Schedule for: 22w5186 - Mathematics and Statistics of Genomic Epidemiology

Beginning on Sunday, November 6 and ending Friday November 11, 2022

All times in Oaxaca, Mexico time, CST (UTC-6).

Sunday, November 6
14:00 - 23:59 Check-in begins (Front desk at your assigned hotel)
19:30 - 22:00 Dinner (Restaurant Hotel Hacienda Los Laureles)
20:30 - 21:30 Informal gathering (Hotel Hacienda Los Laureles)
Monday, November 7
07:30 - 09:15 Breakfast (Restaurant Hotel Hacienda Los Laureles)
09:15 - 09:30 Introduction and Welcome (Conference Room San Felipe)
09:30 - 10:00 Sally Otto: SARS-CoV-2, an evolving pandemic (Zoom)
10:00 - 10:30 Oliver Ratmann: Keeping momentum beyond COVID - genomic surveillance to strengthen HIV public health interventions and lessons from Rakai, Uganda (Zoom)
10:30 - 11:00 Coffee Break (Conference Room San Felipe)
11:00 - 11:30 Daniel Weissman: Crhonic infections likely drive SARS-CoV-2 adaptation (Zoom)
11:30 - 12:00 Marina Escalera-Zamudio: Comparing the evolutionary dynamics of predominant SARS-Cov-2 virus lineages co-circulating in Mexico (Zoom)
12:00 - 13:20 Lunch (Restaurant Hotel Hacienda Los Laureles)
13:20 - 13:30 Group Photo (Hotel Hacienda Los Laureles)
13:30 - 14:00 Philip Gerrish: Heterogeneous vaccination rates and the evolution of vaccine escape (Zoom)
14:00 - 14:30 David Rasmussen: Designing optimal sampling strategies for pathogen genomic surveillance using reinforcement (Zoom)
14:30 - 15:00 Coffee Break (Conference Room San Felipe)
15:00 - 15:30 Jesse Shapiro: Genome-wide association of convergent mutations with SARS-CoV-2 animal host preference (Zoom)
15:30 - 16:00 Yeongseon Park: Epidemiological inference virus lineages using segregating sites (Zoom)
19:00 - 21:00 Dinner (Restaurant Hotel Hacienda Los Laureles)
Tuesday, November 8
07:30 - 09:30 Breakfast (Restaurant Hotel Hacienda Los Laureles)
09:30 - 10:00 Hongzhe Li: Deep learning to predict the biosynthetic gene clusters in bacterial genomes (Zoom)
10:00 - 10:30 Jingyi Jessica Li: PCA outperforms popular hidden variable inference methods for QTL mapping (Zoom)
10:30 - 11:00 Coffee Break (Conference Room San Felipe)
11:00 - 11:30 ZhengZheng Tang: Multi-trait analysis of rare-variant association summary statistics using MTAR (Zoom)
11:30 - 12:00 Xiang Zhou: Likelihood-based Mendelian randomization analysis with automated instrument selection and horizontal pleiotropic modeling (Zoom)
12:00 - 13:30 Lunch (Restaurant Hotel Hacienda Los Laureles)
13:30 - 14:00 Xavier Didelot: Detecting imported cases within a geographically limited genomic sample of an infectious disease (Zoom)
14:00 - 14:30 Celia Greenwood: Two kinds of over-dispersion affect regional DNA methylation patterns (Zoom)
14:30 - 15:00 Coffee Break (Conference Room San Felipe)
15:00 - 15:30 Madikay Senghore: Beyond consensus sequence - a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model (Zoom)
15:30 - 16:00 Aaron King: Exact Phylodynamic Likelihood (Zoom)
19:00 - 21:00 Dinner (Restaurant Hotel Hacienda Los Laureles)
Wednesday, November 9
07:30 - 09:30 Breakfast (Restaurant Hotel Hacienda Los Laureles)
09:30 - 10:00 Kelly Burkett: Using the coalescent tree to define genealogical relationship matrices (Zoom)
10:00 - 10:30 Joshua Herbeck: Are HIV genetic clusters enriched with transmitters? (Zoom)
10:30 - 11:00 Coffee Break (Conference Room San Felipe)
11:00 - 11:30 Olivier Gascuel: Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks (Zoom)
11:30 - 12:00 Ailene MacPherson: Assumptions and Identifiability of Phylodynamic Inference (Zoom)
12:00 - 13:00 Lunch (Restaurant Hotel Hacienda Los Laureles)
13:00 - 18:00 Free Afternoon (Oaxaca)
19:00 - 21:00 Dinner (Restaurant Downton)
Thursday, November 10
07:30 - 09:30 Breakfast (Restaurant Hotel Hacienda Los Laureles)
09:30 - 10:00 Ashley Cooper: Investigating the limits of detection of AMR in agri-food metagenomic samples (Zoom)
10:00 - 10:30 Leonid Chindelevitch: Compiling all publicly available genotype-phenotype data on AMR (Zoom)
10:30 - 11:00 Coffee Break (Conference Room San Felipe)
11:00 - 11:30 John Lees: Bigger is better? Solving problems while working with hundreds of thousands of bacterial genomes (Zoom)
11:30 - 12:00 Maxwell Libbrecht: Accurate and interpretable prediction of drug resistance in M. tuberculosis using deep learning (Zoom)
12:00 - 13:30 Lunch (Restaurant Hotel Hacienda Los Laureles)
13:30 - 14:00 Diana Haider: Different quality thresholds impact the interpretation of measurements of mock microbial communities (Zoom)
14:00 - 14:30 Itsik Pe'er: Probabilistic Models for Microbiome Dynamics (Zoom)
14:30 - 15:00 Coffee Break (Conference Room San Felipe)
15:00 - 15:30 Santiago Castillo-Ramirez: One Health and pan-genomic epidemiology of a superbug (Zoom)
15:30 - 16:00 Lei Liu: A flexible quasi-likelihood model for microbiome abundance count data (Zoom)
19:00 - 21:00 Dinner (Restaurant Hotel Hacienda Los Laureles)
Friday, November 11
07:30 - 09:30 Breakfast (Restaurant Hotel Hacienda Los Laureles)
09:30 - 09:45 Samuel Horsfield: Studying how bacterial accessory genomes evolve using PopPUN (Zoom)
09:45 - 10:00 Rohan Mehta: Detecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes (Zoom)
10:00 - 10:15 Abayomi Olabode: Revisiting the recombinant history of HIV-1 group M with dynamic network community detection (Zoom)
10:15 - 10:30 Leonhardt Unruh: Inferring bacterial strains in metagenomic data (Zoom)
10:30 - 11:00 Coffee Break (Zoom)
11:00 - 11:30 Nicholas Croucher: The impact of intragenomic conflict on pathogen epidemiology (Zoom)
11:30 - 11:40 Closing remarks (Zoom)
11:40 - 12:00 Post-workshop discussion (Zoom)
12:00 - 13:30 Lunch (Restaurant Hotel Hacienda Los Laureles)