Conference agenda

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)
  
  

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.
  
  

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)

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)