• Monday 11 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 (Plenary session)

      17:00 - 18:15

      Session chairs: David Gfeller and Zoltán Kutalik
      Room: Montreal

      • 17:00 – 17:15        
        Welcome words

      • 17:15 - 18:15  KEYNOTE SPEAKER 
        Double Trouble: Inappropriate Image Duplications in Biomedical Publications
        Elisabeth Bik (Science Consultant, Harbers Bik LLC) 

    • [BC]2 Welcome apéro & dinner

      18:45 - 22:30

      The welcome dinner will take place at Werk8, where we will be honoured to have Kaspar Sutter (Head of the Department of Economic, Social and Environment Affairs of the Canton of Basel-Stadt) delivering an official speech.

  • Tuesday 12 September

    • Registration

      08:30 - 09:15
    • Parallel session 1

      09:15 - 10:45
      • Session chairs: Maria Brbic and Raphael Gottardo
        Room: Singapore

        • 09:15 - 09:45  INVITED SPEAKER 

          Comparative analysis of spatially resolved transcriptomics data
          Jean Fan (Department of Biomedical Engineering, Johns Hopkins University - JEFworks Lab, US)

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

          Multi-V-Stain: multiplexed virtual staining of histopathology images using deep learning
          Sonali Andani (ETH Zurich, CH)

          Modeling the tumor microenvironment with graph concept learning
          Santiago Castro Dau (IBM Research Zurich, CH)

          Mapping cells through time and space with moscot  
          Marius Lange (Department of Biosystems Science and Engineering, ETH Zurich, CH)

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

          Digital synthesis of multiplexed stains using unpaired image-to-image translation
          Adriano Luca Martinelli (IBM Research Laboratory Zurich, CH)

          Prediction of cellular neighbourhoods in 3D spatial transcriptomics data using graph neural networks
          Enes Senel (Max Delbrück Center for Molecular Medicine, DE)

          Topological encoding of relations in data from multiplex immunohistochemistry images
          Bernadette Stolz (EPFL, CH)

      • Session chairs: Charlotte Ng and Valentina Boeva 
        Room: Montreal

        • 09:15 - 09:45  INVITED SPEAKER 
          Multi-modal data integration for tumor biology and predictive models
          Sohrab Shah (Memorial Sloan Kettering Cancer Center, US)

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

          Adipose tissue signature in large-scale human obesity cohort
          Adhideb Ghosh (Functional Genomics Center Zurich, ETH Zurich, CH)

          Causes and consequences of telomere shortening: a mendelian randomisation study
          Samuel Moix (Department of Computational Biology, University of Lausanne, CH)

          Can mutations in the non-protein-coding “Dark Matter” of our genome drive tumorigenesis? Insights from 16,000 Genomics England tumours
          Sunandini Ramnarayanan (University College Dublin, IR)

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

          Computational approaches to deconvolve the tumor micro-environment using ATAC-Seq data.
          Aurélie Gabriel (Ludwig Institute for Cancer Research, University of Lausanne, CH)

          Decoding the collective impact of cancer genomic alterations
          Arvind Iyer (Department of Computational Biology, University of Lausanne, CH)

          Charting the hterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics
          Alberto Valdeolivas (Roche Pharma Research and Early Development, CH)

    • Coffee break

      10:45 - 11:15
    • SIB Bioinformatics Awards Ceremony (Plenary session)

      11:15 - 12:30

      Session chair: Robert Waterhouse
      Room: Montreal

      To promote excellence, diversity and innovation in the field of bioinformatics and computational biology, in 2008 SIB created the Bioinformatics Awards to acknowledge international early career bioinformaticians and ground-breaking resources of national or international standing.

      • 11:15 – 11:40        
        PhD Paper Award
        Announcement of awardee and presentation of paper
      • 11:40 – 12:05        
        Early Career Award
        Announcement of awardee and presentation of research
      • 12:05 – 12:30        
        Innovative Resource Award
        Announcement of awardee and presentation of resource
    • Lunch

      12:30 - 14:00
      • The company Novigenix will hold a presentation at the 'Boost your career' corner, from 13:30 until 14:00.

        • 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.

    • Parallel session 2

      14:00 - 15:30
      • Session chairs: Xavier Deupi and Torsten Schwede
        Room: Singapore

        • 14:00 - 14:30  INVITED SPEAKER

          Dynamic, global snapshots of the structural proteome to detect functional and pathological alterations
          Paola Picotti (Institute for Molecular Systems Biology, ETH Zurich, CH)

        • 14:30 - 15:15  SELECTED TALKS (3x15')

          Machine-learning based CVs and OneOPES: the right ingredients for a path-less sampling of protein conformational change?
          Simone Aureli (University of Geneva, CH)

          Covalent Protein-Ligand Docking with Attracting Cavities
          Mathilde Goullieux (SIB Swiss Institute of Bioinformatics, CH)

          DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks
          Felix Teufel (University of Copenhagen, DK)

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

          Challenging the current view on protein prenylation in T helper cells using experimental data and information on protein 3D structures
          Jana Koch (SIAF, University of Zurich,CH)

          AlphaFold-based discovery of novel protein interaction interfaces
          Chop Lee (Institute of Molecular Biology, DE)

          Automated benchmarking of protein-ligand complex prediction
          Xavier Robin (SIB Swiss Institute of Bioinformatics, CH)

      • Session chairs: Santiago Carmona and Marianna Rapsomaniki
        Room: Montreal

        • 14:00 - 14:30  INVITED SPEAKER 

          Deciphering intrinsic and extrinsic determinants of cell fate at single-cell resolution

          Dominic Grün, (Institute of Systems Immunology, University of Würzburg, DE)

        • 14:30 - 15:15  SELECTED TALKS (3x15')

          Semi-supervised integration of single-cell transcriptomics data with STACAS
          Massimo Andreatta (Ludwig Centre for Cancer Research, University of Lausanne, CH)

          scAbsolute: measuring single-cell ploidy and replication status
          Michael Schneider (University of Cambridge, UK)

          CanSig: discovery of shared transcriptional states across cancer patients from single-cell RNA sequencing data
          Florian Barkmann (ETH Zürich, CH)

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

          Metacells facilitate the analysis of single-cell multiomics data
          Léonard Hérault (Ludwig Institute for Cancer research, University of Lausanne, CH)

          A probabilistic framework for parametrizing RNA velocity fields with manifold-consistent cell cycle dynamics
          Alex Lederer (EPFL, CH)

          Generalizing fate mapping to multi-view single-cell data
          Philipp Weiler (Technical University Munich, DE)
    • Poster session 1 and coffee break

      15:30 - 17:00

      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

      On the 'Boost your career' corner, two events will take place: 

      How to prepare for the interview (16:00 - 16:20)
      Dala Egger, ‪Head of People & Culture, SIB

      CV workshop (16:20 - 17:00) 
      Vanessa Monteiro, Sandra Reinders 

  • Wednesday 13 September

    • Parallel session 3

      08:30 - 10:00
      • Session chairs: Marija Buljan and Adrian Egli
        Room: Montreal

        • 08:30 - 09:00  INVITED SPEAKER

          The power of ONE: Immunology in the age of spatial and single cell genomics
          Ido Amit (Department of Immunology at the Weizmann Institute, IL)

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

          A trans-ancestry genomics-based approach to the identification and interpretation of host immune response to sepsis
          Serghei Mangul (University of Southern California, US)

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

          Identification of HIV broadly neutralizing antibodies using a Deep Language Model
          Chiara Rodella (Institute of Biochemistry and Molecular Medicine, University of Bern, CH)

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

          Transcriptome-based classifier identifies tumor CD8 T cell immunophenotype and predicts clinical outcome
          Iakov Davydov (Roche Pharma Research and Early Development, CH)

          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)

          A multiomic single-cell landscape of intratumoral lung NK cells
          Clara Serger (Department of Biomedicine, University of Basel, CH)        
      • Session chairs: Claudia Bank and Roman Arguello 
        Room: Singapore

        • 08:30 - 09:00 INVITED SPEAKER 

          From so simple a molecule, endless forms most beautiful are monitored
          Kristy Deiner (Dep. of Environmental Systems Science, ETH Zurich, CH)

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

          Association study of genetic variation and spectroscopic imaging variants
          Cheng Li (University of Zurich, CH)

          Evolution of chemosensory tissues and cells across ecologically diverse Drosophila
          Bastien Saint-Leandre (Department of Ecology and Evolution, University of Lausanne, CH)

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

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

          The evolution of ant crop milk proteins over independent gains of a social transfer behavior
          Marie-Pierre Meurville (University of Fribourg, CH)

          Scoary2: Rapid association of phenotypic multi-omics data with microbial pan-genomes
          Thomas Roder (University of Bern, CH)

          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 (Plenary session)

      10:30 - 12:00

      Session chairs: Katja Bärenfaller and Zoltán Kutalik
      Room: Montreal

      Deep learning predictions of TCR specificity with TCRpred reveal functional chains in double-alpha T cells
      Giancarlo Croce (Ludwig Centre for Cancer Research, University of Lausanne, CH)

      Expansion of the landscape of small-molecule binding sites by AlphaFold2
      Jürgen Jänes (Institute of Molecular Systems Biology, ETH Zürich, CH)

      CARMEN: A pan-HLA and pan-cancer proteogenomic database on antigen presentation to support cancer immunotherapy
      Ashwin Adrian Kallor (International Center for Cancer Vaccine Science, University of Gdansk, PL)

      Modeling gene regulation using biophysics-informed deep learning on large-scale single-cell genomic data
      Nacho Molina (IGBMC, Institut de génétique, biologie moléculaire et cellulaire, FR)

      The Protein Universe Atlas
      Joana Maria Soares Pereira (Biozentrum, University of Basel, CH)

      CellCharter reveals spatial cell niches associated with tissue remodeling and oncogenic progression
      Marco Varrone (University of Lausanne, Department of Computational Biology, CH)

    • Lunch

      12:00 - 13:00
    • Industry-academia collaborations from scientific and contractual perspectives

      13:00 - 14:15

      Session chairs: Madiha Derouazi and Vincent Zoete
      Room: Montreal
      Zoom link

      • 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 (Plenary session)

      15:45 - 17:00

      Session chairs: Katja Bärenfaller and David Gfeller
      Room: Montreal

      • 15:45 – 16:45  KEYNOTE SPEAKER 
        Learning single-cell dynamics across time and space
        Fabian J. Theis (Helmholtz Munich)

      • 16:45 - 16:50  
        Artwork prize
        Presented by Katrin Arnold, Site Head Pharma R&D, Roche

      • 16:50 - 17:00
        Poster prizes

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

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