Conference agenda

Room: Restaurant - Congress Centre

Organizers:

• Heidi Tschanz-Lischer (Interfaculty Bioinformatics Unit, University of Bern)
• Geert van Geest (Bioinformatics Trainer at the Training group & computational biologist, Interfaculty Bioinformatics Unit, Bern)
• David Miguel Francisco Ferreira (Interfaculty Bioinformatics Unit, University of Bern)

Organizers:

• Marija Dmitrijeva, Postdoctoral Researcher, Microbiome Research Lab, ETH Zurich
• Hans-Joachim Ruscheweyh, Senior Bioinformatician, Microbiome Research Lab, ETH Zurich

Room: Ginger 1 -  Courtyard Mariott Hotel

Room: Workshop 3 - Congress Centre

Schedule:

Organizers:

• Fanny Krebs (Computer-aided Molecular Engineering group, Epalinges)
• Frédérique Lisacek (Group Leader, Proteome Informatics, Geneva)
• Ute Röhrig (Senior Research Scientist, Molecular Modelling group, Lausanne)
• Vincent Zoete (co-Group Leader, Molecular Modelling, Lausanne, and Group Leader, Computer-aided Molecular Engineering, Epalinges)

Room: Juniper - Courtyard Mariott Hotel

Schedule:

Organizers:

• Maïa Berman (Team Lead Communications, Lausanne, SIB Diversity Working group)
• Davide Cirillo (Life Sciences Department, Barcelona Supercomputing Center), external speaker
• Aitana Neves (Team Lead Data Science at SIB clinical bioinformatics, Lausanne, SIB Diversity Working group)
• Xavier Robin, (Senior Software Developer at Computational Structural Biology, Basel, SIB Diversity Working group)
• Julien Roux, (DBM Bioinformatics Core Facility, Basel, SIB Diversity Working group)
• Leonore Wigger (Senior Computational Biologist at Vital-IT, Lausanne, SIB Diversity Working group)

Confirmed instructors: Davide Cirillo (BSC) and Frédéric Schütz (UNIL/SIB)

Speakers: each career path presentation will last approx. 15 minute, followed by a 15-minute Q&A session.

• 13:30 Annika Gable, Bioinformatics Software Engineer at Immunai 
• 13:55 Murat Akhmedov, CEO and Co-Founder of BigOmics Analytics
• 14:25 Amel Bekkar, Bioinformatics Scientist at JSR Life Sciences
• 14:50 Coffee break
• 15:15 David Dylus, Senior Scientist at Roche
• 15:40 Janet Thornton, former Director of EMBL-EBI
• 16:05 Matteo Togninalli, Co-Founder and COO at Visium SA

Moderators: Yannis Nevers, Silvia Prieto-Baños

Room: Workshop 1 - Congress Centre

Structural genome annotation is the process of identifying coding and non-coding elements on a genome. This process is critical to make sense and make use of genomic data but thus far lacks agreed upon standards and is still technically difficult for eukaryotic genomes.

In this session, we will lead the discussion about state-of-the-art in eukaryotic genome annotation and the main challenges it currently faces. We will touch upon the emerging format and quality standards in the community - including recent developments and contributions from major sequencing initiatives. Finally, we will turn the spotlight on the effect of genome annotation on downstream analyses, and share experiences on how to better reduce such technical bias.

Moderators: Marija Buljan, Aurélie Gabriel

Room: Workshop 5 - Congress Centre

Cellular signaling pathways determine cell identity, its response to stimuli and its function both in homeostasis and disease. Even though targeting of cellular pathways is of a high pharmaceutical interest, their comprehensive mapping represents a formidable challenge due to the complexity in signal transduction regulation. In particular, wiring of pathway components is often specific for individual cell types and their functional states. In this session, we want to discuss useful multi-omics datasets, data repositories as well as computational approaches that investigate gene regulatory processes induced by changes in chromatin accessibility, assess kinase signaling cascades and build up on the network inference approaches, which can all be used for the better mapping and understanding of cellular signaling routes.

Moderators: Jonas Grossmann, Katja Bärenfaller

Room: Vereinsaal - Congress Centre

In which direction is the field of proteomics currently developing? How far away are we from getting a complete view on the proteome also considering subproteomes and proteoforms? What aspects are we still missing? How do we move away from 'unbiased cherry picking' in standard approaches? Do we still need bulk proteomics or should we focus more on single-cell proteomics? What research questions can we ask, and what is not possible to answer with the current technologies?

In this interactive “Meet your peers” discussion, we encourage participants to share their expertise and insights on these topics, and to reflect on their experiences, unsuccessful approaches, and potential pitfalls. Additionally, we are keen to hear your thoughts on the developments you would like to see for the proteomics field in the near or distant future.

Moderators: Geert van Geest, Diana Marek

Room: Ginger 1 - Courtyard Mariott Hotel

Do you consider education as an important part of science? Have you ever struggled to re-use educational material? Did you know that the FAIR* principles can be applied to training and education? Do you know what SIB is doing in this area?

In this “Meet your peers“ discussion, learn how the FAIR principles can support education and training. Discover how SIB efforts can be leveraged in this process and discuss ways in which the FAIRification process could be improved and more easily used in education.

This session welcomes anyone involved in education at universities or within institutes in any way (learners, occasional lecturers, teachers) and/or who is interested in open and FAIR education.

During this interactive discussion, the attendees will share their knowledge and ideas of what FAIR in education means. In addition, it will give them guidance on how to re-use existing material and how to apply the FAIR principles to their own education process.

Moderator(s): Philipp Bucher

Room: Restaurant - Congress Centre

This event is organized by the SIB Epigenomics focus group. Discussion topics may include:

(i) interoperability issues (semantic and computational): metadata, ontologies, format standards, federated queries;
(ii) reproducibility and re-usability: workflow sharing, containerization, data longevity, visualization;
(iii) community aspects: Dissemination channels (journals and data repositories), legal aspects, authorship, incentives, role of bioinformatics core facilities, teaching needs.

The intent is to address these questions in a broad context, not limited to epigenomics. We hope to be able to attract a balanced mix of data producers, users and brokers with different background.

Moderators: Robert Waterhouse

Room: Workshop 2 - Congress Centre

The integration of Equity, Diversity, and Inclusion (EDI) policies and best practices into institutional governance structures is increasingly recognised as essential for community cohesion and belonging. As a federated institution, the SIB connects members from many different institutions across Switzerland. In this session, we aim to share SIB Members experiences and understanding of their own institution's EDI initiatives. The goal is to create a map of the status of SIB-affiliates' activities in the domain as a means of cross-pollinating ideas amongst institutions. Emerging from this, we hope to also develop a clearer picture of how the SIB can best serve the needs of SIB Members with respect to EDI integration

Moderators: Remy Bruggmann, Robert Ivanek, Michael Stadler

Room: Cinnamon - Courtyard Mariott Hotel

The "Core Facilities Focus Group" provides a collaborative platform for members of SIB core facilities to exchange experiences and best practices. Alongside topics specific to facilities, like project management, time tracking, and financial models, we also address broader challenges in bioinformatics. This encompasses standardizing data analysis, developing and sharing workflows, and promoting reproducible research. With many institutes adopting embedded bioinformaticians, fostering regular interaction between them and core facilities, and integrating them into the SIB bioinformatics community belongs to our main focus. It serves as a dynamic forum for optimizing processes and sharing knowledge within and beyond bioinformatics cores.

Moderators: Santiago Carmona, Julien Roux

Room: Juniper -  Courtyard Mariott Hotel

Launched in November 2022, the Single-cells Omics focus group organizes hybrid meetings every first Wednesday of the month, aiming at discussing various topics connected to single-cell data analysis and visualization.

This session will be the opportunity to meet in real life with members of the group, and with people interested in joining us. We are planning an informal discussion allowing us to get a better idea of who is working on what type of single cell data at the moment, and collect the topics people would like to hear about in the upcoming meetings.

This session aims at fostering connections between attendees who have interest in the development of single-cell omics technologies.

Moderators: Marc Robinson Rechavi

Room: Workshop 3 - Congress Centre

While scientists as a community sound the alarm about climate change and biodiversity collapse, individual scientists and labs continue to have a large environmental impact. This includes plane travel and, for bioinformatics especially, the carbon footprint of computations.
We will discuss how to balance the environmental footprint of our work with the needs of scientific research and bioinformatics support.

Moderators: Marie-Claude Blätter, Monique Zahn

Room: Ginger 2 - Courtyard Mariott Hotel

Are you passionate about science and want to share it with others? Do you think more scientists should be speaking up about societal issues that can be impacted by their science? Would you like to improve the SIB outreach activities? Would you like to be involved in some way in the SIB's outreach activities?

If you’ve answered yes to any of these questions, this ‘meet your peers’ session is for you.

Over the years, SIB has developed websites (chromosomewalk.ch, lightofevolution.org, ohmygenes.org, drug-designworkshop.ch) and related interactive workshops which are available to teachers, students, as well as the public. The topics covered (genes & proteins, evolution, drug design) allow a public of all ages to discover a wide range of tools and databases developed by the SIB, how they are being used by researchers around the world to answer questions that have an impact on society.

In 2023, 2'300 people participated in more than 120 workshops organized and/or animated by the SIB, in classrooms, during events such as TecDays (by SATW), open days (Mystères de l'UNIL), science fairs (Nuit de la Science), events dedicated to young girls (Enlarge your Horizon) or career orientation programs.

Come and discuss with like-minded peers at SIB how you can communicate with the public!

Moderators: Alex Kanitz, Mark Ibberson, Michael Baudis, Lucy Poveda

Room: Konzertsaal - Congress Centre

The discussion introduces SIB members to community standards and pan-European infrastructure projects for large scale data storage and analytics as well as sensitive data handling with application to biomedical research and personalized medicine. While it is primarily geared towards managers and administrators of computing and data centers and those SIB members that already contribute or would like to contribute in the future to relevant European and/or international organizations, initiatives or projects (e.g., ELIXIR, EOSC, FEGA, GA4GH, RDA), it will address trending topics for anyone involved in the acquisition, governance, and processing of large data volumes, obtained, e.g., through sequencing, mass spectrometry or imaging techniques.

NAVIGATING THE RAPIDLY EXPANDING SPACE OF GENES AND GENOMES

Session chairs: Maria Anisimova and David Francisco
Room: Konzertsaal / Salle des congrès

Session description

• 13:00 - 13:50 ORAL TALKS (3x15')
  
  Integrating DNA language models with explainable graph neural networks to identify causal genes and pathways in human genomic studies
  Ali Saadat (Group: Jacques Fellay, Lausanne)
  
  Robust estimation of cancer and immune cell type proportions from bulk tumor ATAC-Seq data
  Aurélie Gabriel (Group: David Gfeller, Lausanne)
  
  Non-coding variants impact cis-regulatory coordination in a cell type-specific manner
  Olga Pushkareva (Group: Bart Deplancke, Lausanne)
  
  
• 13:50 - 14:00 POSTER PITCHES (3x3')
  
  T2T haplotig phased genome assembly of the Argan tree (Argania spinosa)
  Laurent Falquet (Group Leader, Fribourg)
  
  Immunotherapy response biomarkers in colorectal cancer
  Olesia Kondrateva (Group: Maria Anisimova, Wädenswill)
  
  On the identification of differentially-active transcription factors from ATAC-seq data
  Emanuel Sonder (Group: Mark Robinson, Zurich)
  

INNOVATIVE TOOLS TO ADDRESS BIO-MACROMOLECULAR STRUCTURE AND DYNAMICS

Session chairs: Andrea Cavalli & Joana Pereira
Room: Vereinssaal / Salle des sociétés

Session description

• 13:00 - 13:50 ORAL TALKS (3X15')
  
  ProPose: Generative modelling of ligand-binding protein conformations using flow matching and AlphaFold 
  Peter Skrinjar (Group: Torsten Schwede, Basel)
  
  TCRpcDist: A Cutting-Edge In Silico Algorithm for Advancing Cancer Immunotherapies
  Marta Andreia Da Silva Perez Gomes (Group: Olivier Michielin & Vincent Zoete, Lausanne)
  
  Computational design of lipocalin ligands
  Sara Buscarini (Group: Andrea Cavalli, Bellinzona)
  
  
• 13:50 - 14:00 POSTER PITCHES (3X3')
  
  SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina
  Marine Bugnon (Group: Vincent Zoete, Lausanne)
  
  Computational antigen-targeted antiviral design
  Océane Follonier (Group: Torsten Schwede, Basel)
  
  Protein-Ligand Complex Prediction - Are we there yet?
  Janani Durairaj (Group: Torsten Schwede, Basel)

Session description

• 14:00 - 14:50 ORAL TALKS (3x15')
  
  Metacells facilitate the analysis of single-cell multiomics data
  Léonard Hérault (Group: David Gfeller, Lausanne)
  
  Integration of Imaging Mass Cytometry and Imaging Mass Spectrometry data
  Reto Gerber (Group: Mark Robinson, Zurich)
  
  Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids
  Tülay Karakulak (Group: Abdullah Kahraman, Muttenz) and Hubert Rehrauer (Functional Genomics Center Zurich)
  
  
• 14:50 - 15:00 POSTER PITCHES (3x3')
  
  Bonsai captures and visualizes the structure in single-cell transcriptomics
  Daan de Groot (Group: Erik van Nimwegen, Basel)
  
  Harmonizing cell type classification in the tumor microenvironment
  Josep Garnica Caparrós (Group: Santiago Carmona, Lausanne)
  
  Multi-sample non-negative spatial factorization for spatial transcriptomics data
  Yi Wang (LS2 Intersection, Baltimore)

EVOLUTIONARY MODELLING WITH TREES AND BEYOND

Session chairs: Frederic Bastian and Nina Marchi
Room: Vereinssaal / Salle des sociétés

Session description

• 14:00 - 14:50 ORAL TALKS (3x15')
  
  Community conservatism is present in all microbial Phyla and environments
  Lukas Malfertheiner (Group: Christian von Mering, Zurich)
  
  A competition-detoxification balance controls the evolution of resistance in simple microbial communities
  Massimo Amicone (Group: Sara Mitri, Lausanne)
  
  The interaction between overdominant heterosis and hybrid incompatibilities
  Julio Ayala Lopez (Group: Claudia Bank, Bern)
  
  
• 14:50 - 15:00 POSTER PITCHES (3x3')
  
  Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data
  Felix Thalen (Group: Andreas Ziegler, Davos Wolfgang)
  
  Mutual Information-based feature selection of k-mers for phylogenetic placement
  Nikolai Romashchenko (Group: Christophe Dessimoz & Natasha Glover, Lausanne)
  
  Exploring Indel Patterns in the HIV-1 Genome - A Comparative Analysis of Alignment and Ancestral Sequence Reconstruction Methods
  Clara Iglhaut (Group: Maria Anisimova, Wädenswill)
  

Panel moderators: Daniel Stekhoven and Valérie Barbié 
Special guest: Obi Griffith 
Room: Workshop 5
Panelists:

• Abdullah Kahraman
• Alan Bridge
• Michael Baudis
• Marija Buljan

Session description

PERSONALISED HEALTH AND DISEASE, FROM MOLECULES TO SYSTEMS

Session chairs: Janna Hastings and Patrick Pedrioli
Room: Konzertsaal / Salle des congrès

Session description

• 09:30 - 10:20 ORAL TALKS (3x15')
  
  Somatic short tandem repeat mutations regulate gene expression in colorectal cancer
  Max Verbiest (Group: Maria Anisimova, Wädenswill)
  
  GPT-based Grading of Retinal Inflammation
  Mattia Tomasoni (Alumni, UniL, Lausanne)
  
  Combinatorial in silico algorithm to identify clinically-relevant TCRs for personalized T-cell therapy
  Rémy Pétremand (Group: Vincent Zoete, Lausanne)
  
  
• 10:20 - 10:30 POSTER PITCHES (3x3')
  
  CytoxPred: efficient prediction of cancer cell lines targeted by cytotoxic small molecules
  Alessandro Cuozzo (Group: Vincent Zoete, Lausanne)
  
  Unveiling Novel Adipose Populations Linked to Metabolic Health in Obesity
  Adhideb Ghosh (Group: Hubert Rehrauer, Zurich)
  
  dsMO: enabling non-disclosive federated multi-omics analysis on virtual cohorts
  Thuong Van Du Tran (Group: Mark Ibberson, Lausanne)
  

UNRAVELING ECOSYSTEM COMPLEXITY WITH BIOINFORMATICS

Session chairs: Catalina Chaparro Pedraza & Germán Bonilla-Rosso
Room: Vereinssaal / Salle des sociétés 

Session description

• 09:30 - 10:20 ORAL TALKS (3x15')
  
  Genomic data production systems to catalogue and explore eukaryotic biodiversity
  Robert Waterhouse (Group Leader, Lausanne)
  
  Application of the RDF framework to integrate heterogenous experimental data of a large chemo- and biodiverse collection from a collaborative research project
  Frédéric Burdet (Group: Mark Ibberson, Lausanne)
  
  A meta-analysis of complete microbial genomes reveals differences in assembly quality, taxonomic coverage and serves as a resource to decipher the functions of microbiome isolates
  Christian Ahrens (Group Leader, Zurich)
  
  
• 10:20 - 10:30 POSTER PITCHES (3x3')
  
  The Microbe Atlas database: Global trends and insights into Earth’s Microbial Ecosystems
  Janko Tackmann (Group: Christian von Mering, Zurich)
  
  
  Towards Comparative QTLomics
  Irene Consuelo Julca Chavez (Group: Christophe Dessimoz & Natasha Glover)

MATHEMATICAL AND COMPUTATIONAL APPROACHES TO SOLVE BIOLOGICAL PROBLEMS

Session chairs: Mark Ibberson & Sandra Mitrović
Room: Konzertsaal / Salle des congrès

Session description

• 11:00 - 11:50 ORAL TALKS (3x15')
  
  A simple-to-use R package for mimicking study data by simulation
  George Koliopanos (Group: Andreas Ziegler, Davos Wolfgang)
  
  PolyHoop and SimuCell3D: New tools for cell-based tissue simulation
  Roman Vetter (Group: Dagmar Iber, Basel)
  
  Inference of expression state in bulk and single-cell RNA-Seq using curated intergenic regions
  Alessandro Brandulas Cammarata (Group: Marc Robinson-Rechavi & Frederic Bastian, Lausanne)
  
  
• 11:50 - 12:00 POSTER PITCHES (3x3')
  
  Unlocking the potential of PMC supplementary data
  Julien Gobeill (LS2 Intersection)
  
  CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods
  Ana-Claudia Sima (Group: Vital-IT, Knowledge Representation Unit)
  
  Advancing FAIR meta-analyses of nucleotide sequence data with q2-fondue
  Anja Adamov (ETH, Zurich - LS2 Intersection)

PROTEINS AND PROTEOMES, FROM DATA TO KNOWLEDGE

Session chairs: Frédérique Lisacek and Witold Wolski
Room: Vereinssaal / Salle des sociétés

Session description

• 11:00 - 11:50 ORAL TALKS (3x15')
  
  The Literature-Derived regulatory Networks in the STRING Database
  Damian Szklarczyk (Group: Christian von Mering, Zurich)
  
  Enhancing antimicrobial resistance prediction models with multimodality integration
  Diane Duroux (Group: Niko Beerenwinkel, Zurich)
  
  From a glycome graph to refined protein interactions
  Catherine Hayes (Group: Frédérique Lisacek, Geneva )
  
  
• 11:50 - 12:00 POSTER PITCHES (3x3')
  
  ViralZone enzymes: improved overview of the viral reaction landscape
  Philippe Le Mercier (Group: Alan James Bridge, Geneva)
  
  Recon4IMD: Leveraging UniProt, Rhea, and SwissLipids to develop improved human metabolic models for inherited metabolic diseases
  Anastasia Sveshnikova (Group: Alan James Bridge, Geneva)
  
  A map of predicted mechanistic impacts of human protein missense variants
  Jürgen Jänes (Group: Pedro Beltrao, Zurich)
  

Session description

• Xiang Ge Luo (Group: Niko Beerenwinkel) Mining tumor mutation trees with TreeMHN for evolution-guided precision oncology
• Marco Varrone (Group: Giovanni Ciriello) CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity
• Janani Duraijaj (Group: Torsten Schwede) Protein Universe Atlas
• Stefan Stark (Group: Gunnar Rätsch) Learning Single-Cell Perturbation Responses using Neural Optimal Transport
• Pedro Beltrao (Group: Pedro Beltrao) Clustering predicted structures at the scale of the known protein universe
• Geert van Geest (Groups: Patricia Palagi & IT) Glittr.org: Find and Compare Git Repositories with Bioinformatics Training Materials
• Julien Racle (Groups: David Gfeller & Vincent Zoete) Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes