• Monday 13 June

    • Council of Group Leaders

      14:00 - 17:30
  • Tuesday 14 June

    • Arrival & registration

      09:00 - 09:45

      Croissants and coffee  

    • Welcome speech

      09:45 - 10:00

      Room: Kongresssaal / Salle des congrès

    • Keynote lecture #1: Antonella Santuccione Chadha

      10:00 - 10:40

      Sex and gender differences as a biological variant: the work of the Women's Brain Project.
      Antonella Santuccione Chadha

      Session Chairs: Franziska Singer & Santiago Carmona 
      Room: Kongresssaal / Salle des congrès

    • Parallel session 1

      10:50 - 11:50
      • Navigating the rapidly expanding space of Genes and Genomes

        Session chairs: Evgenia Kriventseva & Damian Szklarczyk
        Room: Kongresssaal / Salle des congrès

        Session description

        Oral presentations

        • 10:50 - 11:05
          Reference genome-independent taxonomic profiling of microbiomes with mOTUs
          Alessio Milanese (Group: Shinichi Sunagawa)

        • 11:05 - 11:20
          Evol-Feat, a bioinformatics tool to map and explore evolutionary-functional correspondences of non-model arthropod genes
          Livio Ruzzante (Group: Robert Waterhouse)

        • 11:20 - 11:35
          Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression
          Arianna Vallerga (Group: Luciano Cascione)

        Poster pitches

        • 11:38 - 11:41
          Evolution of gene expression in the chemosensory tissues of ecologically diverse fly species
          Bastien Saint-Leandre (Group: Roman Arguello)

        • 11:42- 11:45
          Integration and homologous comparison of bulk and single-cell RNA-seq in Bgee
          Frederic Bastian (Group: Marc Robinson-Rechavi & Frédéric Bastian)

        • 11:46 - 11:49
          OpenGenomeBrowser: A reusable database independent and scalable web platform for genome database management and comparative genomics
          Thomas Roder (Group: Rémy Bruggmann)

      • Structural bioinformatics: innovative tools to address bio-macromolecular structure and dynamics

        Session chairs: Andrea Cavalli & Maria Marcaida Lopez
        Room: Vereinssaal / Salle des sociétés

        Session description

        Oral presentations

        • 10:50 - 11:05
          Covalent Ligand Docking with Attracting Cavities
          Mathilde Goullieux (Group: Olivier Michielin and Vincent Zoete)

        • 11:05 - 11:20
          Structure and Plasticity of Indoleamine 2,3-Dioxygenase 1 (IDO1)
          Ute Roehrig (Group: Olivier Michielin and Vincent Zoete)

        • 11:20 - 11:35
          Investigating the critical amino acids differentiating POU5F1B from its parent OCT4
          Anastasia Theodoropoulou (Group: Matteo dal Peraro)

        Poster pitches

        • 11:38- 11:41
          TBvar3D: Mycobacterium tuberculosis resistance variants mapped on protein structures
          Erblin Asllanaj (Group: Torsten Schwede)

        • 11:42 - 11:45
          SwissSimilarity 2021
          Maïa Bragina (Group: Vincent Zoete)

        •  11:46 - 11:49
          Benchmarking ligand structure prediction methods
          Xavier Robin (Group: Torsten Schwede)

      • Standards, analyses and trends in systems biology

        Session chairs: Enkelejda Miho & Daniele Tavernari
        Room: Workshop 1&2

        Session description

        Oral presentations

        • 10:50 - 11:05
          MNXtools – a software tool to diagnose chemistry of metabolites and reactions in genome-scale metabolic networks
          Marco Pagni (Group Vital-IT)

        • 11:05 - 11:20
          OMA Annotation Pipeline
          Sade Bates

        • 11:20 - 11:35
          The super-enhancer landscape reflects molecular subgroups of adrenocortical carcinoma
          Samuel Gunz

        Poster pitches

        • 11:38 - 11:41
          Interpretation of T cell states from single-cell transcriptomics data using reference atlases
          Massimo Andreatta (Group: Santiago Carmona)

        • 11:42 - 11:45
          CanIsoNet: A Database to Study the Functional Impact of Isoform Switching Events in Diseases
          Tülay Karalulak (Group: Christian von Mering)

        • 11:46 - 11:49
          CREMA: Automated modelling of genome-wide chromatin state in terms of local constellations of regulatory sites
          Mikhail Pachkov (Group: Erik van Nimwegen)

      • Room: Workshop 5


        In this ad hoc session, you will learn how to present the SIB Swiss Institute of Bioinformatics and explain its missions, with practical examples.


        • Maïa Berman, Team Lead, Communications 
        • Marie Dangles, Director, Public Relations, Communications, People & Culture & Resource Usability
    • Lunch break

      12:00 - 13:00
    • Parallel session 2

      13:00 - 14:00
      • Ecosystems bioinformatics in ecology and agriculture

        Session chairs: Natasha Glover & Guillem Salazar
        Room: Workshop 1&2

        Session description

        Oral presentations

        • 13:00 - 13:15
          Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity
          Anne-Florence Bitbol (Group: Anne-Florence Bitbol)

        • 13:15 - 13:30
          A global survey of the contribution of ecological factors to rates of horizontal gene transfer
          Marija Dmitrijeva (Group: Christian von Mering)

        • 13:30 -13:45
          Towards taxon-specific growth prediction in microbial communities by metatranscriptomics
          Melanie Stäubli (Group: Shinichi Sunagawa)

        Poster pitches

        • 13:45 - 13:48
          The good the bad and the ugly: the three sequencing approaches to compare microbial communities in aquaculture farms
          Adamandia Kapopoulou (Group: Claudia Bank)

        • 13:48 - 13:51
          Microbe Atlas Project: a global analysis and web resource of microbiome data enabling the characterisation of species habitats and comparative community analysis
          Joao Rodrigues (Group: Christian von Mering)

        • 13:51 - 13:54
          Using microbiome data to assemble a plant-inspired biocontrol community against the potato late blight
          Vivien Pichon

      • Evolutionary modelling with trees and beyond

        Session chairs: Richard Neher & Ana Morales-Arce
        Room: Vereinssaal / Salle des sociétés

        Session description

        Oral presentations

        • 13:00 -13:15
          Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes
          Diana Ivette Cruz Dávalos (Group: Anna-Sapfo Malaspinas)

        • 13:15 -13:30
          TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses
          Pierre Barrat-Charlaix (Group: Richard Neher)

        • 13:30 - 13:45
          Joint Alignment and Tree Inference
          Jūlija Pečerska (Group: Maria Anisimova)

        Poster pitches

        • 13:45 - 13:48
          Benchmarking methods using time-series data to infer selection
          Lucas Anchieri (Group: Anna-Sapfo Malaspinas)

        • 13:48 - 13:51
          ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
          Gholamhossein Jowkar (Group: Maria Anisimova)

        • 13:51 - 13:54
          Epistasis defines the transmission fitness of multidrug-resistant Mycobacterium tuberculosis
          Etthel Windels (Group: Tanja Stadler)
      • Immunology, health and disease

        Session chairs: Valérie Barbié & Giancarlo Croce
        Room: Kongresssaal / Salle des congrès

        Session description

        Oral presentations

        • 13:00 - 13:15
          FollicleFinder: an open source software for automated ovarian follicle detection and measurement
          Kevin Akira Yamauchi

        • 13:15 - 13:30
          SARS-CoV-2 – Two years on: How curation meets the challenge of variants
          Philippe Le Mercier (Group: Swiss-Prot)

        • 13:30 - 13:45
          Responsible sharing of health-related data in multi-center research projects
          Julia Maurer (Group: Personalized Health Informatics)

        Poster pitches

        • 13:45 - 13:48
          TCRpcDist: Estimating the physico-chemical similarity of TCR. Application to TCR repertoire analysis and TCR specificity prediction
          Marta Andreia Da Silva Perez (Group: Vincent Zoete)

        • 13:48 -13:51
          Clinical tools for interpreting genetic variants, SwissGenVar on BioMedIT, Switzerland's secure infrastructure for biomedical research
          Shubham Kapoor  (Group: Personalized Health Informatics)

        • 13:51 - 13:54
          Uncovering the Diverse Roles of Short Tandem Repeat Variation in Colorectal Cancer
          Max Verbiest (Group: Maria Anisimova)
    • Panel discussion - Who is afraid of data sharing?

      14:10 - 15:00

      Session chairs: Katrin Crameri, Franziska Singer, Patricia Palagi
      Room: Kongresssaal / Salle des congrès

      Together with representatives from biomedical research and legal, ethical, and technical experts, we will jointly explore why data-sharing is so essential, what challenges and risks it poses, and what this means for researchers as well as for data-donating citizens and patients. We want to discuss solutions that help ensure data protection and data security and enter into dialogue with the audience about their opinions, concerns, and expectations regarding the reuse of (health) data and the sharing of data in the life-science field in general.

      Our panel speakers are:

    • Poster session 1 - with coffee

      15:00 - 16:15
    • SIB days summer party at Römerhof farm

      17:30 - 01:00

      We will spend the evening at Römerhof, a traditional Bernese farm with mother cow herd, crops and homemade delights. Get close to real-life nature as you embark on a mother cow safari - or test your skills with other entertaining games such as archery and bow shooting - and, last but not least, show us your moves on the dance floor!

  • Wednesday 15 June

    • Prize draw to win a mini beamer

      08:00 - 09:15
    • Workshops & tutorials

      09:15 - 12:00

      Coffee break: 10:15 -10:30

      • Room: restaurant

        This workshop offers an overview of good practice in experimental design for high-throughput experiments. Particularly we focus on pitfalls in the design of projects (e.g. too low sample size or sequencing coverage, or sample batches overlap with biological groups), how to successfully plan an experiment and how to deal with challenges, e.g. batch effects or confounding factors. More


        • Michael Prummer
        • Eva Riegler
        • Franziska Singer 
      • Room: workshop 3

        In this tutorial users will learn about the CREMA theory behind the analysis, and explore in detail how it can be used in practice. CREMA has a large number of interactive possibilities to explore predictions and to generate new analyses of the data which will be demonstrated in the tutorial. More


        Erik van Nimwegen
        Mikhail Pachkov

      • Room: foyer

        The workshop is for beginners and will focus on explaining all the basic concepts required to implement simple workflows. We will briefly introduce a few advanced topics that are particularly useful for common use cases. More


        • Romain Feron 
        • Antonin Thiebaut 
      • Room: workshop 1

        In this tutorial, you will learn about the most recent advances in protein structure prediction, starting with a short presentation introducing the current state of the art. A hands-on tutorial will then focus on web based tools that can go from one or more input protein sequences to an accurate 3D model of a single protein chain or a protein complex. Topics covered will include homology modelling with SWISS-MODEL and deep learning powered modelling with AlphaFold. More


        • Gabriel Studer
        • Joana Pereira
        • Gerardo Tauriello
      • Room: vereinssaal

        In this tutorial, you will learn different approaches to simplify single-cell RNA-Seq data by merging highly similar, and possibly biologically redundant cells into metacells. These will include the SuperCell method developed in the Computational Cancer Biology Group's lab. More


        • David Gfeller
        • Mariia Bilous
        • Aurélie Gabriel
        • Léonard Hérault
      • Room: Kongresssaal

        This workshop will teach the participants how to describe the work they do and its impact on society; plan an activity that introduces the general public to their work and prepare a brief communication around the activity.


        • Marie-Claude Blatter
        • Natasha Glover
        • Monique Zahn
      • Room: workshop 5

        In this workshop, you will investigate the hidden biases that might exist in our bioinformatics daily practices, be it in the use of particular data repositories, the curation process, the way we design experiments and implement models, or the analysis approaches we undertake and the interpretation of their results. More


        SIB Diversity working group:

        • Aitana Lebrand (Chair)
        • Maïa Berman
        • Ute Roehrig
        • Julien Roux
        • Gerardo Tauriello
        • Robert Waterhouse
      • Room: workshop 2

        The aims of this workshop are:

        • Learning from participants about common practices and challenges in re-using published epigenomics data
        • Discussing FAIRness issues in epigenomics with colleagues
        • Raising awareness of FAIR principles among younger scientists
        • Initiating a SIB focus group to continue the discussions initiated at the workshop
        • Information on related initiatives: SwissBioData ecosystem, FAIRtracks


        • Philipp Bucher
        • Michael Stadler
      • Room: foyer

        In this workshop, you will discuss the challenges of implementing a rapid genomic surveillance strategy that can be activated in case of emergencies. The discussions will focus on three target areas: rapid data generation, practical analyses and effective communication. More


        • Louis du Plessis
        • Chaoran Chen
        • Cecilia Valenzuela Agüi
        • Adrian Lison
    • Lunch break

      12:00 - 13:00
    • Keynote lecture #2: Johannes Rainer

      13:00 - 13:40

      The Power of Open Software Development in Metabolomics Research

      A personal view on advantages of reproducible research and open software development in mass spectrometry data analysis.

      Session chairs: Etthel Windels & Robert Waterhouse
      Room: Kongresssaal / Salle des congrès

      With ever more comprehensive data sets and complex analysis algorithms, reproducibility is becoming increasingly important to ensure trust in research results. Availability and stability of the employed software algorithms are, along with data availability, crucial aspects of reproducible research. Open and collaborative software development can increase stability and long term support of software as the development is not carried out by a single research group and hence maintenance is less dependent on individual developers or funding of a single research group. Heavily interdisciplinary sciences, such as for example metabolomics, also benefit from open collaborative software development, as researchers with different background will contribute functionality from their specific expert areas resulting thus in a potentially more complete software solution.

      In this presentation Johannes Rainer will share his own experiences with reproducible research and open software development in metabolomics research. He will discuss advantages, but also potential pitfalls of open software development and highlight opportunities that openness and collaborative efforts bring to modern data science.

    • Parallel session 3

      13:50 - 14:50
      • Mathematical and computational approaches to solve biological problems

        Session chairs: Patrick Ruch & Sarah Brüningk    
        Room: Kongresssaal / Salle des congrès

        Session description

        Oral presentations

        • 13:50 - 14:05
          Metacells untangle large and complex single-cell transcriptome networks
          Mariia Bilous (Group: David Gfeller)

        • 14:05 - 14:20
          Protein language models trained on multiple sequence alignments learn phylogenetic relationships
          Umberto Lupo 

        • 14:20 - 14:35
          Bayesian phylodynamic inference of multi-type population trajectories using genomic data
          Timothy Vaughan (Group: Tanja Stadler)

        Poster pitches

        • 14:38 - 14:41
          Classification of oncology treatment responses from radiology reports with supervised machine learning
          Luc Mottin (Group: Patrick Ruch)

        • 14:42 - 14:45
          Taxonbridge: an algorithm for the creation and analysis of custom taxonomies
          Werner Pieter Veldsman (Group: Marc Robinson-Rechavi & Frédéric Bastian)

        • 14:46 - 14:48
          Somatic Copy Number Alteration Data Calibration
          Hangjia Zhao (Group: Michael Baudis)
      • Proteins and proteomes, from data to knowledge

        Session chairs: Bernd Wollscheid & Fanny Krebs
        Room: Vereinssaal / Salle des sociétés

        Session description

        Oral presentations

        • 13:50 - 14:05
          Disentangling phylogeny and optimization contributions in protein sequences
          Nicola Dietler

        • 14:05 - 14:20
          Glycan-protein interaction motifs: A semantic based annotation method
          Catherine Hayes (Group: Frédérique Lisacek) 

        • 14:20 - 14:35
          Proteogenomics identifies conserved and lineage-specific novel small proteins in clinical Mycobacterium tuberculosis reference strains
          Benjamin Heiniger (Group: Christian Ahrens)

        Poster pitches

        • 14:38 - 14:41
          Swiss-PO and its upcoming updates
          Fanny Krebs (Group: Vincent Zoete)

        • 14:42 - 14:45
          Delineation of kinase signaling networks in tumor-associated macrophages
          Tiberiu Totu  (Group: Marija Buljan)

        • 14:46 - 14:49
          Protein detection sensitivity in 2D electrophoresis experiments strongly depends on imaging parameters
          Sonja Voordjik (Group: Valérie Barbié)
      • Room: Workshop 1&2

        Objective: This informal session will provide the opportunity to exchange knowledge and best practices around the management of small or bigger projects.

        • Part 1 - Being agile with the Scrum framework (20 min) 

        Séverine Duvaud, Team Lead, Resource Usability & Support and Software Developer 

        Description: In this presentation, we will describe the principles of the Scrum framework and its main components. In particular, we will focus on what the framework does, what it does not do, and what it is and is not for. Breaking down myths, giving a new perspective on project management, and perhaps inspiring some of you, will be the overall goals of this session.   

        • Part 2 – Demo of the tool Click-up: how to organise your project and collaborate (20 min) 

        Maïa Berman, Team Lead, Communications 

        Description: Recurring meetings, releases, reports… Processes, in particular collaborative ones, can get messy, and it is easy to forget a task and get lost across tools. In this session, find out how ClickUp has help us in the Communication and Scientific events team to (somewhat) streamline our workflows, and get ideas on how to structure your own work.  

        • Q&A (10 min) 
    • Poster session 2 - with Beers & Bretzels

      14:50 - 16:00

      Posters and software demonstrations served with beer and bretzel.

    • Poster prizes and closing remarks

      16:00 - 16:15
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