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)