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2020 – today
- 2024
[j43]Karthik Gangavarapu
, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard:
Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinform. 40(2) (2024)- [j42]Egill A. Fridgeirsson, Ross D. Williams, Peter R. Rijnbeek, Marc A. Suchard, Jenna Marie Reps:
Comparing penalization methods for linear models on large observational health data. J. Am. Medical Informatics Assoc. 31(7): 1514-1521 (2024) - [j41]Jianxiao Yang, Martijn J. Schuemie, Xiang Ji, Marc A. Suchard:
Massive Parallelization of Massive Sample-Size Survival Analysis. J. Comput. Graph. Stat. 33(1): 289-302 (2024) - [i1]Tianyu Xie, Frederick A. Matsen IV, Marc A. Suchard, Cheng Zhang:
Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions. CoRR abs/2408.05058 (2024) - 2023
- [j40]Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H. Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV:
A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm. Algorithms Mol. Biol. 18(1): 10 (2023) - [j39]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:
Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study. J. Am. Medical Informatics Assoc. 30(5): 859-868 (2023) - [j38]Qiong Wu, Martijn J. Schuemie, Marc A. Suchard, Patrick B. Ryan, George Hripcsak, Charles A. Rohde, Yong Chen:
Padé approximant meets federated learning: A nearly lossless, one-shot algorithm for evidence synthesis in distributed research networks with rare outcomes. J. Biomed. Informatics 145: 104476 (2023) - [j37]Evangelos K. Oikonomou, Phyllis M. Thangaraj, Deepak L. Bhatt, Joseph S. Ross, Lawrence H. Young, Harlan M. Krumholz, Marc A. Suchard, Rohan Khera:
An explainable machine learning-based phenomapping strategy for adaptive predictive enrichment in randomized clinical trials. npj Digit. Medicine 6 (2023) - [j36]Zhenyu Zhang, Akihiko Nishimura, Nídia S. Trovão, Joshua L. Cherry, Andrew J. Holbrook, Xiang Ji, Philippe Lemey, Marc A. Suchard:
Accelerating Bayesian inference of dependency between mixed-type biological traits. PLoS Comput. Biol. 19(8) (2023) - [c6]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:
Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research. MedInfo 2023: 966-970 - 2022
- [j35]Andrew J. Holbrook, Xiang Ji, Marc A. Suchard:
From viral evolution to spatial contagion: a biologically modulated Hawkes model. Bioinform. 38(7): 1846-1856 (2022) - [c5]Tara V. Anand, Marc A. Suchard, George Hripcsak:
Reproducibility in comparative effectiveness and safety of ACE inhibitors and thiazides for modified monotherapy treatment criteria. AMIA 2022 - 2021
- [j34]Nicola De Maio, Alexander V. Alekseyenko, William J. Coleman-Smith, Fabio Pardi, Marc A. Suchard, Asif U. Tamuri, Jakub Truszkowski, Nick Goldman:
A phylogenetic approach for weighting genetic sequences. BMC Bioinform. 22(1): 285 (2021) - [j33]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:
A standardized analytics pipeline for reliable and rapid development and validation of prediction models using observational health data. Comput. Methods Programs Biomed. 211: 106394 (2021) - [j32]Martijn J. Schuemie, Patrick B. Ryan, Nicole Pratt, Ruijun Chen, Seng Chan You, Harlan M. Krumholz, David Madigan, George Hripcsak, Marc A. Suchard:
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. 28(1): 196 (2021) - [j31]Andrew J. Holbrook, Philippe Lemey, Guy Baele, Simon Dellicour, Dirk Brockmann, Andrew Rambaut, Marc A. Suchard:
Massive Parallelization Boosts Big Bayesian Multidimensional Scaling. J. Comput. Graph. Stat. 30(1): 11-24 (2021) - [j30]Eric S. Kawaguchi, Jenny I. Shen, Marc A. Suchard, Gang Li:
Scalable Algorithms for Large Competing Risks Data. J. Comput. Graph. Stat. 30(3): 685-693 (2021) - [j29]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:
Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model. PLoS Comput. Biol. 17(3) (2021) - [j28]Andrew J. Holbrook, Charles E. Loeffler, Seth R. Flaxman, Marc A. Suchard:
Scalable Bayesian inference for self-excitatory stochastic processes applied to big American gunfire data. Stat. Comput. 31(1): 4 (2021) - 2020
- [j27]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:
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. Bioinform. 36(7): 2098-2104 (2020) - [j26]Martijn J. Schuemie, Patrick B. Ryan, Nicole Pratt, Ruijun Chen, Seng Chan You, Harlan M. Krumholz, David Madigan, George Hripcsak, Marc A. Suchard:
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. 27(8): 1268-1277 (2020) - [j25]Martijn J. Schuemie, Patrick B. Ryan, Nicole Pratt, Ruijun Chen, Seng Chan You, Harlan M. Krumholz, David Madigan, George Hripcsak, Marc A. Suchard:
Principles of Large-scale Evidence Generation and Evaluation across a Network of Databases (LEGEND). J. Am. Medical Informatics Assoc. 27(8): 1331-1337 (2020) - [j24]Michael D. Karcher, Luiz Max Carvalho, Marc A. Suchard, Gytis Dudas, Vladimir N. Minin:
Estimating effective population size changes from preferentially sampled genetic sequences. PLoS Comput. Biol. 16(10) (2020) - [j23]Eric S. Kawaguchi, Jenny I. Shen, Gang Li, Marc A. Suchard:
A Fast and Scalable Implementation Method for Competing Risks Data with the R Package fastcmprsk. R J. 12(2): 163 (2020) - [c4]Ruijun Chen, Martijn J. Schuemie, Marc A. Suchard, Anna Ostropolets, Linying Zhang, Patrick B. Ryan, George Hripcsak:
Evaluation of Large-scale Propensity Score Modeling and Covariate Balance on Potential Unmeasured Confounding in Observational Research. AMIA 2020
2010 – 2019
- 2019
- [j22]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:
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15(4) (2019) - 2018
- [j21]Jenna Marie Reps, Martijn J. Schuemie, Marc A. Suchard, Patrick B. Ryan, Peter R. Rijnbeek:
Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data. J. Am. Medical Informatics Assoc. 25(8): 969-975 (2018) - 2017
- [j20]Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A. Suchard:
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinform. 33(12): 1798-1805 (2017) - [j19]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:
Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nat. 544(7650): 309-315 (2017) - [j18]Daniel Magee, Marc A. Suchard, Matthew Scotch:
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. 13(2) (2017) - 2016
- [j17]Michael D. Karcher, Julia A. Palacios, Trevor Bedford, Marc A. Suchard, Vladimir N. Minin:
Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. PLoS Comput. Biol. 12(3) (2016) - [j16]Trevor R. Shaddox, Patrick B. Ryan, Martijn J. Schuemie, David Madigan, Marc A. Suchard:
Hierarchical models for multiple, rare outcomes using massive observational healthcare databases. Stat. Anal. Data Min. 9(4): 260-268 (2016) - 2015
- [j15]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:
Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nat. 523(7559): 217-220 (2015) - [c3]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:
Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. MedInfo 2015: 574-578 - 2014
- [j14]Filip Bielejec, Philippe Lemey, Luiz Carvalho, Guy Baele, Andrew Rambaut, Marc A. Suchard:
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinform. 15: 133 (2014) - [j13]Remco R. Bouckaert, Joseph Heled, Denise Kühnert, Timothy G. Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond:
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput. Biol. 10(4) (2014) - [j12]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:
The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates. PLoS Comput. Biol. 10(4) (2014) - 2013
- [j11]Marc A. Suchard, Shawn E. Simpson, Ivan Zorych, Patrick B. Ryan, David Madigan:
Massive Parallelization of Serial Inference Algorithms for a Complex Generalized Linear Model. ACM Trans. Model. Comput. Simul. 23(1): 10:1-10:17 (2013) - [c2]Bram Vrancken, Andrew Rambaut, Guy Baele, Anne-Mieke Vandamme, Kristel Van Laethem, Eric Van Wijngaerden, Alexei J. Drummond, Marc A. Suchard, Philippe Lemey:
Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework. IWBBIO 2013: 555-556 - 2012
- [j10]Philippe Lemey, Vladimir N. Minin, Filip Bielejec, Sergei L. Kosakovsky Pond, Marc A. Suchard:
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinform. 28(24): 3248-3256 (2012) - [j9]Yu-Nong Gong, Guang-Wu Chen, Marc A. Suchard:
A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. Comput. Biol. Chem. 39: 20-28 (2012) - 2011
- [j8]Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey:
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinform. 27(20): 2910-2912 (2011)
2000 – 2009
- 2009
- [j7]Marc A. Suchard, Andrew Rambaut:
Many-core algorithms for statistical phylogenetics. Bioinform. 25(11): 1370-1376 (2009) - [j6]Li-Jung Liang, Robert E. Weiss, Benjamin D. Redelings, Marc A. Suchard:
Improving phylogenetic analyses by incorporating additional information from genetic sequence databases. Bioinform. 25(19): 2530-2536 (2009) - [j5]Christina M. R. Kitchen, Jing Kroll, Daniel R. Kuritzkes, Erik Bloomquist, Steven G. Deeks, Marc A. Suchard:
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. 53(3): 766-775 (2009) - [j4]Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard:
Bayesian Phylogeography Finds Its Roots. PLoS Comput. Biol. 5(9) (2009) - 2007
- [j3]Fang Fang, Jing Ding, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman:
cBrother: relaxing parental tree assumptions for Bayesian recombination detection. Bioinform. 23(4): 507-508 (2007) - [c1]Misha L. Rajaram, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman:
Hot and Cold: Spatial Fluctuation in HIV-1 Recombination Rates. BIBE 2007: 707-714 - 2006
- [j2]Marc A. Suchard, Benjamin D. Redelings:
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinform. 22(16): 2047-2048 (2006) - 2005
- [j1]Vladimir N. Minin, Karin S. Dorman, Fang Fang, Marc A. Suchard:
Dual multiple change-point model leads to more accurate recombination detection. Bioinform. 21(13): 3034-3042 (2005)
Coauthor Index
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last updated on 2024-10-07 22:12 CEST by the dblp team
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