Schedule for: 20w5222 - Mathematics and Statistics of Genomic Epidemiology (Online)
Beginning on Monday, November 9 and ending Friday November 13, 2020
All times in Oaxaca, Mexico time, CST (UTC-6).
| Monday, November 9 | |
|---|---|
| 09:50 - 10:00 | Introduction by BIRS/CMO staff and the workshop organizers (Zoom) |
| 10:00 - 10:20 | Trevor Bedford: Genomic tracking of SARS-CoV-2 evolution and spread (Zoom) |
| 10:20 - 10:40 | Lindi Wahl: How different is the flu you transmit from the flu you received? (Zoom) |
| 10:40 - 10:50 | Virtual tea break - session 1 (evolution) (Zoom) |
| 10:50 - 11:10 | Nicholas Croucher: The evolution of multi-strain bacterial populations (Zoom) |
| 11:10 - 11:30 | Jimmy Liu: High-resolution characterization of global Salmonella subpopulations (Zoom) |
| 11:30 - 12:30 | Discussion for session 1 (evolution) (Zoom) |
| 12:30 - 12:50 | Aaron King: Phylodynamics and genealogy-valued Markov processes (Zoom) |
| 12:50 - 13:10 | Liangliang Wang: Bayesian inference of parameters in transmission models (Zoom) |
| 13:10 - 13:20 | Virtual tea break - session 2 (transmission) (Zoom) |
| 13:20 - 13:40 | Robert Beiko: Mapping the shared evolutionary trajectories of resistance genes and other (possibly!) bad actors (Zoom) |
| 13:40 - 14:00 | Jianhong Wu: COVID-19: implication of multi-waves (Zoom) |
| 14:00 - 15:00 | Discussion for session 2 (transmission) (Zoom) |
| Tuesday, November 10 | |
|---|---|
| 10:00 - 10:20 | Olivier Gascuel: Large-scale phylogeography of hCoV-19 (Zoom) |
| 10:20 - 10:40 | Carmen Murall: Genomic epidemiology of SARS-CoV-2 in Quebec (Zoom) |
| 10:40 - 10:50 | Virtual tea break - session 3 (COVID-19) (Zoom) |
| 10:50 - 11:10 | Melodie Monod: Estimating the age groups that sustain resurging COVID-19 epidemics in the United States (Zoom) |
| 11:10 - 11:30 | Maribel Hernández Rosales: Insights on the Effects of Contact and Mobility Network Dynamics in the Mexican COVID-19 Epidemics (Zoom) |
| 11:30 - 12:25 | Discussion for session 3 (COVID-19) (Zoom) |
| 12:25 - 12:30 | Group photo (screenshot) (Zoom) |
| 12:30 - 12:50 | David Rasmussen: Decomposing the sources of SARS-CoV-2 fitness variation using phylodynamics (Zoom) |
| 12:50 - 13:10 | Katia Koelle: Phylodynamic inference - with and without phylogenies? (Zoom) |
| 13:10 - 13:20 | Virtual tea break - session 4 (viral phylodynamics) (Zoom) |
| 13:20 - 13:40 | Vladimir Minin: Bayesian modeling and data integration in infectious disease phylodynamics (Zoom) |
| 13:40 - 14:00 | Art Poon: Optimizing the genetic clustering of viruses for public health surveillance (Zoom) |
| 14:00 - 15:00 | Discussion for session 4 (viral phylodynamics) (Zoom) |
| Wednesday, November 11 | |
|---|---|
| 10:00 - 10:20 | Xavier Didelot: Additive uncorrelated relaxed clock models (Zoom) |
| 10:20 - 10:40 | Mark Achtman: Hierarchical population genomic structure of bacterial pathogens in EnteroBase (Zoom) |
| 10:40 - 10:50 | Virtual tea break - session 5 (phylogenetics) (Zoom) |
| 10:50 - 11:10 | Oliver Ratmann: Estimating population level transmission dynamics from pathogen deep sequence data: a case study around HIV hotspots in sub Saharan-Africa (Zoom) |
| 11:10 - 11:30 | Alexandre Bouchard: Distribution continuum methods for phylogenetic inference (Zoom) |
| 11:30 - 12:30 | Discussion for session 5 (phylogenetics) (Zoom) |
| 12:30 - 12:50 | John Lees: Hardware-accelerated genome sketching enables real-time genomic epidemiology of pathogens (Zoom) |
| 12:50 - 13:10 | Pierre Mahé: Improving the interpretability of k-mer-based signatures for antibiotic resistance prediction (Zoom) |
| 13:10 - 13:20 | Virtual tea break - session 6 (next-gen sequencing) (Zoom) |
| 13:20 - 13:40 | Zamin Iqbal: Revealing hidden genetic variation in the bacterial accessory genome (Zoom) |
| 13:40 - 14:00 | Jingyi Jessica Li: mbImpute: an accurate and robust imputation method for microbiome data (Zoom) |
| 14:00 - 15:00 | Discussion for session 6 (next-gen sequencing) (Zoom) |
| Thursday, November 12 | |
|---|---|
| 10:00 - 10:20 | Kevin Ma: Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae (Zoom) |
| 10:20 - 10:40 | Tatum Mortimer: Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae (Zoom) |
| 10:40 - 10:50 | Virtual tea break - session 7 (antimicrobial resistance) (Zoom) |
| 10:50 - 11:10 | Santiago Castillo-Ramirez: Population genomics of A. baumannii reveals a licentious and highly mobile resistome (Zoom) |
| 11:10 - 11:30 | Brian Ingalls: Synthetic biology approaches to suppression of antibiotic resistance (Zoom) |
| 11:30 - 12:30 | Discussion for session 7 (antimicrobial resistance) (Zoom) |
| 12:30 - 12:50 | Irina Ostrovnaya: Identifying prognostic pairwise relationships among bacterial species in microbiome studies (Zoom) |
| 12:50 - 13:10 | Celia Greenwood: Bayesian community modelling of the microbiome (Zoom) |
| 13:10 - 13:20 | Virtual tea break - session 8 (bacterial genomics and metagenomics) (Zoom) |
| 13:20 - 13:40 | Leonid Chindelevitch: Interpretable machine learning methods for predicting drug resistance (Zoom) |
| 13:40 - 14:00 | Edward Feil: The adaptation and transmission of Klebsiella species and strains in human, animal and environmental settings (Zoom) |
| 14:00 - 15:00 | Discussion for session 8 (bacterial genomics and metagenomics) (Zoom) |
| Friday, November 13 | |
|---|---|
| 10:00 - 10:05 | Paul Gordon: Considerations for estimating Rt in Alberta, Canada (Zoom) |
| 10:05 - 10:10 | Marco Hamins-Puertolas: Inference of Multiscale Selection using a Continuous Type Birth Death Model (Zoom) |
| 10:10 - 10:15 | Lenora Kepler: Using phylodynamics and decision trees to estimate the effects of mutation on viral fitness (Zoom) |
| 10:15 - 10:20 | Adrian Cazares: Combining sequencing technologies and data mining to study (mega)plasmid families (Zoom) |
| 10:20 - 10:25 | Alpha Forna: Case fatality imputation using machine learning (Zoom) |
| 10:25 - 10:30 | Dongyuang Song: PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data (Zoom) |
| 10:30 - 10:35 | Miles Xi: Benchmarking computational doublet-detection methods for single-cell RNA sequencing data (Zoom) |
| 10:35 - 10:40 | Daniel Anderson: In-browser genome sketching for secure real-time genomic epidemiology (Zoom) |
| 10:40 - 10:45 | Morteza Mahmoudisaber: Do machine learning predictors of microbial phenotype from genotype identify causal variants? (Zoom) |
| 10:45 - 10:50 | Sam Horsfield: ggCaller: a gene caller for bacterial pangenome graphs (Zoom) |
| 10:50 - 10:55 | Maryam Hayati: Deep clustering of bacterial tree images (Zoom) |
| 10:55 - 11:00 | Xueting Qiu: Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host (Zoom) |
| 11:00 - 12:00 | General discussion and workshop wrap-up (Zoom) |
