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) |
