Conference agenda

Programme overview

  • Monday 8 September

    • Registration for the tutorial & workshops

      08:15 - 09:00

      Location: at Biozentrum, Basel.

    • Tutorials & workshops

      09:00 - 16:15

      The tutorials and workshops take place at the Biozentrum in Basel. 

      Check out the full list.

    • Council of Group Leaders

      14:30 - 16:30

      For SIB GLs only
      Room: Osaka + Samarkand (2nd floor)

    • Registration for the conference

      16:00 - 17:00

    • Conference opening and keynote lecture

      17:00 - 18:00

      Session chairs: David Gfeller, Catherine Jutzeler
      Room: Montreal

      • 17:00 – 17:10       
        Intro and Welcome words

      • 17:10 - 18:00  KEYNOTE SPEAKER 
        Advances in understanding mutational processes in whole genome sequencing data and implications for cancer clinical trials
        Serena Nik-Zainal (University of Cambridge, UK) 

    • [BC]2 Welcome apéro & dinner

      18:15 - 22:30

      The welcome dinner will take place at bambusnest, where we will be honoured by an official speech from Kaspar Sutter, Head of the Department of Economic Affairs, Social Affairs and the Environment of the Canton of Basel-Stadt 

  • Tuesday 9 September

    • Registration

      08:00 - 09:00

    • Parallel session 1

      09:00 - 10:30

      • Session chairs: Emma Hodcroft and Jacques Fellay 
        Room: Singapore

        • 09:00 - 09:30  INVITED SPEAKER 

          Genome-wide prioritization of human 5'UTR variants: insights into Human resistance to tuberculosis
          Aurélie Cobat (Institut Imagine | INSERM, France)

        • 09:30- 10:15  SELECTED TALKS (3x15')


          Co-circulating Respiratory Viruses and their Phylogenies in Switzerland: A case for Global Representation?
          Charlyne Bürki (ETHZ, D-BSSE, Switzerland)

          Bacteriophage host prediction via genome-wide large language models
          Andrea Di Gioacchino (Phagos, France)

          Recombination in Vaccine-Derived Polioviruses: Insights from Public Sequencing Data
          Keno Strotjohann (Swiss Tropical and Public Health Institute, Switzerland)

        • 10:15 - 10:30  SELECTED POSTER PITCHES (3x5')

          Decoding immune repertoires by integrating immune sequencing techniques and large-scale functional antibody repertoire profiling methods
          Hesham El Abd (Institute of Clinical Molecular Biology, Germany)

          Cross-scale effect of microbiome dynamics on resistance
          Lisa Pagani (Integrative Biology, ETH Zurich, Switzerland)

          Clonal Hematopoiesis in People Living With HIV: Association With Aging and Inflammation
          Valeriia Timonina (EPFL SV GHI GR-FE, Switzerland)

      • Session chairs: Valentina Boeva and Santiago Carmona
        Room: Montreal

        • 09:00 - 09:30  INVITED SPEAKER 

          Dissecting intra-tumor heterogeneity by single cell and spatial transcriptomics
          Itay Tirosh (Weizmann Institute of Science, Israel)

        • 09:30 -10:15   SELECTED TALKS  (3x15')

          Deciphering TCR Specificity with deep learning
          Giancarlo Croce (Ludwig Centre for Cancer Research, UNIL, Switzerland)

          Spatio-morphological profiling of glioblastoma
          Zuzanna Lottenbach (ETH Zürich, Switzerland)

          Spatial Profiling of the Prostate Cancer Microenvironment: Integrating Vision-Based and Graph-Based Modeling
          Adriano Martinelli (Centre hospitalier universitaire vaudois CHUV, Switzerland)

        • 10:15 - 10:30  SELECTED POSTER PITCHES (3x5')

          Associating cancer-specific single nucleotide variants with methylation changes using models based on convolutional neural networks
          Halimat Atanda (Mater Research Institute-University of Queensland, Australia)

          Resolving malignant cell heterogeneity in tumor bulk RNA-seq data with CDState
          Agnieszka Kraft (ETH Zurich, Switzerland)

          Generalizable AI predicts immunotherapy outcomes across cancers and treatments
          Daniel Marbach (Roche Innovation Center Basel, Switzerland)

    • Coffee break

      10:30 - 11:00

    • SIB Bioinformatics Awards and Remarkable Outputs recognition

      11:00 - 12:30

      Session chair: Luciano Cascione
      Room: Montreal

      To promote excellence and innovation in bioinformatics and computational biology, SIB established the Bioinformatics Awards in 2008 to recognise international early-career bioinformaticians and impactful resources. Additionally, since 2019, the SIB Remarkable Outputs programme annually highlights up to 10 notable contributions from members, enhancing the visibility and importance of bioinformatics.   

      • 11:00 – 11:15      
        PhD Paper Award
        Announcement of awardee and presentation of paper
           
      • 11:15 – 11:30  
        Early Career Award
        Announcement of awardee and presentation of research
           
      • 11:30 – 11:45    
        Innovative Resource Award
        Announcement of awardee and presentation of resource

      • 11:15 - 12:30
        SIB Remarkable Outputs
        Short presentation of each output

    • Lunch

      12:30 - 13:45

      • Discover scientific innovations and research advancements from industry experts, who will share insights on transcriptomics breakthroughs, explore challenges in personalized healthcare, present precision medicine approaches in cancer diagnostics, and showcase novel bioinformatics applications in pharmaceutical research.

        • Riccardo Dainese, CEO and Co-Founder, Alithea Genomics
        • Noushin Hadadi, Chief Data Officer, Novigenix
        • Lian Huang, Senior Patent Counsel specializing in Personalized Healthcare and Computational Sciences, Genentech
        • Petra Schwalie, Principal Bioinformatics Scientist, Roche

    • Parallel session 2

      13:45 - 15:15

      • Session chairs: Marianna Rapsomaniki and Julien Roux
        Room: Singapore

        • 13:45 - 14:15  INVITED SPEAKER

          Learning compact representations of protein motions
          Elodie Laine (Sorbonne Université, France)

        • 14:15 - 15:00 SELECTED TALKS (3x15')

          Multi-objective genetic algorithms for metalloprotein design
          Simon Duerr (HES-SO Valais-Wallis, Switzerland)

          Protein Alphabets from Language Models (PALM): quantization of pLM embeddings to enable fast and sensitive sequence screening
          Lorenzo Pantolini (Biozentrum, University of Basel, Switzerland)

          Improved Molecular Predictions with Ontology-derived Knowledge Injection
          Charlotte Tumescheit (University of Zurich, Switzerland)


        • 15:00 - 15:15  SELECTED POSTER PITCHES (3x5')

          From bytes to binders: design, score and optimize
          Océane Follonier (Biozentrum, University of Basel, Switzerland)

          Prosit-XL: Accurate Fragment Intensity Prediction and Enhanced Cross-Linked Peptide Identification for Protein Structural and Interaction Studies
          Mostafa Kalhor (Friedrich-Loeffler-Institut, Switzerland)

          Integrated sequence-structure Deep Learning framework for single-residue property prediction in antibody-antigen complexes
          Kevin Michalewicz (Imperial College London, UK)

      • Session chairs: Valérie Barbié and Laura Azzimonti 
        Room: Montreal

        • 13:45 - 14:15  INVITED SPEAKER 

          Technology and Data-driven precision medicine – a research and infrastructure perspective
          Päivi Östling (Karolinska Institute, SciLifeLab, Sweden)

        • 14:15 - 15:00  SELECTED TALKS (3x15')

          Deciphering fluorescence microscopy datasets with AI
          Elisa Messori (Idiap, Switzerland)

          Towards Precision Drug Dosage: Exploring Pharmacogenomic Interactions in the All of Us Research Program
          Jan Matthias (Stanford, USA)

          Unravelling associations between HLA peptidome divergence and patient outcomes in diseases
          Julien Racle (University of Lausanne, Switzerland)

        • 15:00 - 15:15  SELECTED POSTER PITCHES (3x5')

          KidsCan_01: In depth tumor profiling for children with high-risk, progressive & relapsed malignancies
          Linda Grob (University Children's Hospital Zürich, Switzerland)

          Exploring Obesity Variability through Machine Learning-Driven Patient Segmentation
          Anne Hoffmann (Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), Germany)

          Deep Hierarchical Subtyping of Multi-Organ Systemic Sclerosis Trajectories
          Cécile Trottet (Krauthammerlab, Switzerland)

    • Poster session 1 and coffee break

      15:15 - 16:30

      Browse our Poster Gallery to see who will present and get in touch with your fellow scientists to discuss your and their latest research projects in front of the poster. 

      • Take the opportunity to meet with a member of SIB’s People and Culture team for personalized career guidance! Whether you are looking for feedback on your CV or cover letter, preparing for interviews, or wondering how to best present your academic background, our HR professionals, and the Director of an SIB group will be available to help you.

        When?
        - Tuesday 9 September, from 15:15 to 16:30
        - Wednesday 10 September, from 14:45 to 16:00

        You may upload your CV and/or cover letter in advance to help us provide more targeted feedback or send it to peopleandculture@sib.swiss.

        Slots are limited and assigned on a first-come, first-served basis - book yours using this form.

    • Keynote lecture

      16:30 - 17:15

      Session chairs: Abdullah Kahraman, David Gfeller 
      Room: Montreal

      Peer Bork (EMBL Heildelberg, Germany)

  • Wednesday 10 September

    • Parallel session 3

      09:00 - 10:30

      • Session chairs: Anne-Florence Bitbol and Anna-Sapfo Malaspinas
        Room: Singapore

        • 09:00 - 09:30  INVITED SPEAKER

          Molecular natural history – an interdisciplinary prism into the past
          Eline Lorenzen (University of Copenhagen, Denmark)

        • 09:30 - 10:15  SELECTED TALKS (3 x 15')

          RECOPHY: Detecting Genetic Recombination and its Population Structure among Prokaryotic Genomes
          Ludovico Calabrese (Biozentrum, University of Basel, Switzerland)

          Fate of duplicated genes through expression profiling and structural analysis
          Irene Consuelo Julca Chavez (University of Lausanne, Switzerland)

          Relative Lotka-Volterra: A Novel Approach for Modeling Microbiome Dynamics from Relative Abundance Data
          Tristan Gollmart (Max Planck Institute for Intelligent Systems, Germany)

        • 10:15 - 10:30  SELECTED POSTER PITCHES (3x5') 

          Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes 
          Marco Molari (Biozentrum, University of Basel, Switzerland)

          Phylogenetic and Recombination Analysis of Non-Polio Enteroviruses to Develop a Scalable Nomenclature System
          Nadia Neuner-Jehle (Swiss Tropical and Public Health Institute, Switzerland)

          Lightning-Fast Simulations on Large Fitness Landscapes
          Jacob Riina (University of Bern, Switzerland)

      • Session chairs: Marianna Rapsomaniki and Julien Roux
        Room: Montreal

        • 09:00 - 09:30 INVITED SPEAKER 

          Scalable computational tools for spatial omics data
          Stephanie Hicks (Johns Hopkins Bloomberg School of Public Health, USA)

        • 09:30 - 10:15  SELECTED TALKS (3x15')

          The Recurrent Tissue States Across Adult Gliomas as Revealed by Spatial Transcriptomics
          Anna Mathioudaki (German Cancer Research Centre DKFZ, Germany)

          A call for reproducibility and systematic benchmarking in single cell perturbation tools
          Jean Radig (Heidelberg University, Germany)

          Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering
          Jieran Sun (Centre hospitalier universitaire vaudois (CHUV), Switzerland,)

        • 10:15 - 10:30  POSTER PITCHES (3x15')

          Perturbation screens reveal a spectrum of cell type-specific signal transduction response in human organoids
          Nadezhda Azbukina (ETH Zurich, Switzerland)

          Comparative single-cell transcriptomics in dozens of species
          Frederic Bastian (SIB Swiss Institute of Bioinformatics, Switzerland)

          Transcriptional regulation of cell fate plasticity in hematopoiesis
          Aryan Kamal (University of Basel, Switzerland)

    • Coffee break

      10:30 - 11:00

    • [BC]2 Highlights - Top abstracts across all scientific themes

      11:00 - 12:30

      Session chairs: Katja Bärenfaller, Abdullah Kahraman
      Room: Montreal

      The [BC]² Highlight session features top-ranked abstracts selected from across the six scientific themes of the conference. Talks are chosen for their scientific excellence, broad relevance, and clarity—showcasing impactful research that is accessible to a wide audience beyond specialized fields.

      • 11:00 – 11:15      
        Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation
        Francesco Craighero (EPFL, Switzerland)

      • 11:15 - 11:30
        Cracking the animal venom code using phylogenetic big data
        Athina Gavriilidou (University of Lausanne, Switzerland)

      • 11:30 - 11:45
        Spatial lipidomics-transcriptomics integration reveals multi-omics cell states and spatial domains
        Sander Goossens (Delft University of Technology, Netherlands)

      • 11:45 - 12:00
        Integrative spatial analysis of human IDHm glioma reveals differentiation of cancer cell states at the invasive front
        Rouven Hoefflin (University of Freiburg, Germany)

      • 12:00 - 12:15
        From multiomic discovery to real-time rapid diagnostics: Pediatric sepsis and rare diseases at the children's hospital
        Dylan Lawless (University of Zürich, Switzerland)

      • 12:15 - 12:30
        Have protein-ligand co-folding methods moved beyond memorisation?
        Peter Skrinjar (University of Basel, Switzerland)

    • Lunch

      12:30 - 13:30

    • From academia to industry: launching your bioinformatics startup

      13:30 - 14:45

      Session chairs: Abdullah Kahraman, Elif Özkırımlı and Vincent Zoete
      Room: Montreal

      • 13:30 - 13:35 Session opening

      • 13:35 - 13:45: Business models
        Robert Van Kommer, Innovation mentor, Association Alliance (TBC)

      • 13:45 - 13:55: Intellectual property
        Kamran Houshang Pour, Swiss Federal Institute of Intellectual Property

      • 13:55 - 14:05: Legal & regulatory considerations
        Sevan Antreasyan, Lenz & Staehelin law firm

      • 14:05 - 14:15: Funding opportunities
        Markus Ehrat, Innosuisse

      • 14:15 - 14:35: Start-up case studies

      • 14:35 - 14:45: Q&A

    • Poster session 2 and Bier&Bretz'n

      14:45 - 16:00

      Browse our Poster Gallery to see who will present and get in touch with your fellow scientists to discuss your and their latest research projects in front of the poster.

      • Take the opportunity to meet with a member of SIB’s People and Culture team for personalized career guidance! Whether you are looking for feedback on your CV or cover letter, preparing for interviews, or wondering how to best present your academic background, our HR professionals, and the Director of an SIB group will be available to help you.

        When?
        - Tuesday 9 September, from 15:15 to 16:30
        - Wednesday 10 September, from 14:45 to 16:00

        You may upload your CV and/or cover letter in advance to help us provide more targeted feedback or send it to peopleandculture@sib.swiss.

        Slots are limited and assigned on a first-come, first-served basis - book yours using this form.

    • Keynote lecture

      16:00 - 16:45

      Session chairs: Katja Bärenfaller and Catherine Jutzeler
      Room: Montreal

      • Affinity maturation: Against the odds
        Julia Merkenschlager (Harvard Medical School, USA)

    • Poster & bingo prizes | Closing words

      16:45 - 17:00
      • 16:45 - 16:55
        Poster & Bingo prizes 
        Catherine Jutzeler

      • 16:55 - 17:00
        Closing words
        Christophe Dessimoz, Executive Director of SIB