Location: at Biozentrum, Basel.
Conference agenda
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Monday 11 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 (Plenary session)
17:00 - 18:15Session 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)
- 17:00 – 17:15
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[BC]2 Welcome apéro & dinner
18:45 - 22:30The 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.
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Tuesday 12 September
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Registration
08:30 - 09:15 -
Parallel session 1
09:15 - 10:45-
Track A: Machine Learning algorithms for advancing spatial biology
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)
- 09:15 - 09:45 INVITED SPEAKER
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Track B: Precision medicine: harnessing big data for cancer and other complex diseases
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)
- 09:15 - 09:45 INVITED SPEAKER
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Coffee break
10:45 - 11:15 -
SIB Bioinformatics Awards Ceremony (Plenary session)
11:15 - 12:30Session 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
- 11:15 – 11:40
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Lunch
12:30 - 14:00-
Informal session with Elisabeth Bik (for students only)
- 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.
- 13:30 - 14:00
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'Charting the Future: AI in Precision Medicine and Career Opportunities' by Novigenix
The company Novigenix will hold a presentation at the 'Boost your career' corner, from 13:30 until 14:00.
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Parallel session 2
14:00 - 15:30-
Track A: Proteins in 3D: the dynamics of protein structures and their interactions
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)
- 14:00 - 14:30 INVITED SPEAKER
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Track B: Methods in single-cell data analysis: from pre-processing to biological inference
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)
- 14:00 - 14:30 INVITED SPEAKER
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Poster session 1 and coffee break
15:30 - 17:00Browse 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, SIBCV workshop (16:20 - 17:00)
Vanessa Monteiro, Sandra Reinders
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Wednesday 13 September
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Parallel session 3
08:30 - 10:00-
Track A: Dynamics of immune processes: from responses to pathogens to immunotherapy
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)
- 08:30 - 09:00 INVITED SPEAKER
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Track B: Deciphering ecology and evolution with creative genomics approaches
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)
- 08:30 - 09:00 INVITED SPEAKER
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Coffee break
10:00 - 10:30 -
[BC]2 Highlights (Plenary session)
10:30 - 12:00Session chairs: Katja Bärenfaller and Zoltán Kutalik
Room: MontrealDeep 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 - 14:15Session 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
- 13:00 - 13:10 Clément Parisato, Legal & Technology transfer, SIB Swiss Institute of Bioinformatics
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Poster session 2 and Bier&Bretz'n
14:15 - 15:45Browse 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
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Closing session (Plenary session)
15:45 - 17:00Session 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
- 15:45 – 16:45 KEYNOTE SPEAKER
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