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  • center
  • program_project
  • nrc
  • whocc
  • project
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  • Associate Professor
  • Clinical Research Assistant
  • Clinician Researcher
  • Department Manager
  • Full Professor
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  • Lab assistant
  • Non-permanent Researcher
  • Permanent Researcher
  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Project Manager
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  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
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© Research
Course

Phylogenetics, Molecular Epidemiology and Phylodynamics – Montevideo 2021

Scientific Fields
Diseases
Organisms
Applications
Technique
Starting Date
03
Dec 2021
Ending Date
10
Dec 2021
Time
09:00:00
Ave Julio Herrera y Reissig 565, 11300 Montevideo, Departamento de Montevideo, Uruguay
Address
2021-12-03 09:00:00 2021-12-10 17:00:00 Europe/Paris Phylogenetics, Molecular Epidemiology and Phylodynamics – Montevideo 2021 This course was a part of IRL IFUMI project. Teachers Paul Bastide (PB ‐ IMAG, Montpellier, France) Gonzalo Bello (GB – Instituto Oswaldo Fiocruz, RJ, Brazil) Miraine Davila Felipe (MDF – UTC, Compiègne, France) […] Ave Julio Herrera y Reissig 565, 11300 Montevideo, Departamento de Montevideo, Uruguay Anna Zhukova anna.zhukova@pasteur.fr

This course was a part of IRL IFUMI project.

Teachers

  • Paul Bastide (PB ‐ IMAG, Montpellier, France)
  • Gonzalo Bello (GB – Instituto Oswaldo Fiocruz, RJ, Brazil)
  • Miraine Davila Felipe (MDF – UTC, Compiègne, France)
  • Olivier Gascuel (OG – CNRS & MNHN, Paris, France)
  • Martin Grana (MG – Instituto Pasteur, Montevideo, Uruguay)
  • Enrique Lessa (EL – Universidad de Montevideo, Uruguay)
  • Daiana Mir (DM – Universidad de Salto, Uruguay)
  • Gonzalo Moratorio (GM – Institut Pasteur Montevideo, Uruguay)
  • Hugo Naya (HN – Instituto Pasteur, Montevideo, Uruguay)
  • Hector Romero (HR – Universidad de Montevideo, Uruguay)
  • Anna Zhukova (AZ – Institut Pasteur, France)
Program

Friday 12/3: Introduction to evolution for mathematicians (EL)

Monday 12/6: Phylogenetic tree inference in a likelihood framework

  • Molecular evolution, speciation, selection, pathogen evolution (EL)
  • Continuous time Markov models, model selection (LRT, AIC, BIC) (MDF)
  • Models for DNA and proteins, likelihood calculation (OG)
  • The 10h gene of HIV (OG)
  • Hands‐on, ML tree inference using Seaview/IQ‐TREE (OG, AZ, MG, HR)

Tuesday 12/7: Ancestral character reconstruction, dating, phylogeography

  • The spread of pathogens (GB)
  • Unrooted, rooted and dated trees, molecular clock models (OG)
  • Methods and algorithms for ancestral character reconstructions (ACR) (AZ)
  • HIV‐1 CRF19 epidemics in Cuba (AZ)
  • Hands‐on, dating using LSD2, ACR with PastML (AZ, OG, HR)Wednesday 12/8: The comparative approach

Wednesday 12/8: The comparative approach

  • Heritability of traits (HN)
  • Stochastic processes on trees: Brownian motion and beyond (MDF)
  • Phylogenetic regression (mixed models, ANOVA) (PB)
  • Heritability of viral load in HIV (PB)

Thursday 12/9: Modeling and reconstructing the evolution of traits

  • Pathogen spread, continuous phylogeography (HR)
  • Heterogeneous and multidimensional models (PB)
  • Bayesian analysis of continuous traits (MCMC, HMC, Beast) (PB)
  • Hands‐on using Beast: Yellow fever virus (Beast tutorial) (PB, GB, HR)

Friday 12/10: Molecular epidemiology, phylodynamics

  • Mathematical epidemiology, virus evolution, variant tracking (HR)
  • Tree models (MDF)
  • Phylodynamics inference and applications (AZ)
  • HIV spread and phylodynamics (DM)
  • Math‐oriented seminars (pedigree, differential equations in phylodynamics…)

Location

Location: Ave Julio Herrera y Reissig 565, 11300 Montevideo, Departamento de Montevideo, Uruguay