng Chan You, Harlan M. Krumholz, David Madigan, George Hripcsak, Marc A. Suchard
2020 J jnl
Principles of Large-scale Evidence Generation and Evaluation across a Network of Databases (LEGEND).
J. Am. Medical Informatics Assoc.
Martijn J. Schuemie, Patrick B. Ryan, Nicole Pratt, Ruijun Chen, Seng Chan You, Harlan M. Krumholz, David Madigan, George Hripcsak, Marc A. Suchard
2019 J jnl
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
PLoS Comput. Biol.
Remco R. Bouckaert, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David A. Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond
2018 J jnl
Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data.
J. Am. Medical Informatics Assoc.
Jenna Marie Reps, Martijn J. Schuemie, Marc A. Suchard, Patrick B. Ryan, Peter R. Rijnbeek
2017 J jnl
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.
Bioinform.
Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A. Suchard
2017 J jnl
Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.
PLoS Comput. Biol.
Daniel Magee, Marc A. Suchard, Matthew Scotch
2017 J jnl
Virus genomes reveal factors that spread and sustained the Ebola epidemic.
Nat.
Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D'Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart L. Haagmans, Julian A. Hiscox, Umaru Jah, Jeffrey R. Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke W. Meredith, James Qu, Joshua Quick, Suzan D. Pas, My V. T. Phan, Georgios Pollakis, Chantal B. Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. G. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson, Kendra West, Shannon Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia O. Blyden, Fatorma Bolay, Miles W. Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian T. Happi, Edward C. Holmes, Brima Kargbo, Sakoba Keïta, Paul Kellam, Marion Koopmans, Jens H. Kuhn, Nicholas J. Loman, N'Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo F. Palacios, Oliver G. Pybus, Pardis C. Sabeti, Amadou Sall, Ute Ströher, Isatta Wurie, Marc A. Suchard, Philippe Lemey, Andrew Rambaut
2016 J jnl
Hierarchical models for multiple, rare outcomes using massive observational healthcare databases.
Stat. Anal. Data Min.
Trevor R. Shaddox, Patrick B. Ryan, Martijn J. Schuemie, David Madigan, Marc A. Suchard
2016 J jnl
Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.
PLoS Comput. Biol.
Michael D. Karcher, Julia A. Palacios, Trevor Bedford, Marc A. Suchard, Vladimir N. Minin
2015 J jnl
Global circulation patterns of seasonal influenza viruses vary with antigenic drift.
Nat.
Trevor Bedford, Steven Riley, Ian G. Barr, Shobha Broor, Mandeep Chadha, Nancy J. Cox, Rodney S. Daniels, C. Palani Gunasekaran, Aeron C. Hurt, Anne Kelso, Alexander Klimov, Nicola S. Lewis, Xiyan Li, John W. McCauley, Takato Odagiri, Varsha Potdar, Andrew Rambaut, Yuelong Shu, Eugene Skepner, Derek J. Smith, Marc A. Suchard, Masato Tashiro, Dayan Wang, Xiyan Xu, Philippe Lemey, Colin A. Russell
2015 — conf
Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.
MedInfo
George Hripcsak, Jon D. Duke, Nigam H. Shah, Christian G. Reich, Vojtech Huser, Martijn J. Schuemie, Marc A. Suchard, Rae Woong Park, Ian Chi Kei Wong, Peter R. Rijnbeek, Johan van der Lei, Nicole Pratt, G. Niklas Norén, Yu-Chuan Li, Paul E. Stang, David Madigan, Patrick B. Ryan
2014 J jnl
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.
PLoS Comput. Biol.
Remco R. Bouckaert, Joseph Heled, Denise Kühnert, Timothy G. Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond
2014 J jnl
The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates.
PLoS Comput. Biol.
Bram Vrancken, Andrew Rambaut, Marc A. Suchard, Alexei J. Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, Philippe Lemey
2014 J jnl
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.
BMC Bioinform.
Filip Bielejec, Philippe Lemey, Luiz Carvalho, Guy Baele, Andrew Rambaut, Marc A. Suchard
2013 J jnl
Massive Parallelization of Serial Inference Algorithms for a Complex Generalized Linear Model.
ACM Trans. Model. Comput. Simul.
Marc A. Suchard, Shawn E. Simpson, Ivan Zorych, Patrick B. Ryan, David Madigan
2013 — conf
Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework.
IWBBIO
Bram Vrancken, Andrew Rambaut, Guy Baele, Anne-Mieke Vandamme, Kristel Van Laethem, Eric Van Wijngaerden, Alexei J. Drummond, Marc A. Suchard, Philippe Lemey
2012 J jnl
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.
Bioinform.
Philippe Lemey, Vladimir N. Minin, Filip Bielejec, Sergei L. Kosakovsky Pond, Marc A. Suchard
2012 J jnl
A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses.
Comput. Biol. Chem.
Yu-Nong Gong, Guang-Wu Chen, Marc A. Suchard
2011 J jnl
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics.
Bioinform.
Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey
2009 J jnl
Bayesian Phylogeography Finds Its Roots.
PLoS Comput. Biol.
Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard
2009 J jnl
Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.
Bioinform.
Li-Jung Liang, Robert E. Weiss, Benjamin D. Redelings, Marc A. Suchard
2009 J jnl
Many-core algorithms for statistical phylogenetics.
Bioinform.
Marc A. Suchard, Andrew Rambaut
2009 J jnl
Two-way Bayesian hierarchical phylogenetic models: An application to the co-evolution of gp120 and gp41 during and after enfuvirtide treatment.
Comput. Stat. Data Anal.
Christina M. R. Kitchen, Jing Kroll, Daniel R. Kuritzkes, Erik Bloomquist, Steven G. Deeks, Marc A. Suchard
2007 C conf
Hot and Cold: Spatial Fluctuation in HIV-1 Recombination Rates.
BIBE
Misha L. Rajaram, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman
2007 J jnl
cBrother: relaxing parental tree assumptions for Bayesian recombination detection.
Bioinform.
Fang Fang, Jing Ding, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman
2006 J jnl
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.
Bioinform.
Marc A. Suchard, Benjamin D. Redelings
2005 J jnl
Dual multiple change-point model leads to more accurate recombination detection.
Bioinform.
Vladimir N. Minin, Karin S. Dorman, Fang Fang, Marc A. Suchard