Publications by authors named "Andrew Holbrook"

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BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference.
Guy Baele, Xiang Ji, Gabriel W Hassler, John T McCrone, Yucai Shao, Andrew J Holbrook

Nat Methods· August 2025

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Tau drives cell specific functional isolation of the hippocampal formation.
Theodore J Zwang, Jasen Zhang, Rudy Gelb-Bicknell, Nina Wolf, Viktor Chanchykov, Andrew J Holbrook

bioRxiv· August 2025

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Quantum Speedups for Multiproposal MCMC.
Chin-Yi Lin, Kuo-Chin Chen, Philippe Lemey, Marc A Suchard, Andrew J Holbrook

Bayesian Anal· August 2025

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A SPATIALLY VARYING HIERARCHICAL RANDOM EFFECTS MODEL FOR LONGITUDINAL MACULAR STRUCTURAL DATA IN GLAUCOMA PATIENTS.
By Erica Su, Robert E Weiss, Kouros Nouri-Mahdavi, Andrew J Holbrook

Ann Appl Stat· December 2024

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Parallel MCMC algorithms: theoretical foundations, algorithm design, case studies.
Nathan E Glatt-Holtz, Andrew J Holbrook, Justin A Krometis, Cecilia F Mondaini

Trans Math Appl· December 2024

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Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations.
Andrew F Magee, Andrew J Holbrook, Jonathan E Pekar, Itzue W Caviedes-Solis, Fredrick A Matsen Iv

Syst Biol· September 2024

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ANTsX neuroimaging-derived structural phenotypes of UK Biobank.
Nicholas J Tustison, Michael A Yassa, Batool Rizvi, Philip A Cook, Andrew J Holbrook

Sci Rep· April 2024

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On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2.
Gustavo Didier, Nathan E Glatt-Holtz, Andrew J Holbrook, Andrew F Magee, Marc A Suchard

Proc Natl Acad Sci U S A· January 2024

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ANTsX neuroimaging-derived structural phenotypes of UK Biobank.
Nicholas J Tustison, Michael A Yassa, Batool Rizvi, Philip A Cook, Andrew J Holbrook

Res Sq· October 2023

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Random-effects substitution models for phylogenetics via scalable gradient approximations.
Andrew F Magee, Andrew J Holbrook, Jonathan E Pekar, Itzue W Caviedes-Solis, Fredrick A Matsen Iv

ArXiv· September 2023

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Accelerating Bayesian inference of dependency between mixed-type biological traits.
Zhenyu Zhang, Akihiko Nishimura, Nídia S Trovão, Joshua L Cherry, Andrew J Holbrook

PLoS Comput Biol· August 2023

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A quantum parallel Markov chain Monte Carlo.
Andrew J Holbrook

J Comput Graph Stat· April 2023

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Generating MCMC proposals by randomly rotating the regular simplex.
Andrew J Holbrook

J Multivar Anal· March 2023

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Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis.
Gabriel W Hassler, Brigida Gallone, Leandro Aristide, William L Allen, Max R Tolkoff, Andrew J Holbrook

Methods Ecol Evol· October 2022

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From viral evolution to spatial contagion: a biologically modulated Hawkes model.
Andrew J Holbrook, Xiang Ji, Marc A Suchard

Bioinformatics· March 2022

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BAYESIAN MITIGATION OF SPATIAL COARSENING FOR A HAWKES MODEL APPLIED TO GUNFIRE, WILDFIRE AND VIRAL CONTAGION.
Andrew J Holbrook, Xiang Ji, Marc A Suchard

Ann Appl Stat· March 2022

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The ANTsX ecosystem for quantitative biological and medical imaging.
Nicholas J Tustison, Philip A Cook, Andrew J Holbrook, Hans J Johnson, John Muschelli

Sci Rep· April 2021

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Scalable Bayesian inference for self-excitatory stochastic processes applied to big American gunfire data.
Andrew J Holbrook, Charles E Loeffler, Seth R Flaxman, Marc A Suchard

Stat Comput· January 2021

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Flexible Bayesian Dynamic Modeling of Correlation and Covariance Matrices.
Shiwei Lan, Andrew Holbrook, Gabriel A Elias, Norbert J Fortin, Hernando Ombao

Bayesian Anal· December 2020

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Longitudinal Mapping of Cortical Thickness Measurements: An Alzheimer's Disease Neuroimaging Initiative-Based Evaluation Study.
Nicholas J Tustison, Andrew J Holbrook, Brian B Avants, Jared M Roberts, Philip A Cook

J Alzheimers Dis· October 2020

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Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics.
Xiang Ji, Zhenyu Zhang, Andrew Holbrook, Akihiko Nishimura, Guy Baele

Mol Biol Evol· October 2020

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Anterolateral entorhinal cortex thickness as a new biomarker for early detection of Alzheimer's disease.
Andrew J Holbrook, Nicholas J Tustison, Freddie Marquez, Jared Roberts, Michael A Yassa

Alzheimers Dement (Amst)· August 2020

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Massive parallelization boosts big Bayesian multidimensional scaling.
Andrew J Holbrook, Philippe Lemey, Guy Baele, Simon Dellicour, Dirk Brockmann

J Comput Graph Stat· June 2020

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Neural network gradient Hamiltonian Monte Carlo.
Lingge Li, Andrew Holbrook, Babak Shahbaba, Pierre Baldi

Comput Stat· March 2019

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Geodesic Lagrangian Monte Carlo over the space of positive definite matrices: with application to Bayesian spectral density estimation.
Andrew Holbrook, Shiwei Lan, Alexander Vandenberg-Rodes, Babak Shahbaba

J Stat Comput Simul· December 2017

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