Publications

Preprints

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  Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling

  Medina CM, Palacios JA, Minin VM

  arXiv:2407.18432

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  Exact Bayesian Gaussian Cox Processes Using Random Integral

  Tang B, Palacios JA

  arXiv:2406.19722

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  Multiple merger coalescent inference of effective population size

  Zhang J, Palacios JA

  arXiv:2407.14976

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  Statistical summaries of unlabelled evolutionary trees

  Samyak R, Palacios JA

  Biometrika 2024 in press

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  The Tajima heterochronous n-coalescent: inference from heterochronously sampled molecular data

  Cappello L, Veber A, Palacios JA

  Journal of the American Statistical Society 2024 in press

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  Scalable Bayesian change point detection with spike and slab priors

  Cappello L, Madrid-Padilla OH, Palacios JA

  Journal of Computational and Graphical Statistics 2023 in press

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  adaPop: Bayesian inference of dependent population dynamics in coalescent models

  Cappello L, Kim J, Palacios JA

  PLOS Computational Biology 2023 in press

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  CRP-Tree: A phylogenetic association test for binary traits

  Zhang J, Preising GA, Schumer M, Palacios JA

  Journal of the Royal Statistical Society Series C: Applied Statistics 2023 in press

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  Statistical Challenges in Tracking the Evolution of SARS-CoV-2

  Cappello L, Kim J, Liu S, Palacios JA

  Statistical Science 2022 in press

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  Enumeration of binary trees compatible with a perfect phylogeny

  Palacios JA, Bhaskar A, Disanto F, Rosenberg NA

  Journal of Mathematical Biology 2022 in press

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  An adjacent-swap Markov chain on coalescent trees

  Simper M, Palacios JA

  Journal of Applied Probability 2022 in press

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  Deconvoluting complex correlates of COVID19 severity with a multi-omic pandemic tracking strategy

  Victoria Parikh, Alexander Ioannidis, David Jimenez-Morales, John Gorzynski, Hannah De Jong, Xiran Liu, Jonasel Roque, Victoria Cepeda-Espinoza, Kazutoyo Osoegawa, Christopher Hughes, Shirley Sutton, Nathan Youlton, Ruchi Joshi, David Amar, Yosuke Tanigawa, D. Russo, J. Wong, Jessica Lauzon, J. Edelson, D. Montserrat, Y. Kwon, S. Rubinacci, Olivier Delaneau, L. Cappello, Jaehee Kim, M. Shoura, Archana Raja, Nathaniel Watson, Nathan Hammond, Elizabeth Spiteri, K. Mallempati, G. Montero-Martin, Jeffrey Christle, J. Kim, A. Kirillova, Kinya Seo, Yong Huang, Chunli Zhao, S. Moreno-Grau, S. Hershman, Karen Dalton, Jimmy Zhen, Jack Kamm, Karan Bhatt, Alina Isakova, M. Morri, Thanmayi Ranganath, Catherine Blish, Angela Rogers, Kari Nadeau, Samuel Yang, A. Blomkalns, Ruth O'Hara, Norma Neff, C. DeBoever, Sandor Szalma, Matthew Wheeler, Christopher Gates, K. Farh, Gary Schroth, Phillip Febbo, F. deSouza, Omar Cornejo, Marcelo Fernandez-Vina, Amy Kistler, J. Palacios, Benjamin Pinsky, Carlos Bustamante, Manuel Rivas, and Euan Ashley

  Nature Communications 2022 in press

• 

  Adaptive preferential sampling in phylodynamics

  Cappello L, Palacios JA

  Journal of Computational and Graphical Statistics 2021 in press

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  Discussion on “Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories” by James R. Faulkner, Andrew F. Magee, Beth Shapiro, and Vladimir N. Minin

  Cappello, L, Ghosh, S, Palacios JA

  Biometrics 2020 in press

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  Sequential Importance Sampling for Multi-Resolution Kingman-Tajima Coalescent Counting

  Cappello L, Palacios JA

  The Annals of Applied Statistics 2020 in press

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  Distance metrics for ranked evolutionary trees

  Kim J, Rosenberg NA, Palacios JA

  PNAS 2020 in press

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  Bayesian Estimation of Population Size Changes by Sampling Tajima's Trees

  Palacios JA, Veber A, Cappello L, Wang Z, Wakeley J, Ramachandran S

  Genetics 2019 in press

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  No Evidence for Recent Selection at FOXP2 among Diverse Human Populations

  Atkinson EG, Audesse AJ,Palacios JA, Bobo DM, Webb AE, Ramchandran S, and Henn BM

  Cell 2018 in press

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  Exact Limits of Inference in Coalescent Models

  Johndrow, J, Palacios JA

  Theoretical Population Biology 2018 in press

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  phylodyn: an R package for phylodynamic simulation and inference

  Karcher, MD, Palacios JA, Lan S, and Minin, VN

  Molecular Ecology Resources 2017 in press

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  Quantifying and mitigating the effect of preferential sampling on phylodynamic inference

  Karcher, MD, Palacios JA, Bedford T, Suchard MA and Minin, VN

  PLOS Computational Biology 2016 in press

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  An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

  Lan S, Palacios JA, Karcher, M, Minin VN, Babak Shahbaba

  Bioinformatics 2015 Vol. 112:1265-1272

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  Bayesian nonparametric inference of population size changes from sequential genealogies

  Palacios, JA, Wakeley, J, and Ramachandran, S

  Genetics 2015 Vol. 201:281-304

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  Gaussian process-based Bayesian nonparametric inference of population trajectories from gene genealogies

  Palacios JA, Minin VN

  Biometrics 2013 69: 8 – 18. DOI: 10.1111/biom.12003

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  Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of southeastern Mexico

  Leaché A, Palacios JA, Minin VN, Bryson, Jr.R

  Biological Journal of the Linnean Society 2013 BJLS-2868.R1

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  Integrated nested Laplace approximation for Bayesian nonparametric phylodynamics

  Palacios JA, Minin VN

  Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence 2012

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  Bayesian nonparametric phylodynamics, in Bayesian Phylogenetics: Methods, Algorithms, and Applications

  Palacios JA, Gill MS, Suchard MA, and Minin VN

  Edited by Chen MH, Kuo L, Lewis PO