Infection Biology Across Scales
February 3, 2025 @ 08:00 – February 4, 2025 @ 17:00 CET
An EMBL-SciLifeLab-MIMS workshop on infection
The European Molecular Biology Laboratory (EMBL), SciLifeLab and the Laboratory for Molecular Infection Medicine Sweden (MIMS) invite you to an in-person workshop on infection biology on 3-4 February 2025 in Umeå.
The workshop will focus on exploring complementary platforms and capabilities of the three organizations in light of the most important scientific challenges facing infection research. We are also eager to foster exchange between EMBL and Swedish scientists more widely, with a particular emphasis on the next generation of future research leaders from Swedish excellence initiatives who are at a similar career stage as EMBL group leaders.
Please join us for this one-and-a-half-day workshop to meet the researchers, engage in discussions, network with experts across a range of infectious disease research and related services and platforms, accompanied by refreshments!
Program
| 3 February 2025, Rotundan | |
|---|---|
| 11:30 | Soft landing with lunch, Brashörnan |
| 13:00 | Welcome and opening words Oliver Billker, MIMS Director, Jan Ellenberg, SciLifeLab Director, and Maria Bernabeu, EMBL, Infection Biology Transversal Theme |
| 13:15 | Session I: From pathogen genomes to pandemic preparedness Chairs: Stefan Bertilsson, SciLifeLab/SLU and John Lees, Uppsala University |
| Introduction Stefan Bertilsson, SciLifeLab/SLU and John Lees, Uppsala University | |
| 13:20 | Resources for assembly and annotation of metagenomes Rob Finn, EMBL-EBI Tools for modelling and epidemiology of pathogens John Lees, EMBL-EBI |
| 13:45 | Resolving microbial genomes in complex communities at the single-cell level Laura Carroll, SciLifeLab/Umeå University and MIMS |
| 14:05 | Coffee Break |
| 14:20 | Functional annotation of malaria parasite genomes at scale Ellen Bushell, Umeå University and MIMS |
| 14:40 | A Large Language Model for studying bacterial genome architecture, population structure and epidemiology Sam Horsfield, EMBL-EBI |
| 15:00 | Viral metagenomics Tobias Allander, Karolinska Institutet/SciLifeLab |
| 15:20 | Meet the facilities & infrastructures Venue: Galaxen. Coffee and cake served. |
| 16:00 | Session II: Imaging infection – from organisms to structure Chairs: Maria Bernabeu and Lars-Anders Carlson |
| Introduction Breaking and entering: capturing T. gondii invasion by multi-modal imaging Simone Mattei, EMBL | |
| 16:25 | Bioengineered models for malaria pathogenesis research Maria Bernabeu, EMBL |
| 16:40 | Resolving Enterobacterial Pathogenesis by Gut Organoid Imaging Mikael Sellin, SciLifeLab/Uppsala University |
| 16:55 | Coffee Break |
| 17:10 | Structural Biology with Neutrons at the European Spallation Source Esko Oksanen, European Spallation Source (ESS) and Lund University |
| 17:30 | Replication organelles of arboviruses through the lens of a cryo-electron microscope Lars-Anders Carlson, Umeå University and MIMS |
| 17:50 | Mechanistic insight into mycobacterial Type VII Secretion Matthias Wilmanns, EMBL |
| 18:15 | Bus transfer to Bildmuseet (contemporary art museum) for social activity; guided introduction followed by walk to see exhibition |
| 20:00 | Dinner in Bildmuseet |
| 4 February 2025, Rotundan | |
|---|---|
| 08:30 | Soft landing with coffee |
| 09:00 | Session III: Microbiome Chairs: Luisa Hugerth, SciLifeLab/Uppsala University and Rob Finn, EMBL-EBI |
| Introduction Leveraging large human cohorts to understand links between the gut microbiome and health Tove Fall, Uppsala University | |
| 09:25 | Systems ecology of the human microbiome in health and disease: from molecules to mechanisms Paul Wilmes, University of Luxemburg |
| 09:50 | Facilitating Microbial Research with High-Throughput Approaches & Automation Alexandra Koumousti, EMBL |
| 10:05 | Coffee Break |
| 10:20 | The effects of bugs and drugs during early life Nele Brusselaers, Karolinska Institutet |
| 10:35 | Drug resistance and metabolism of gut commensals at strain resolution Mariia Beliaeva, EMBL |
| 10:50 | Dietary suppression of Muc2-dependent host-microbiota mutualism in the small intestine George Birchenough, University of Gothenburg |
| 11:05 | Mechanistic insight into diet-dependent mucus modulation by the gut microbiota Björn Schröder, Umeå University and MIMS |
| 11:20 | Lunch |
| 12:15 | Session IV: Antimicrobial resistance Chairs: Nassos Typas and Linus Sandegren |
| 12:20 | Heteroresistance – a complex and insidious antibiotic resistance phenotype Dan Andersson, Uppsala University |
| 12:45 | Rapid imaging-based antibiotic susceptibility testing for UTI, sepsis, and tuberculosis Johan Elf, SciLifeLab/Uppsala University |
| 13:10 | Coffee Break |
| 13:25 | Breaking intrinsic antibiotic resistance by targeting bacterial defense mechanisms Michaela Wenzel, Chalmers |
| 13:45 | Gut microbiota (counter)-selects for antibiotic resistant strains at a personalized manner Michael Knopp, EMBL |
| 14:05 | Reflection and Closing words Audience, Session Chairs, and Oliver Billker, MIMS |
| 14:30 | Departure |
Organizers
Committee
Maria Bernabeu, EMBL
Nassos Typas, EMBL
Oliver Billker, Nordic EMBL Partnership, Umeå University, MIMS, DDLS
Ulf Ribacke, Karolinska Institutet, SciLifeLab
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