Overview
The IVI Bioinformatics Day is a new symposium with a focus on Genomics and Bioinformatics that aims to bring together participants from the Institute of Virology and Immunology (IVI) and the University of Bern to discuss key applications of Genomics and Bioinformatics across different disciplines. The symposium will showcase select projects currently underway at the IVI, covering diverse topics such as pathogen diagnostics and surveillance, single cell sequencing analysis, and spatial transcriptomics. Complementary to the research at the IVI, scientists from core facilities and other institutes at the University of Bern have been invited to present their research, skills, and services in Genomics, Bioinformatics, and Data Science. 
The symposium is intended to strengthen collaboration among researchers from different institutes at the University of Bern and create a network of researchers who are interested in Genomics and Bioinformatics across disciplines. The symposium will be followed by a Networking event and Apéro riche. 
Whether you are an expert or just curious to hear how Genomics and Bioinformatics could be applied in your area, registration is free and everyone is welcome!
Key Information

Current Bioinformatics Projects in Diagnostics, Virology and Immunology @IVI *

The morning session will be focused on the projects ongoing at the Institute of Virology and Immunology.


Technologies, Skills, and Services *

The afternoon session will be focused on next-generation sequencing technologies and computational services provided at the University of Bern, including the Next Generation Sequencing Platform (NGSP), Interfaculty Bioinformatics Unit (IBU), and the Data Science Lab (DSL).

*Presentations will be held in English


Networking Event and Apéro Riche
IVI Bioinformatics Day, April 30, 2024
9:30-10:00 Welcome and Reception ☕
10:00-10:15Bioinformatics in Diagnostics, Virology and Immunology 
  • Jakub Kubacki (Head of the Vector-borne Diseases Group, IVI)
  • Jenna Kelly (Group Leader Virus Bioinformatics, IVI)
  • Stephanie Talker (Group Leader Comparative Immunology, IVI)


Current Bioinformatics Projects in Diagnostics, Virology and Immunology @IVI
Diagnostics, Surveillance, and Phylogenetics
10:15-10:30 Assessing the diversity of Avian Influenza Virus: From long reads to characterization
  • Michele Wyler (Bioinformatician, Group Bachofen, IVI)
  • Keywords: Assembly, phylogenetics, SNPs, frameshifts

10:30-10:45 Tracking influenza A virus evolution using phylogenetics
  • Mike Mwanga (PhD student, Group Kelly/Dijkman, IVI/IFIK)
  • Keywords: Influenza, phylogenetics, public health

10:45-11:00 Development and evaluation of novel metagenomic approaches for pathogen surveillance at the human-animal interface 
  • Jean Claude Makangara (PhD student, Group Kelly/Dijkman, IVI/IFIK)
  • Keywords: Metagenomics, nanopore sequencing, bioinformatics pipeline, pathogen discovery, One Health


11:00-11:15 Coffee Break ☕🍪

Single Cell Sequencing, Spatial Transcriptomics, and Beyond
11:15-11:30Leveraging single-cell data to study virus infection in airway epithelial cells of different species
  • Vera Flück (PhD student, Group Kelly/Thiel, IVI)
  • Keywords: single-cell, transcriptomics, non-model species, infectious diseases

11:30-11:45Navigating cross-species single-cell transcriptomics of the mononuclear phagocyte system: challenges and insights
  • Marius Botos (PhD student, Group Talker/Summerfield, IVI)
  • Keywords: single-cell, transcriptomics, integration, machine learning

 11:45-12:00BCR repertoire sequencing: applications in characterizing African swine fever virus infection
  • Francisco Brito (Post-doc, Group Summerfield, IVI)
  • Keywords: repertoire sequencing, single-cell, bulk, immunology, ASFV

12:00-12:15Navigating tissue complexity with spatial omics and machine learning
  • Demeter Túrós (PhD student, Group Thiel/Rottenberg, IVI/ITPA)
  • Keywords: spatial transcriptomics, machine learning, spatial biology, host-pathogen interactions


12:15-13:15 Lunch (NOT PROVIDED)
Technologies, Skills, and Services
13:15-13:45Novel technologies and services at the NGSP
  • Pamela Nicholson (Scientific Associate, Next Generation Sequencing Platform (NGSP), Bern)

13:45-14:15IBU - Bioinformatics Solutions | Research | Education (Part 1)
  • Rémy Bruggmann (Head of Interfaculty Bioinformatics Unit (IBU), Bern)

Flash talks by IBU members:
  • Heidi Tschanz-Lischer
  • Marco Kreuzer
  • Alexander Nater
  • Sara Krättli


14:15-14:30 Coffee Break ☕🍪
14:30-15:00IBU - Bioinformatics Solutions | Research | Education (Part 2) Level up your bioinformatic skills: A guide to short courses and learning resources
  • Geert van Geest (IBU, Bioinformatics trainer, Training Group SIB Swiss Institute of Bioinformatics)

15:00-15:30Data Science Lab: Making advanced data analysis methods accessible to researchers
  • Guillaume Witz (Data Science Lab (DSL), Bern)

15:30-16:00Flash talks by external Bioinformaticians (list of presenters will be updated)
  • Ambre Baillou (Vetsuisse Faculty, IVI)
  • Andrej Benjak (Faculty of Medicine, DBMR)
  • Daniel Sánchez Taltavull (Faculty of Medicine, DBMR)
  • Hugo Armando Guillen Ramirez  (Faculty of Medicine, DBMR)
  • Jing Zhang (Vetsuisse Faculty, IVB)
  • Simone Oberhänsli (Vetsuisse Faculty, FIWI/NGSP)
  • Tural Yarahmadov (Faculty of Medicine, DBMR)
  • Vidhya Jagannathan (Vetsuisse Faculty, Institute of Genetics)
  • Cedric Walker (Vetsuisse Faculty, ITPA)


Networking Event and Apéro Riche
Registration (due to limited physical space first come first served policy)*
If you plan to attend the meetup, please register here

*Deadline for registration: 25th of April (Applies only to "In-person")

Key Information
Organizing Committee