Conference agenda

  • 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.

    • Registration for the conference

      16:00 - 17:00

    • Conference opening

      17:00 - 18:15

      Session chairs: David Gfeller and ??
      Room: Montreal

      • 17:00 – 17:15        
        Welcome words

      • 17:15 - 18:15  KEYNOTE SPEAKER
        Title
        Serena Nik-Zainal (University of Cambridge, UK) 

    • [BC]2 Welcome apéro & dinner

      18:45 - 22:30

      The welcome dinner will take place at bambusnest, where we will be honoured to have [keynote] delivering an official speech.

  • Tuesday 9 September

    • Registration

      08:00 - 08:30

    • Parallel session 1

      08:30 - 10:00

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

        • 09:15 - 09:45  INVITED SPEAKER 

          Comparative analysis of spatially resolved transcriptomics data
          Aurélie Cobat (Institut Imagine | INSERM, France)

        • 09:45- 10:30  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)

        • 10:30 - 10:45  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

        • 09:15 - 09:45  INVITED SPEAKER 
          Title TBD
          Itay Tirosh (Weizmann Institute of Science, Israel)

        • 09:45 -10:30   SELECTED TALKS  (3x15')

          Title
          Firstname Name (Institution, Country)

          Title
          Firstname Name (Institution, Country)

          Title
          Firstname Name (Institution, Country)

        • 10:30 - 10:45  SELECTED POSTER PITCHES (3x5')

          Title
          Firstname Name (Institution, Country)

          Title
          Firstname Name (Institution, Country)

          Title
          Firstname Name (Institution, Country)

    • Coffee break

      10:00 - 10:30

    • SIB Bioinformatics Awards and Remarkable Outputs recognition

      10:30 - 12:00

      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.   

      • 10:30 – 10:50        
        PhD Paper Award
        Announcement of awardee and presentation of paper
           
      • 10:50 – 11:10      
        Early Career Award
        Announcement of awardee and presentation of research
           
      • 11:10 – 11:30        
        Innovative Resource Award
        Announcement of awardee and presentation of resource

      • 11:30 - 12:00
        SIB Remarkable Outputs
        Shot presentation of each output

    • Lunch

      12:00 - 13:30
        • 13:30 - 14:00
          Exclusively tailored for students, this informal session presents a rare opportunity to engage with renowned keynote speaker, Elisabeth Bik. Limited spots will be allocated through a lucky draw; selected students will receive a special card during registration. Seize this unique chance to interact, exchange ideas, and gain insights in a relaxed lunchtime atmosphere.

      • The company Novigenix will hold a presentation at the 'Boost your career' corner, from 13:30 until 14:00.

    • Spotlight on scientific innovations & research advancements in industry

      12:45 - 13:15

      Discover how to transform an academic project into a successful start-up. Experts and entrepreneurs will share their experiences on key aspects such as intellectual property management, business models, legal considerations, and securing funding. This session features key stakeholders from intellectual property offices, incubators, funding agencies, and successful bioinformatics start-ups, providing practical guidance and real-world case studies.

      Presenters: 

      • Riccardo Dainese, CEO and Co-Founder, Alithea Genomics
      • Daniel von der Mühll, Executive director, PHRT

    • Parallel session 2

      13:30 - 15:00

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

        • 14:00 - 14:30  INVITED SPEAKER

          Title TBD
          Elodie Laine (Sorbonne Université, France)

        • 14:30 - 15:15  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)


        • 15:15 - 15:30  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

        • 14:00 - 14:30  INVITED SPEAKER 

          Title TBC
          Päivi Östling (Karolinska Institute, SciLifeLab, Sweden)

        • 14:30 - 15:15  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)

        • 15:15 - 15:30  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

      15:00 - 16:30

      Browse our Poster Gallery to see who will present – on-site and virtually – and get in touch with your fellow scientists to discuss your and their latest research projects in front of the poster. Download list of posters

    • Keynote lecture (16:30 - 17:15)

      16:30 - 17:15

      Session chairs: 
      Room: Montreal

      Peer Bork (EMBL Heildelberg, Germany)

  • Wednesday 10 September

    • Parallel session 3

      08:30 - 10:00

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

        • 08:30 - 09:00  INVITED SPEAKER

          Title TBC
          Eline Lorenzen (University of Copenhagen, Denmark)

        • 09:00 - 09:45  SELECTED TALKS (3 x 15')

          Title
          Firstname Name (Affiliation, Country)

          Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes
          Julien Racle (University of Lausanne, CH)

          Title
          Firstname Name (Affiliation, Country)

        • 09:45 - 10:00  SELECTED POSTER PITCHES (3x5') 

          Title
          Firstname Name (Affiliation, Country)

          GeneSelectR: A Machine Learning-Based R Package for Enhanced Feature Selection and Biological Assessment in RNAseq Analysis of Complex Biological Datasets
          Damir Zhakparov (Swiss Institute of Allergy and Asthma Research, SIAF)

          Title
          Firstname Name (Affiliation, Country)

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

        • 08:30 - 09:00 INVITED SPEAKER 

          Title TBC
          Stephanie Hicks (Johns Hopkins Bloomberg School of Public Health, USA)

        • 09:00 - 09:45  SELECTED TALKS (3x15')

          Title
          Firstname Name (Affiliation, Country)

          Title
          Firstname Name (Affiliation, Country)

          Nanopore squiggle analysis for environmental monitoring
          Lara Urban (Helmholtz AI, DE)

        • 09:45 - 10:00  POSTER PITCHES (3x15')

          Title
          Firstname Name (Affiliation, Country)

          Title
          Firstname Name (Affiliation, Country)

          The Swiss Pathogen Surveillance Platform – a nation-wide One-health sequencing data platform
          Adrian Egli (University of Zurich, CH)



    • Coffee break

      10:00 - 10:30

    • [BC]2 Highlights

      10:30 - 12:00

      Session chairs: Katja Bärenfaller and ??
      Room: Montreal

      Title
      Name presenter (Institution, CH)

      Title
      Name presenter (Institution, CH)

      Title
      Name presenter (Institution, CH)

      Title
      Name presenter (Institution, CH)

      Title
      Name presenter (Institution, CH)

      Title
      Name presenter (Institution, CH)

    • Lunch

      12:00 - 13:30

    • From academia to industry: launching your bioinformatics startup

      13:00 - 14:15

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

      • 13:00 - 13:10 Clément Parisato, Legal & Technology transfer, SIB Swiss Institute of Bioinformatics 
         Ensuring successful Academic-Industry Partnerships through balanced contractual frameworks
        + 5' Q&A

      • 13:15 - 13:25 Thomas Martignier, Innosuisse
        Moving the world with Swiss innovation
        + 5' Q&A

      • 13:30 - 13:40 Oliver Hartley, University of Geneva
        CTI/Innosuisse support for protein and peptide innovation: views from either side of the academia/industry divide
        + 5' Q&A

      • 13:45 - 13:55 David Dylus, Roche
        The Immunology Incubator: A close collaboration with academic experts that benefits academia and industry
        + 5' Q&A

      • 14:00 - 14:10 Natasha Glover, SIB Swiss Institute of Bioinformatics
        Pioneering Partnerships: Insights and Best Practices from Academic-Industry Collaborations in Crop Science
        + 5'  Q&A


    • Poster session 2 and Bier&Bretz'n

      14:15 - 15:45

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

      Download list of posters


    • Closing session

      15:45 - 17:00

      Session chairs: Katja Bärenfaller and David Gfeller
      Room: Montreal

      • 15:45 – 16:45  KEYNOTE SPEAKER 
        title
        Julia Merkenschlager (Harvard Medical School, USA)

      • 16:45 - 16:50  
        Artwork prize
        Presented by xxxxx, poste,company

      • 16:50 - 17:00
        Poster prizes

      • 17:00 - 17:10
        Closing words
        Christophe Dessimoz, Executive Director of SIB