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Preliminary_agenda_2018_Genomic_epi_20180213

Preliminary course agenda

Genomic

Genomic Epidemiology of Infectious Diseases DAY 3 AGENDA WEDNESDAY, JUNE 20 Time 9.00-10.00AM 10.00-10.30AM 10.30-11.15AM 11.15AM-12.00PM Within-host diversity J Shapiro Coffee Break Molecular clocks and dating A Gonçalves da Silva Journal club M Behr, A Gonçalves da Silva, R Lee, I Levade, T Seemann 12.00-12.45PM 12.45-1.30PM 1.30-3.00PM 3.00-3.30PM Lunch Making inferences about transmission and study design considerations in genomic epidemiology R Lee Practical Exercise: Phylogenetic trees, SNP matrices and epi data - inferring (refuting) transmission R Lee Coffee Break 3.30-5.00PM Practical Exercise (continued): Phylogenetic trees, SNP matrices and epi data - inferring (refuting) transmission R Lee 4

Genomic Epidemiology of Infectious Diseases DAY 4 AGENDA THURSDAY, JUNE 21 Time 9.00-9.30AM 9.30-10.00AM 10.00-10.30AM 10.30AM-11.15AM Mechanisms of antimicrobial resistance M Behr How we currently predict antimicrobial resistance using genomic data T Seemann Coffee Break Metagenomics – analysis and applications J Shapiro 11.15-12.00PM 12.00-12.45PM 12.45-1.30PM 1.30-2.00PM 2.00PM-2.45PM 2.45-3.15PM Journal Club M Behr, A Gonçalves da Silva, R Lee, I Levade, T Seemann Lunch Practical Exercise: Predicting antimicrobial resistance T Seemann Practical Exercise: Metagenomics (16S) T Seemann Other approaches for predicting resistance W Hanage Coffee break 3.15PM-4.00PM 4.00PM-5.00PM Nanopore sequencing – applications L Cowley Practical Exercises: Working with nanopore data 5

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