Location: at Biozentrum, Basel.


Conference agenda
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Monday 8 September
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Registration for the tutorial & workshops
08:15 - 09:00 -
Tutorials & workshops
09:00 - 16:15The tutorials and workshops take place at the Biozentrum in Basel.
Check out the full list.
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Registration for the conference
16:00 - 17:00 -
Conference opening
17:00 - 18:15Session chairs: David Gfeller
Room: Montreal- 17:00 – 17:15
Welcome words
- 17:15 - 18:15 KEYNOTE SPEAKER
Title TBC
Serena Nik-Zainal (University of Cambridge, UK)
- 17:00 – 17:15
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[BC]2 Welcome apéro & dinner
18:45 - 22:30The welcome dinner will take place at bambusnest, where we will be honoured by an official speech from a representative of the Canton of Basel.
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Tuesday 9 September
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Registration
08:00 - 08:30 -
Parallel session 1
08:30 - 10:00-
Track A: Bioinformatics in infectious diseases: Tackling Challenges from Hosts to Pathogen
Session chairs: Emma Hodcroft and Jacques Fellay
Room: Singapore- 09:15 - 09:45 INVITED SPEAKER
Title TBD
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)
- 09:15 - 09:45 INVITED SPEAKER
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Track B: Bioinformatics for cancer research
Session chairs: Valentina Boeva and Santiago Carmona
Room: Montreal- 09:15 - 09:45 INVITED SPEAKER
Dissecting intra-tumor heterogeneity by single cell and spatial transcriptomics
Itay Tirosh (Weizmann Institute of Science, Israel) - 09:45 -10:30 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)
- 10:30 - 10:45 SELECTED POSTER PITCHES (3x5')
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)
Biostatistical approaches to single-cell perturbation screens to create a prospective map of mutational impact
Magdalena Strauss (University of Exeter, United Kingdom)
- 09:15 - 09:45 INVITED SPEAKER
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Coffee break
10:00 - 10:30 -
SIB Bioinformatics Awards and Remarkable Outputs recognition
10:30 - 12:00Session chair: Luciano Cascione
Room: MontrealTo 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
- 10:30 – 10:50
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Lunch
12:00 - 13:30 -
Spotlight on scientific innovations & research advancements in industry
12:45 - 13:15Discover 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
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Parallel session 2
13:30 - 15:00-
Track A: Protein design and modeling molecular assemblies: breakthroughs and applications in computational structural biology
Session chairs: Marianna Rapsomaniki and Julien Roux
Room: Singapore- 14:00 - 14:30 INVITED SPEAKER
Learning compact representations of protein motions
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)
- 14:00 - 14:30 INVITED SPEAKER
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Track B: Clinical data science: advancements in diagnostics and patient care
Session chairs: Valérie Barbié and Laura Azzimonti
Room: Montreal- 14:00 - 14:30 INVITED SPEAKER
Technology and Data-driven precision medicine – a research and infrastructure perspective
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)
- 14:00 - 14:30 INVITED SPEAKER
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Poster session 1 and coffee break
15:00 - 16:30Browse 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.
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Keynote lecture (16:30 - 17:15)
16:30 - 17:15Session chairs:
Room: MontrealPeer Bork (EMBL Heildelberg, Germany)
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Wednesday 10 September
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Parallel session 3
08:30 - 10:00-
Track A: Integrative Bioinformatics for Evolutionary and Environmental Processes
Session chairs: Anne-Florence Bitbol and Anna-Sapfo Malaspinas
Room: Singapore- 08:30 - 09:00 INVITED SPEAKER
Molecular natural history – an interdisciplinary prism into the past
Eline Lorenzen (University of Copenhagen, Denmark) - 09:00 - 09:45 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) - 09:45 - 10:00 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)
- 08:30 - 09:00 INVITED SPEAKER
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Track B: Computational methods for single-cell and spatial omics: from data to biological insights
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')
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)
Consensus among spatially-aware clustering methods: a non-benchmark
Jieran Sun (Biomedical Data Science Center, Switzerland)
- 09:45 - 10:00 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)
- 08:30 - 09:00 INVITED SPEAKER
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Coffee break
10:00 - 10:30 -
[BC]2 Highlights
10:30 - 12:00Session chairs: Katja Bärenfaller
Room: MontrealCracking the animal venom code using phylogenetic big data
Athina Gavriilidou (University of Lausanne, Switzerland)Spatial lipidomics-transcriptomics integration reveals multi-omics cell states and spatial domains
Sander Goossens (Delft University of Technology, Netherlands)Integrative spatial analysis of human IDHm glioma reveals differentiation of cancer cell states at the invasive front
Rouven Hoefflin (University of Freiburg, Germany)From multiomic discovery to real-time rapid diagnostics: Pediatric sepsis and rare diseases at the children's hospital
Dylan Lawless (University of Zürich, Switzerland)
Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation
Mohan Vamsi Nallapareddy (EPFL, Switzerland)Have protein-ligand co-folding methods moved beyond memorisation?
Peter Skrinjar (University of Basel, Switzerland) -
Lunch
12:00 - 13:30 -
From academia to industry: launching your bioinformatics startup
13:00 - 14:15Session chairs: Abdullah Kahraman, Elif Özkırımlı and Vincent Zoete
Room: Montreal- 13:00-13:05 Session opening
- 13:05-13:15: Intellectual property
Kamran Houshang Pour, Swiss Federal Institute of Intellectual Property - 13:15-13:25: Business models
Speaker to be confirmed - 13:25-13:35: Legal & regulatory considerations
Speaker to be confirmed - 13:35-13:45: Funding opportunities
Markus Ehrat, Innosuisse 13:45-14:05: Start-up case studies
14:05-14:15: Q&A
- 13:00-13:05 Session opening
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Poster session 2 and Bier&Bretz'n
14:15 - 15:45Browse 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.
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Closing session
15:45 - 17:00Session chairs: Catherine Jutzeler and Abdullah Kahraman
Room: Montreal- 15:45 – 16:45 KEYNOTE SPEAKER
title TBC
Julia Merkenschlager (Harvard Medical School, USA)
- 16:50 - 17:00
Poster prizes - 17:00 - 17:10
Closing words
Christophe Dessimoz, Executive Director of SIB
- 15:45 – 16:45 KEYNOTE SPEAKER
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