VEME2022 – Phylogenetic inference module

Responsible
Brittany Rife Magalis and Marta Giovanetti

TIME

CONTENT

SPEAKERS

SUNDAY 21 AUGUST

14:00
to
16:00

Registration.

16:00
to
16:40

Welcome to VEME.

Jairo Mendez, Luiz Alcantara, Tulio de Oliveira, Juan Miguel Pascale, Ana Riviere, Luis Sucre

16:40
to
17:00

Keynote lecture 1: Genomic pathogen surveillance in Panama, from research to public health, Gorgas Memorial Institute experience

Alexander Martinez

17:00
to
17:20

Keynote lecture 2: PAHO Genomic Surveillance Regional Networks: genomics to support public health response for the world

Juliana Leite

17:20
to
17:30

Questions & Answers

A. Martinez and J. Leite

17:30
to
19:00

Keynote lecture 3: Collaboration in South Africa to help the world on the characterisation of pandemics and epidemics

Tulio de Oliveira

19:00
to
21:30

VEME Cocktail

Monday 22 AUGUST

8:30
to
9:00

Welcome and practical instructions.

L. Franco and L. Alcantara

9:00
to
10:30

Fundamentals of molecular evolution

M Salemi

10:30
to
11:00

Coffee break.

11:00
to
12:30

Constructing a proper dataset: practical

M Giovanetti and E Wilkinson

12:30
to
14:00

Lunch.

14:00
to
16:00

Alignment algorithms.

S van Wyk

16:00
to
17:00

Coffee break + poster session.

17:00
to
17:40

Keynote lecture 4: A transdisciplinary approach to pandemic preparedness

A-M Vandamme

17:40
to
18:20

Keynote lecture 5: Portable DNA sequencing: impacting the response to emerging and re-emerging viral pathogens on the ground

M. Giovanetti

Tuesday 23 AUGUST

8:30
to
9:30

Sequence alignments and editing: practical

S Van Wyk and E Wilkinson

9:30
to
10:30

Phylogenetic signal and phylogenetic noise: theory

H. Schmidt

10:30
to
11:00

Coffee break.

11:00
to
12:30

Phylogenetic signal and phylogenetic noise: practical

M Giovanetti and E Wilkinson

12:30
to
13:30

Lunch.

13:30
to
14:30

Evolutionary models: theory

H. Schmidt

14:30
to
15:30

Testing evolutionary models: practical

E Wilkinson and M Giovanetti

15:30
to
16:00

Coffee break.

16:00
to
16:50

Free computer time.

M. Giovanetti and E. Wilkinson

16:50
to
17:10

Keynote lecture 7: Project VigenDA: Genomic Surveillance of Dengue in the Americas

Jorge L. Munoz

17:10
to
18:10

Keynote lecture 8: Putting ecology into virus evolution​​

Edward Holmes

Wednesday 24 AUGUST

8:00
to
8:30

Keynote lecture 9: Modernizing Pathogen Surveillance with Fully Automated Genomic Sequencing and Data Ecosystem​​​​

Sasan Amini

8:30
to
10:30

Methods for phylogenetic tree reconstruction

H. Schmidt

10:30
to
11:00

Coffee break.

11:00
to
12:30

Constructing phylogenetic trees: practical (NJ)

M Giovanetti, E Wilkinson and L Santos

12:30
to
13:30

Lunch.

13:30
to
15:00

Hypothesis testing and ML methods

H Schmidt

15:00
to
16:00

Hypothesis testing and ML methods: practical

M Giovanetti and E Wilkinson

16:00
to
17:00

Coffee break + poster session.

17:00
to
17:40

Keynote lecture 10: Quick and Accurate identification of SARS-CoV-2 Variants and Lineages in Africa​

H Tegally​

17:40
to
18:20

Keynote lecture 11: Modeling and forecasting virus evolution and pathogenesis in the XXI century: from genomic epidemiology to single cell sequencing

M Salemi

Thursday 25 August

8:00
to
8:30

Keynote lecture 6: Molecular Epidemiology based on Ampliseq Technology: SARS-CoV 2 and Beyond

Gonzalo Sepulveda

8:30
to
9:30

Reconstructing ancestral states

E Wilkinson

9:30
to
10:30

Reconstructing ancestral states: practical

E Wilkinson and M Giovanetti

10:30
to
11:00

Coffee break.

11:00
to
12:30

Free computer time

M Giovanetti and E Wilkinson, R Kato L Santos, and L Alcantara

12:30
to
13:30

Lunch.

13:30
to
15:30

Molecular Clocks

M Salemi

15:30
to
16:00

Coffee break.

16:00
to
17:30

Introduction to phylodynamics

M Giovanetti

18:30
to
20:30

Course teachers dinner