Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
from
Monday 29 May 2023 (09:00)
to
Friday 23 June 2023 (18:00)
Monday 29 May 2023
12:50
Welcome
Welcome
12:50 - 13:00
Room: Floor 4, 4205
13:00
Introductory lecture - Stochastic epidemic models: the homogeneous case
-
Tom Britton
(
Stockholm University
)
Introductory lecture - Stochastic epidemic models: the homogeneous case
Tom Britton
(
Stockholm University
)
13:00 - 13:50
Room: Floor 4, 4205
14:00
Introductory lecture - Stochastic epidemic models: introducing heterogeneities
-
Lorenzo Pellis
(
University of Manchester
)
Introductory lecture - Stochastic epidemic models: introducing heterogeneities
Lorenzo Pellis
(
University of Manchester
)
14:00 - 14:50
Room: Floor 4, 4205
15:00
Coffee Break
Coffee Break
15:00 - 15:30
Room: Floor 4
15:30
Introductory lecture - Role of epidemic models in public health policy support
-
Mirjam Kretzschmar
(
University Medical Center Utrecht
)
Introductory lecture - Role of epidemic models in public health policy support
Mirjam Kretzschmar
(
University Medical Center Utrecht
)
15:30 - 16:20
Room: Floor 4, 4205
16:30
Introductory lecture - Statistical inference for epidemic models
-
Daniela De Angelis
Introductory lecture - Statistical inference for epidemic models
Daniela De Angelis
16:30 - 17:20
Room: Floor 4, 4205
17:30
Reception
Reception
17:30 - 19:30
Room: Proviant
Tuesday 30 May 2023
09:00
Research lecture - Mitigation of Superspreader driven epidemics - Chair: Prof Tom Britton, Stockholm University
-
Kim Sneppen
(
Copenhagen University
)
Research lecture - Mitigation of Superspreader driven epidemics - Chair: Prof Tom Britton, Stockholm University
Kim Sneppen
(
Copenhagen University
)
09:00 - 09:50
Room: Floor 4, 4205
10:00
Research lecture - Modeling spatial transmission of infectious diseases - Chair: Prof Tom Britton, Stockholm University
-
Sen Pei
(
Columbia University
)
Research lecture - Modeling spatial transmission of infectious diseases - Chair: Prof Tom Britton, Stockholm University
Sen Pei
(
Columbia University
)
10:00 - 10:50
Room: Floor 4, 4205
11:00
Coffee Break
Coffee Break
11:00 - 11:30
Room: Floor 4
11:30
Research lecture - Time-since-infection models for contact tracing and waning immunity - Chair: Prof Daniela De Angelis, University of Cambridge
-
Francesca Scarabel
(
University of Leeds
)
Research lecture - Time-since-infection models for contact tracing and waning immunity - Chair: Prof Daniela De Angelis, University of Cambridge
Francesca Scarabel
(
University of Leeds
)
11:30 - 12:20
Room: Floor 4, 4205
12:30
Lunch break. NB! Before lunch we take a group photo and make a visit to the NORDITA (6 floor).
Lunch break. NB! Before lunch we take a group photo and make a visit to the NORDITA (6 floor).
12:30 - 14:00
14:00
Research lecture - Jointly modelling epidemics and the economy, with an application to COVID-19 - Chair: Prof Daniela De Angelis, University of Cambridge
-
Otilia Boldea
(
Tilburg University
)
Research lecture - Jointly modelling epidemics and the economy, with an application to COVID-19 - Chair: Prof Daniela De Angelis, University of Cambridge
Otilia Boldea
(
Tilburg University
)
14:00 - 14:50
Room: Floor 4, 4205
15:00
Coffee break
Coffee break
15:00 - 15:30
Room: Floor 6
Wednesday 31 May 2023
09:00
Research lecture - From Pandemic to endemic: the interplay of immunity, viral evolution, and seasonality -Chair: Prof Lorenzo Pellis, University of Manchester
-
Richard Neher
(
University of Basel
)
Research lecture - From Pandemic to endemic: the interplay of immunity, viral evolution, and seasonality -Chair: Prof Lorenzo Pellis, University of Manchester
Richard Neher
(
University of Basel
)
09:00 - 09:50
Room: Floor 4, 4205
10:00
Research lecture - Overdispersed allele frequency fluctuations illuminate disease transmission networks in an ongoing pandemic - Chair: Prof Lorenzo Pellis, University of Manchester
-
Oskar Hallatschek
(
University of Leipzig
)
Research lecture - Overdispersed allele frequency fluctuations illuminate disease transmission networks in an ongoing pandemic - Chair: Prof Lorenzo Pellis, University of Manchester
Oskar Hallatschek
(
University of Leipzig
)
10:00 - 10:50
Room: Floor 4, 4205
11:00
Coffee Break
Coffee Break
11:00 - 11:30
Room: Floor 4
11:30
ONLINE Research lecture - Antigenic evolution and evolutionary consequences of vaccination against SARS CoV-2 - Chair: Prof Lorenzo Pellis, University of Manchester
-
Igor Rouzine
ONLINE Research lecture - Antigenic evolution and evolutionary consequences of vaccination against SARS CoV-2 - Chair: Prof Lorenzo Pellis, University of Manchester
Igor Rouzine
11:30 - 12:20
Room: Room 5
12:30
Lunch Break
Lunch Break
12:30 - 14:00
14:00
Research lecture - Investigating COVID-19 dynamics with agent-based models - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht
-
Francesco Di Ruscio
(
Norwegian Institute of Public Health
)
Research lecture - Investigating COVID-19 dynamics with agent-based models - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht
Francesco Di Ruscio
(
Norwegian Institute of Public Health
)
14:00 - 14:50
Room: Floor 4, 4205
15:00
Research lecture - Estimating the incidence and prevalence of hepatitis C virus among at-risk groups in Norway to monitor progress towards elimination - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht
-
Jørgen Eriksson Midtbø
(
Norwegian Institute of Public Health
)
Research lecture - Estimating the incidence and prevalence of hepatitis C virus among at-risk groups in Norway to monitor progress towards elimination - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht
Jørgen Eriksson Midtbø
(
Norwegian Institute of Public Health
)
15:00 - 15:50
Room: Floor 4, 4205
16:00
Coffee Break
Coffee Break
16:00 - 16:30
Room: Floor 4
16:30
Research lecture - Modelling the importance of population behaviour and seasonality on SARS-CoV-2 spread using Google community mobility reports and weather data - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht
-
Hilde Kjelgaard Brustad
(
University of Oslo
)
Research lecture - Modelling the importance of population behaviour and seasonality on SARS-CoV-2 spread using Google community mobility reports and weather data - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht
Hilde Kjelgaard Brustad
(
University of Oslo
)
16:30 - 17:20
Room: Floor 4, 4205
19:00
Dinner at Knut restaurant
Dinner at Knut restaurant
19:00 - 21:30
Thursday 1 June 2023
11:00
Discussion - Inference and identifiability in infectious disease models
-
Daniela De Angelis
Otilia Boldea
Sen Pei
Discussion - Inference and identifiability in infectious disease models
Daniela De Angelis
Otilia Boldea
Sen Pei
11:00 - 12:00
Room: Albano 3: 6228 - Mega (22 seats)
12:00
Lunch Break
Lunch Break
12:00 - 13:30
13:30
Discussion - Multiscale (within-and-between host) and multi-strain models
-
Lorenzo Pellis
Francesca Scarabel
Discussion - Multiscale (within-and-between host) and multi-strain models
Lorenzo Pellis
Francesca Scarabel
13:30 - 14:30
Room: Albano 3: 6228 - Mega (22 seats)
14:30
Research seminar - Rate of evolution and fitness landscape of SARS-CoV-2
-
Richard Neher
Research seminar - Rate of evolution and fitness landscape of SARS-CoV-2
Richard Neher
14:30 - 15:20
Room: Albano 3: 6228 - Mega (22 seats)
Friday 2 June 2023
09:00
Research seminar - Gradual waning of immunity in SIRS models - Chair: Dr Jørgen Eriksson Midtbø, FHI
-
Mohamed El Khalifi
(
Stockholm University
)
Research seminar - Gradual waning of immunity in SIRS models - Chair: Dr Jørgen Eriksson Midtbø, FHI
Mohamed El Khalifi
(
Stockholm University
)
09:00 - 09:40
Room: Floor 4, 4205
09:50
Research seminar -Application of network science in the infectious disease research - Chair: Dr Jørgen Eriksson Midtbø, FHI
-
Veronika Halász
(
Heidelberg University
)
Research seminar -Application of network science in the infectious disease research - Chair: Dr Jørgen Eriksson Midtbø, FHI
Veronika Halász
(
Heidelberg University
)
09:50 - 10:30
Room: Floor 4, 4205
10:40
Coffee Break
Coffee Break
10:40 - 11:10
Room: Floor 4
11:10
Research seminar -Model-based evaluation of post-pandemic vaccination strategies to reduce COVID-19 in patients with chronic diseases - Chair: Dr Jørgen Eriksson Midtbø, FHI
-
Ilse Westerhof
(
University Medical Center Utrecht
)
Research seminar -Model-based evaluation of post-pandemic vaccination strategies to reduce COVID-19 in patients with chronic diseases - Chair: Dr Jørgen Eriksson Midtbø, FHI
Ilse Westerhof
(
University Medical Center Utrecht
)
11:10 - 11:50
Room: Floor 4, 4205
Saturday 3 June 2023
10:00
Social activity: Vasa Museum
Social activity: Vasa Museum
10:00 - 13:00
Room: Albano 3: 6228 - Mega (22 seats)
Sunday 4 June 2023
Monday 5 June 2023
14:00
Research seminar - Models of pathogens interaction - Chair: Prof Pejman Rohani, University of Georgia
-
Lulla Opatowski
(
Institut Pasteur
)
Research seminar - Models of pathogens interaction - Chair: Prof Pejman Rohani, University of Georgia
Lulla Opatowski
(
Institut Pasteur
)
14:00 - 14:50
Room: Floor 4, 4205
15:00
Research seminar - Development of trait-based models for understanding and approximating pathogen spillover systems - Chair: Prof Pejman Rohani, University of Georgia
-
Marina Treskova
(
Heidelberg University
)
Research seminar - Development of trait-based models for understanding and approximating pathogen spillover systems - Chair: Prof Pejman Rohani, University of Georgia
Marina Treskova
(
Heidelberg University
)
15:00 - 15:40
15:50
Coffee Break
Coffee Break
15:50 - 16:20
Room: Floor 4
16:20
Research seminar - Estimating transmission trees while allowing for multiple introductions, applied to SARS-CoV-2 in Dutch mink farms - Chair: Prof Pejman Rohani, University of Georgia
-
Bastiaan Van der Roest
(
University Medical Center Utrecht
)
Research seminar - Estimating transmission trees while allowing for multiple introductions, applied to SARS-CoV-2 in Dutch mink farms - Chair: Prof Pejman Rohani, University of Georgia
Bastiaan Van der Roest
(
University Medical Center Utrecht
)
16:20 - 17:00
17:30
Reception at Proviant
Reception at Proviant
17:30 - 20:00
Tuesday 6 June 2023
10:00
Social activity: Skansen Museum
Social activity: Skansen Museum
10:00 - 14:00
Room: Albano 3: 6228 - Mega (22 seats)
Wednesday 7 June 2023
13:30
Research seminar - Inferring the ecological and evolutionary determinants of pathogen re-emergence - Chair: Prof Joacim Rocklöv, Heidelberg University
-
Pejman Rohani
(
University of Georgia
)
Research seminar - Inferring the ecological and evolutionary determinants of pathogen re-emergence - Chair: Prof Joacim Rocklöv, Heidelberg University
Pejman Rohani
(
University of Georgia
)
13:30 - 14:20
Room: Floor 4, 4205
14:30
Research seminar - Impact of human behavior on ITNs control strategies to prevent the spread of vector borne diseases - Chair: Prof Joacim Rocklöv, Heidelberg University
-
Manalebish Debalike Asfaw
(
Addis Ababa University
)
Research seminar - Impact of human behavior on ITNs control strategies to prevent the spread of vector borne diseases - Chair: Prof Joacim Rocklöv, Heidelberg University
Manalebish Debalike Asfaw
(
Addis Ababa University
)
14:30 - 15:00
Room: Floor 4, 4205
15:10
Coffee Break
Coffee Break
15:10 - 15:40
Room: Floor 4
15:40
Research seminar - Challenges in modeling complex multi-host infectious diseases: West Nile virus spread and its dependence on climatic conditions - Chair: Prof Joacim Rocklöv, Heidelberg University
-
Julian Heidecke
(
Heildelberg University
)
Research seminar - Challenges in modeling complex multi-host infectious diseases: West Nile virus spread and its dependence on climatic conditions - Chair: Prof Joacim Rocklöv, Heidelberg University
Julian Heidecke
(
Heildelberg University
)
15:40 - 16:20
Room: Floor 4, 4205
16:30
Research seminar - Epidemic models with manual and digital contact tracing - Chair: Prof Joacim Rocklöv, Heidelberg University
-
Dongni Zhang
(
Stockholm University
)
Research seminar - Epidemic models with manual and digital contact tracing - Chair: Prof Joacim Rocklöv, Heidelberg University
Dongni Zhang
(
Stockholm University
)
16:30 - 17:00
Room: Floor 4, 4205
19:00
Dinner at Fotografiska
Dinner at Fotografiska
19:00 - 21:30
Thursday 8 June 2023
09:00
Research seminar - Inclusion of environmental drivers in dynamical models - Chair: Prof Lulla Opatowski, Institut Pasteur
-
Joacim Rocklöv
(
Heidelberg University
)
Research seminar - Inclusion of environmental drivers in dynamical models - Chair: Prof Lulla Opatowski, Institut Pasteur
Joacim Rocklöv
(
Heidelberg University
)
09:00 - 09:50
Room: Floor 4, 4205
10:00
Research seminar - Modeling effect of interventions on HIV transmission among men who have sex with men in the Netherlands - Chair: Prof Lulla Opatowski, Institut Pasteur
-
Alexandra Teslya
(
University Medical Center Utrecht
)
Research seminar - Modeling effect of interventions on HIV transmission among men who have sex with men in the Netherlands - Chair: Prof Lulla Opatowski, Institut Pasteur
Alexandra Teslya
(
University Medical Center Utrecht
)
10:00 - 10:50
Room: Floor 4, 4205
11:00
Coffee Break
Coffee Break
11:00 - 11:30
Room: Floor 4
11:30
Research seminar - Stochastic invasion of Variants of Concern in a Population with Heterogeneous Immunity - Chair: Prof Lulla Opatowski, Institut Pasteur
-
Jacob Curran-Sebastian
(
University of Copenhagen
)
Research seminar - Stochastic invasion of Variants of Concern in a Population with Heterogeneous Immunity - Chair: Prof Lulla Opatowski, Institut Pasteur
Jacob Curran-Sebastian
(
University of Copenhagen
)
11:30 - 12:10
Room: Floor 4, 4205
12:20
Lunch break
Lunch break
12:20 - 13:20
13:20
Discussion - Modeling ecological interactions of viruses
-
Lulla Opatowski
Pejman Rohani
Discussion - Modeling ecological interactions of viruses
Lulla Opatowski
Pejman Rohani
13:20 - 14:20
Room: Albano 3: 6228 - Mega (22 seats)
14:20
Practical introduction to MCMC (includes breaks)
-
Lorenzo Pellis
(
The University of Manchester
)
Practical introduction to MCMC (includes breaks)
Lorenzo Pellis
(
The University of Manchester
)
14:20 - 16:20
Room: Albano 3: 6228 - Mega (22 seats)
Friday 9 June 2023
09:00
Research seminar - Arboviruses in a Changing Environment - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
-
Nicholas DeFelice
(
Icahn School of Medicine at Mount Sinai
)
Research seminar - Arboviruses in a Changing Environment - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
Nicholas DeFelice
(
Icahn School of Medicine at Mount Sinai
)
09:00 - 09:50
Room: Floor 4. 4205
10:00
Research seminar - Simplified within host and dose-response models of SARS-CoV-2 Infection - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
-
Jingsi Xu
(
University of Manchester
)
Research seminar - Simplified within host and dose-response models of SARS-CoV-2 Infection - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
Jingsi Xu
(
University of Manchester
)
10:00 - 10:40
Room: Floor 4, 4205
10:50
Coffee Break
Coffee Break
10:50 - 11:20
Room: Floor 4
11:20
Research seminar - The impact of Urban Heat Islands on the outbreak potential of mosquito-borne diseases spread by Culex pipiens and Aedes albopictus in Europe - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
-
Pratik Singh
(
Heidelberg University
)
Research seminar - The impact of Urban Heat Islands on the outbreak potential of mosquito-borne diseases spread by Culex pipiens and Aedes albopictus in Europe - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
Pratik Singh
(
Heidelberg University
)
11:20 - 12:00
Room: Floor 4, 4205
12:10
Research seminar - Model-based evaluation of school measures on SARS-CoV-2 transmission during the pandemic - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
-
Benedetta Canfora
(
University Medical Center Utrecht & Lisbon University
)
Research seminar - Model-based evaluation of school measures on SARS-CoV-2 transmission during the pandemic - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata
Benedetta Canfora
(
University Medical Center Utrecht & Lisbon University
)
12:10 - 13:00
Room: Floor 4, 4205
Saturday 10 June 2023
10:00
Social activity: Nobel Prize Museum
Social activity: Nobel Prize Museum
10:00 - 13:00
Room: Albano 3: 6228 - Mega (22 seats)
Sunday 11 June 2023
Monday 12 June 2023
09:00
Introductory lecture - Virus evolution between transmission pairs - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht
-
Katia Koelle
(
Emory University
)
Introductory lecture - Virus evolution between transmission pairs - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht
Katia Koelle
(
Emory University
)
09:00 - 09:50
Room: Floor 4, 4205
10:00
Introductory lecture - Within-host evolution of viruses - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht
-
Katrina Lythgoe
(
University of Oxford
)
Introductory lecture - Within-host evolution of viruses - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht
Katrina Lythgoe
(
University of Oxford
)
10:00 - 10:50
Room: Floor4, 4205
11:00
Coffee Break
Coffee Break
11:00 - 11:30
Room: Floor 4
11:30
Introductory lecture - Modeling the evolutionary dynamics of novel infectious diseases - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht
-
Troy Day
(
Queen's University
)
Introductory lecture - Modeling the evolutionary dynamics of novel infectious diseases - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht
Troy Day
(
Queen's University
)
11:30 - 12:20
Room: Floor 4, 4205
12:20
Lunch Break
Lunch Break
12:20 - 13:20
13:20
Introductory lecture - Methods for detecting and characterizing emerging SARS-CoV-2 variants - Chair: Prof Tom Britton, Stockholm University
-
Erik Volz
(
Imperial College London
)
Introductory lecture - Methods for detecting and characterizing emerging SARS-CoV-2 variants - Chair: Prof Tom Britton, Stockholm University
Erik Volz
(
Imperial College London
)
13:20 - 14:10
Room: Floor 4, 4205
17:30
Reception at Proviant
Reception at Proviant
17:30 - 19:30
Tuesday 13 June 2023
09:00
Research lecture - The speed of adaptation to vaccination - Chair: Prof Katia Koelle, Emory University
-
Sylvain Gandon
(
CNRS
)
Research lecture - The speed of adaptation to vaccination - Chair: Prof Katia Koelle, Emory University
Sylvain Gandon
(
CNRS
)
09:00 - 09:50
Room: Floor 4, 4205
10:00
Research lecture - Natural selection and evolution in seasonal epidemic models - Chair: Prof Katia Koelle, Emory University
-
Viggo Andreasen
(
Roskilde University
)
Research lecture - Natural selection and evolution in seasonal epidemic models - Chair: Prof Katia Koelle, Emory University
Viggo Andreasen
(
Roskilde University
)
10:00 - 10:50
Room: Floor 4, 4205
11:00
Coffee Break
Coffee Break
11:00 - 11:30
Room: Floor 4
11:30
Research lecture - Spatially extended SIR models and quadratic growth - Chair: Prof Katia Koelle, Emory University
-
Axel Brandenburg
Research lecture - Spatially extended SIR models and quadratic growth - Chair: Prof Katia Koelle, Emory University
Axel Brandenburg
11:30 - 12:20
Room: Floor 4, 4205
12:30
Lunch Break
Lunch Break
12:30 - 14:00
14:00
Research lecture - Diversity in humans and pathogens: implications for the dynamics of epidemics and the impact of interventions - Chair: Prof Rustom Antia, Emory University
-
Chiara Poletto
(
University of Padova
)
Research lecture - Diversity in humans and pathogens: implications for the dynamics of epidemics and the impact of interventions - Chair: Prof Rustom Antia, Emory University
Chiara Poletto
(
University of Padova
)
14:00 - 14:50
Room: Floor 4, 4205
15:00
Coffee Break
Coffee Break
15:00 - 15:30
Room: Floor 4
15:30
Research lecture - Within- and between host processes of phenotype dynamics of zoonotic pathogens - Chair: Prof Rustom Antia, Emory University
-
Henrik Sjödin
(
Umeå University
)
Research lecture - Within- and between host processes of phenotype dynamics of zoonotic pathogens - Chair: Prof Rustom Antia, Emory University
Henrik Sjödin
(
Umeå University
)
15:30 - 16:20
Room: Floor 4, 4205
Wednesday 14 June 2023
09:00
Research lecture - Incorporating immune waning and boosting into models of viral infections - Chair: Dr Viggo Andreasen, Roskilde University
-
Rustom Antia
(
Emory University
)
Research lecture - Incorporating immune waning and boosting into models of viral infections - Chair: Dr Viggo Andreasen, Roskilde University
Rustom Antia
(
Emory University
)
09:00 - 09:50
Room: Floor 4, 4205
10:00
Research lecture - An epidemic model with short-lived mixing groups - Chair: Dr Viggo Andreasen, Roskilde University
-
Frank Ball
(
University of Nottingham
)
Research lecture - An epidemic model with short-lived mixing groups - Chair: Dr Viggo Andreasen, Roskilde University
Frank Ball
(
University of Nottingham
)
10:00 - 10:50
Room: Floor 4, 4205
11:00
Coffee Break
Coffee Break
11:00 - 11:30
Room: Floor 4
11:30
Research lecture - Inferring SARS-CoV-2 virus loads in sewage in the Netherlands and quantifying its relation to hospital admission data - Chair: Dr Viggo Andreasen, Roskilde University
-
Michiel van Boven
(
University Medical Center Utrecht
)
Research lecture - Inferring SARS-CoV-2 virus loads in sewage in the Netherlands and quantifying its relation to hospital admission data - Chair: Dr Viggo Andreasen, Roskilde University
Michiel van Boven
(
University Medical Center Utrecht
)
11:30 - 12:20
Room: Floor 4, 4205
12:30
Lunch Break
Lunch Break
12:30 - 14:00
14:00
Research lecture - Statistical Genetics and Direct Coupling Analysis - Chair: Prof Troy Day, Queen's University
-
Erik Aurell
(
KTH Royal Institute of Technology
)
Research lecture - Statistical Genetics and Direct Coupling Analysis - Chair: Prof Troy Day, Queen's University
Erik Aurell
(
KTH Royal Institute of Technology
)
14:00 - 14:50
Room: Floor 4, 4205
15:00
Coffee Break
Coffee Break
15:00 - 15:30
Room: Floor 4, 4205
15:30
Research lecture - Inference of fitness landscape (online) - Chair: Prof Troy Day, Queen's University
-
Igor Rouzine
(
Sechenov Institute of Evolutionary Physiology and Biochemistry
)
Research lecture - Inference of fitness landscape (online) - Chair: Prof Troy Day, Queen's University
Igor Rouzine
(
Sechenov Institute of Evolutionary Physiology and Biochemistry
)
15:30 - 16:20
Room: Lecture room 5
20:00
Dinner at Ulla Winbladh
Dinner at Ulla Winbladh
20:00 - 22:30
Thursday 15 June 2023
09:00
Computer Woskhop 1 - Who infected whom? Hands-on experience on outbreak analysis with phybreak to combine genetic and epidemiological data
-
Mirjam Kretzschmar
Martin Bootsma
Computer Woskhop 1 - Who infected whom? Hands-on experience on outbreak analysis with phybreak to combine genetic and epidemiological data
Mirjam Kretzschmar
Martin Bootsma
09:00 - 13:15
Room: Floor 4, 4205
Knowledge of who infected whom during an outbreak of an infectious disease is important to determine risk factors for transmission and to design effective control measures. Our software package phybreak infers transmission links that show how an infection went from person to person, based on both epidemiological and genetic data. During this workshop you will get experienced with phybreak and how to use it yourselves. Requirements: you need to bring your laptop. Materials are attached. The link to the google colab is: bit.ly/phybreakworkshop_colab
13:15
Lunch Break
Lunch Break
13:15 - 14:00
14:00
Discussion - Anticipating and identifying adaptive evolution in SARS-CoV-2 and other acute viral pathogens
-
Katia Koelle
Katrina Lythgoe
Sylvain Gandon
Discussion - Anticipating and identifying adaptive evolution in SARS-CoV-2 and other acute viral pathogens
Katia Koelle
Katrina Lythgoe
Sylvain Gandon
14:00 - 15:00
Room: Albano 3: 6228 - Mega (22 seats)
Friday 16 June 2023
09:00
Computer workshop 2 - Introduction to BEAST: phylodynamic analysis of molecular sequences
-
Jantien Backer
Ganna Rozhnova
Computer workshop 2 - Introduction to BEAST: phylodynamic analysis of molecular sequences
Jantien Backer
Ganna Rozhnova
09:00 - 13:15
Room: Floor 4, 4202
Summary: A phylodynamic analysis uses molecular sequences sampled at different times to learn about the population history of a virus. We will use BEAST 2 (Bayesian Evolutionary Analysis by Sampling Trees) to guide you through all steps of the analysis, from reconstructing phylogenies to choosing the appropriate population model. At the end of the course you will do a phylodynamic analysis by yourself. Requirements: Participants are requested to have the following programs installed prior to the workshop: BEAST 2: a program for Bayesian analysis of molecular sequences using MCMC. You can download the latest version from http://beast2.org/ This download will also include Beauti and TreeAnnotator that will be used during the practical. Tracer: a program to inspect the trace file of parameters that are logged during the BEAST analysis You can download the latest version from http://beast.community/tracer FigTree: a program to view annotated phylogenetic trees You can download the latest version from https://github.com/rambaut/figtree/releases Note that under Windows you need to be allowed to run .exe files for these programs to run.
Saturday 17 June 2023
10:00
Social activity: Boat trip (times TBA)
Social activity: Boat trip (times TBA)
10:00 - 14:00
Room: Albano 3: 6228 - Mega (22 seats)
Sunday 18 June 2023
Monday 19 June 2023
13:00
Research seminars - Host Heterogeneity and Punctuated Evolution of SARS-CoV-2 - Chair: Dr Michiel van Boven, University Medical Center Utrecht
-
Bjarke Frost Nielsen
(
Roskilde University
)
Research seminars - Host Heterogeneity and Punctuated Evolution of SARS-CoV-2 - Chair: Dr Michiel van Boven, University Medical Center Utrecht
Bjarke Frost Nielsen
(
Roskilde University
)
13:00 - 13:40
Room: Floor 4, 4205
13:50
Research seminars - Inferring epidemiological dynamics using temporal patterns of genetic variation, with application to SARS-CoV-2 - Chair: Dr Michiel van Boven, University Medical Center Utrecht
-
Yeongseon Park
(
Emory University
)
Research seminars - Inferring epidemiological dynamics using temporal patterns of genetic variation, with application to SARS-CoV-2 - Chair: Dr Michiel van Boven, University Medical Center Utrecht
Yeongseon Park
(
Emory University
)
13:50 - 14:30
Room: Floor 4, 4205
14:40
Coffee Break
Coffee Break
14:40 - 15:10
Room: Floor 4
15:10
Discussion - Modeling evolutionary and epidemiological dynamics of viruses: role of vaccination and human behavior - Chair: Dr Michiel van Boven, University Medical Center Utrecht
-
Troy Day
Mirjam Kretzschmar
Discussion - Modeling evolutionary and epidemiological dynamics of viruses: role of vaccination and human behavior - Chair: Dr Michiel van Boven, University Medical Center Utrecht
Troy Day
Mirjam Kretzschmar
15:10 - 16:10
Room: Floor 4, 4205
16:20
Discussion - Modeling evolutionary and epidemiological dynamics of viruses: role of host immune system - Chair: Dr Michiel van Boven, University Medical Center Utrecht
-
Rustom Antia
Viggo Andreasen
Michiel van Boven
Discussion - Modeling evolutionary and epidemiological dynamics of viruses: role of host immune system - Chair: Dr Michiel van Boven, University Medical Center Utrecht
Rustom Antia
Viggo Andreasen
Michiel van Boven
16:20 - 17:20
Room: Floor 4, 4205
17:30
Reception at Proviant
Reception at Proviant
17:30 - 19:30
Tuesday 20 June 2023
14:00
Research lecture - Multiscale time-since-infection models in epidemiology and evolution - Chair: Prof Frank Ball, University of Nottingham
-
Lorenzo Pellis
Research lecture - Multiscale time-since-infection models in epidemiology and evolution - Chair: Prof Frank Ball, University of Nottingham
Lorenzo Pellis
14:00 - 14:50
Room: Floor 4, 4205
15:00
Research lecture - Pathogen evolution and emergence in zoonotic spillover events - Chair: Prof Frank Ball, University of Nottingham
-
Peter Fransson
(
Heidelberg University
)
Research lecture - Pathogen evolution and emergence in zoonotic spillover events - Chair: Prof Frank Ball, University of Nottingham
Peter Fransson
(
Heidelberg University
)
15:00 - 15:50
Room: Floor 4, 4205
Wednesday 21 June 2023
14:00
Research lecture - The importance of vaccinated individuals to population- level evolution of pathogens - Chair: Prof Erik Aurell, KTH Royal Institute of Technology
-
Maria Gutierrez
(
University of Cambridge
)
Research lecture - The importance of vaccinated individuals to population- level evolution of pathogens - Chair: Prof Erik Aurell, KTH Royal Institute of Technology
Maria Gutierrez
(
University of Cambridge
)
14:00 - 14:40
Room: Floor 4, 4205
14:50
Research lecture - Early warning signals for SARS-CoV-2 epidemic waves - Chair: Prof Erik Aurell, KTH Royal Institute of Technology
-
Kieran Drake
(
Imperial College London
)
Research lecture - Early warning signals for SARS-CoV-2 epidemic waves - Chair: Prof Erik Aurell, KTH Royal Institute of Technology
Kieran Drake
(
Imperial College London
)
14:50 - 15:40
Room: Floor 4, 4205
18:30
Dinner at Eataly
Dinner at Eataly
18:30 - 21:00
Thursday 22 June 2023
09:00
Research lecture - A fitness landscape model for understanding why chronic infections contribute to population-level SARS-CoV-2 evolution: Chair - Prof Tom Britton, Stockholm University
-
Amber Coats
(
Emory University
)
Research lecture - A fitness landscape model for understanding why chronic infections contribute to population-level SARS-CoV-2 evolution: Chair - Prof Tom Britton, Stockholm University
Amber Coats
(
Emory University
)
09:00 - 09:40
Room: Floor 4, 4205
09:50
Research lecture - The evolution of infectious diseases: connecting within- and between-host processes: Chair - Prof Tom Britton, Stockholm University
-
Willian T. A. F. Silva
(
Swedish University of Agricultural Sciences
)
Research lecture - The evolution of infectious diseases: connecting within- and between-host processes: Chair - Prof Tom Britton, Stockholm University
Willian T. A. F. Silva
(
Swedish University of Agricultural Sciences
)
09:50 - 10:30
Room: Floor 4, 4205
10:40
Coffee Break
Coffee Break
10:40 - 11:10
11:10
Discussion - Household, network and other models with heterogeneity: Chair - Prof Tom Britton, Stockholm University
-
Frank Ball
Tom Britton
Discussion - Household, network and other models with heterogeneity: Chair - Prof Tom Britton, Stockholm University
Frank Ball
Tom Britton
11:10 - 12:10
Room: Albano 3: 6228 - Mega (22 seats)
Friday 23 June 2023
10:00
Social activity: Royal Palace
Social activity: Royal Palace
10:00 - 14:00
Room: Albano 3: 6228 - Mega (22 seats)