News archive:

• [May 2024] Isaac Goldstein defended his dissertation. He is starting his postdoctoral appointment at Stanford Department of Statistics in Summer 2024. Even before moving to Stanford Isaac managed to have won a competitively awarded Postdoctoral Fellowship from Stanford Center for Computational, Evolutionary and Human Genomics. Double congrats to Isaac!
• [June 2024] Thanasi Bakis has become a PhD candidate by successfully passing his Advancement to Candidacy exam! Congrats!
• [April 2024] Isaac Goldstein's first dissertation chapter is officially published: Incorporating testing volume into estimation of effective reproduction number dynamics.
• [Dec 2023] Catalina Medina has successfully passed her Advancement to Candidacy exam! Congrats to the newly minted PhD candidate!
• [Jun 2023] Damon Bayer and Yushang Lai have successfully defended their disserations. Congradulations to the first UC Irvine PhD graduates of the group!
• [May 2023] Isaac Goldstein receives the Beall Family Foundation Graduate Student Social Impact Award in Statistics from the Donald Bren School of Information and Computer Sciences. Congrats to Isaac!
• [April 2023] Catalina Medina is recognized at the Latino Excellence and Achievement Awards Dinner (LEAD). Every year one graduate student from each of UCI Schools is chosen to be recognized for their academic and/or research achievements.
• [Jan 2023] A manuscript describing Catalina Medina's and my collaboration with Daniel Parker on exposure to Aedes mosquitoes is published: https://doi.org/10.1016/j.actatropica.2023.106829.
• [Jan 2023] Two first author papers of recent group alumni, Mingwei Tang and Andy Magee are officially published:
1. Magee AF, Karcher MD, Matsen FA, Minin VM. How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error, Bayesian Analysis, in press, software: treess.
2. Tang M, Dudas G, Bedford T, Minin VN. Fitting stochastic epidemic models to gene genealogies using linear noise approximation, Annals of Applied Statistics, 17, 1 – 22, software: LNAphyloDyn.
• [Sep 2022] Isaac Goldstein has successfully passed his Advancement to Candidacy exam and became a PhD candidate today! Congrats!
• [Aug 2022] Isaac Goldstein, Jon Wakefield, and I wrote a paper about estimating changes in effective reproduction number while accounting for changes in the number of people testing: arXiv:2208.04418.
• [July 2022] Biometrics Co-Editors recognized our paper "Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories" as one the best published in the journal during 2020 – 2022 and selected it for presentation in the Biometrics Showcase session at the the International Biometric Conference 2022.
• [Mar 2022] We received a UC Health CDPH COVID-19 Modeling Consortium grant to support our project "Improving accuracy and precision of forecasts and scenarios by fitting mechanistic transmission models to multiple disaggregated surveillance data sources."
• [May 2022] Congratulations to the newly minted PhD Candidate Damon Bayer! who passed his Advancement to Candidacy exam with flying colors
• [Mar 2022] It was a lot of fun and an incredible honor to give The Spring 2022 Jon A. Wellner Lecture at the University of Idaho. It was a very special visit for me for two personal reasons: 1) It was my great fortune to have Jon Wellner as my senior collegue during my 10 years at the University of Washington, Seattle; 2) My first academic home in US was the University of Idaho Masters program in Mathematics, so it was great to see old friends and mentors!
• [Mar 2022] Humbled and honored to have recieved Latino Excellence and Achievement Outstanding Faculty Mentorship Award by UC Irvine Office of Inclusive Excellence
• [10/30/2021] We, Damon Bayer, Isaac Goldstein (UCI Statisitcs PhD students), Jon Fintzi (group alum), and many other co-authors, updated our Orange County, CA modeling paper. Check out this twitter thread for a short walk through.
• [06/01/2021] Jessica George, who worked as a Research Assistant in our group, recieved an Information and Computer Sciences Outstanding Contribution to Research Award. Jessica graduated from UC Irvine with a BS in Data Science and now works as a Data Scientist at the Biopharmaceutical Company AbbVie.
• [05/11/2021] Andy Magee, who worked with Eric Matsen and me, has defended his dissertation! Congratulations, Dr. Magee! Andy will start his postdoc in Marc Suchard's group this summer.
• [01/16/2021] Catalina Medina and I collaborated with Daniel Parker and other talented people on analyzing Orange County, CA COVID-19 surveillance data
• [09/15/2020] In collaboration with lots of great people, Damon Bayer, Isaac Goldstein (UCI Statisitcs PhD students), and I created two COVID-19 online resources:
  
  
  1. COVID-19 Trends by UC Irvine
     Media coverage: LA Times, LA Times/Daily Pilot, CBS Los Angeles, OC Register, OC Business Journal, UCI News
  2. Orange County, CA COVID-19 Situation Report
     Media coverage: OC Business Journal, KUCI Radio, UCI News
and released a methodological paper with a retrospective analysis of Orange County COVID-19 surveilance data as a pre-print:


• Using multiple data streams to estimate and forecast SARS-CoV-2 transmission dynamics, with application to the virus spread in Orange County, California


• [01/15/2020] New work with Jon Fintzi and Jon Wakefield: A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts. Jon Fintzi won 2020 ASA Section on Statistics in Epidemiology Norman Breslow Prize for this work!
• [11/25/2019] Andy Magee, Sebastian Höhna, Tetyana I. Vasylyeva, Adam D. Leaché, and I developed Markov random field priors for birth-death processes.
• [03/28/2019] Michael Karcher, Marc Suchard, Gytis Dudas and I have a sequel to our preferential sampling model/paper: Estimating effective population size changes from preferentially sampled genetic sequences. Now implemented in BEAST and with ability to include time-varying covariates.
• [03/05/2019] Jon Fintzi, Luis Lomeli, Jon Wakefield, and I wrote a discussion of Bayesian Analysis paper "Dynamic Bayesian Influenza Forecasting in the United States with Hierarchical Discrepancy"
• [02/24/2019] Mingwei Tang, Gytis Dudas, Trevor Bedford, and I have a new preprint on fitting stochastic epidemic models to genealogies/phylogenies. This paper received ASA Section on Bayesian Statistical Science student paper award.
• [08/14/2018] Jim Faulkner, Andy Magee, and I put together a new Bayesian nonparametric model for reconstructing population size dynamics. Beth Shapiro helped us analyze her cool bison data.
• [02/20/2018] Amrit Dhar, Kristian Davidsen, Erick Matsen, and I developed a CSI-style enhance button for B cell amino acid profiles.
• [02/02/2018] Theo Kypraios and I co-edited a Statistical Science special section on infectious diseases.
• [07/01/2017] After ten wonderful years at the University of Washington, I am moving to UC Irvine this summer. Very excited about my next academic adventure!
• [11/17/2017] Another new work on B cells, this time focusing on the somatic hypermutation, with Jean Feng, David Shaw, Noah Simon, and Erick Matsen.
• [08/30/2017] New work with Will DeWitt, Erick Matsen, and other talented people on reconstructing B cell phylogenies.
• [07/03/2017] Jason Xu and I were lucky to be able to help Paredez lab with statistical analysis in their work on cytokinesis in Giardia, an important, but still in many ways mysterious protozoan parasite.
• [10/26/2016] Two new papers on arxiv:
  
  
  • Statistical inference in partially observed stochastic compartmental models with application to cell lineage tracking of in vivo hematopoiesis - second-to-last research chapter from Jason Xu's dissertation.
  • phylodyn: an R package for phylodynamic simulation and inference - software note written in collaboration with Mike Karcher, Julia Palacios, and Shiwei Lan.
• [09/26/2016] New work with Amrit Dhar: Calculating higher-order moments of phylogenetic stochastic mapping summaries in linear time.
• [08/01/2016] Jason Xu defended his dissertation and started his NSF Mathematical Sciences Postdoctoral Research Fellowship at UCLA.
• [07/18/2016] Jon Fintzi won the first place in the oral category of the 2016 WNAR Student Paper Competition. The competition took place during the XXVIIIth Internation Biometric Conference, where Jon presented the paper Efficient data augmentation for fitting stochastic epidemic models to prevalence data.
• [06/29/2016] New work with Jon Fintzi and Jon Wakefield: Efficient data augmentation for fitting stochastic epidemic models to prevalence data.
• [03/11/2016] New work with Lam Ho, Marc Suchard, Forrest Crawford, and Jason Xu: Birth(death)/birth-death processes and their computable transition probabilities with statistical applications.
• [01/15/2016] Jason Xu, Statistics Ph.D. student working with me, is awarded NSF Mathematical Sciences Postdoctoral Research Fellowship. His mentor with be Dr. Kenneth Lange at UCLA.
• [12/21/2015] New work with QERM Ph.D. student Jim Faulkner: Bayesian trend filtering: adaptive temporal smoothing with shrinkage priors.

Last modified: September, 2021