Ascona Workshop: Spatial and temporal statistical modeling in molecular biology
8-13 September 2024 at Congressi Stefano Franscini on Monte Verità in Ascona, CH
Organizers: Niko Beerenwinkel (ETH), Valentina Boeva (ETH), Peter Bühlmann (ETH), Wolfgang Huber (EMBL)
Scope
Living systems operate in space and time, and recent developments in technologies, including spatial omics of tissues and organs, cell-scale structural biology, and planet-scale molecular sampling, are creating exciting new challenges for mathematical modeling, statistical inference and data science. This workshop has two main objectives:
- to bring together scientists close to data generation and scientists with advanced modeling and theoretical perspectives, and
- to explore conceptual and methodological analogies between different data types and spatiotemporal scales.
At the micrometer scale, it is now becoming possible to bridge from individual macromolecules to whole cells using light and electron microscopy and tomography, merging structural biology with cell biology; at the millimeter scale, we can image hundreds of biomolecules in tissues and organ(oid)s using multiplexed immunohistochemistry, fluorescence hybridization or spatially resolved mass spectrometry; at kilo- and megameter scale, systematic sampling of soil, sediment, (waste) water, air, or of model organisms characterizes species diversity, and molecular and genetic variation.
This progress in data acquisition creates novel elementary challenges including data size, exploration and visualization, calibration and harmonization. There are also new conceptual and theoretical challenges to develop suitable mathematical descriptions and models of the underlying biological systems. How can they optimally and practically be fit to the data? How can we use the results to understand the underlying dynamics of the biological systems? What are the important variables (“coarse graining”)? Can we use our models for prediction? How can such insights be used for interventions (e.g., maintenance of health, therapy against disease, bioengineering to improve crop yield, regulation to keep an ecosystem intact)?
These questions will be explored by an interdisciplinary group of speakers and participants.
Keynote Speakers
- Peer Bork, EMBL
- Maria Cristina Gambetta, Univ. of Lausanne
- Shila Ghazanfar, Univ. of Sydney
- Stephanie Hicks, Johns Hopkins University
- Dmitry Kobak, Univ. of Tübingen
- Anna Kreshuk, EMBL
- Andreas Moor, ETH
- Emma Schymanski, Univ. of Luxemburg
- Ewa Szczurek, Univ. of Warsaw
- Virginie Uhlmann, Univ. of Zürich
- Lara Urban, Technical University Munich / Helmholtz Center
How to participate
Pre-registration is now closed. Following pre-registration, abstracts will be selected by the program committee. Pre-registration is non-binding and at no cost. Successful applications will be invited to register by mid-May.
Dates
Deadline for pre-registration: 05 May 2024, 23:59 CEST
Notification and invitation to register: before 20 May 2024
Deadline for registration: 31 July 2024
Workshop: 8-13 September 2024 (Sunday evening till Friday noon)
Location
Congressi Stefano Franscini, Monte Verità, Ascona, Switzerland
For more information on how to get there, visit https://csf.ethz.ch/monte-verita/by-train.html.
We will provide you with additional travel information shortly.
Registration fees (not due until final registration)
Academia 300 CHF
Industry 900 CHF
Important: Accommodation and full board will be available at the conference venue, and will be charged directly to you. Usually, most but not all conference attendees use this option. The venue is in Ascona, a lively tourist town, and in walking distance to many additional accommodation options.
Contact
Preliminary Programm
| Sept 8 | 15:00 - 19:00 | Arrival and Check-in | |
|---|---|---|---|
| 18:00 - 19:00 | Welcome Drinks | ||
| 19:00 | Dinner | ||
| Sept 9 | 8:45 – 9.00 | Welcome | |
| 9:00 – 9:50 | Keynote talk: Shila Ghanzanfar | ||
| 9:50 - 10:15 | Contributed talk: Davide Risso | SpaceTrooper, an R package for the preprocessing and quality control of imaging-based spatial transcriptomics data | |
| 10:15 – 10:45 | Coffee break | ||
| 10:45 – 11:35 | Keynote talk: Andreas Moor | ||
| 11:35 - 12:00 | Contributed talk: Helena Crowell | Whole-transcriptome spatial molecular imaging of Tubullovillous adenomas: Towards new vistas on their emergence and progression to colorectal cancer | |
| 12:15 | Lunch | ||
| Unstructured time | |||
| 15:30 – 16:00 | Coffee and cake | ||
| 16:00 – 16:50 | Keynote talk: Stefanie Hicks | ||
| 17:00 – 19.00 | Poster session | ||
| 19:00 | Dinner | ||
| Sept 10 | 9:00 – 9:50 | Keynote talk: Lara Urban | |
| 9:50 – 10:15 | Contributed talk:
|
Statistical challenges in spatial transcriptomicss | |
| 10:15 – 10:45 | Coffee break | ||
| 10:45 – 11:35 | Keynote talk: Dmitry Kobak | ||
| 11:35 - 12:00 | Contributed talk: Constantin Ahlmann-Eltze | Analysis of multi-condition single-cell data with latent embedding multivariate regression | |
| 12:15 | Lunch | ||
| Unstructured time | |||
| 15:30 – 16:00 | Coffee and cake | ||
| 16:00 – 16:50 | Keynote talk: Ewa Szczurek | ||
| 17:00 – 19:00 | Poster session | ||
| 19:00 | Dinner | ||
| Sept 11 | 9:00 – 9:50 | Keynote talk: Peer Bork | |
| 9:50 – 10:15 | Contributed talk: Simon van Vliet | From molecules to communities: predicting the emergent properties of spatially structured microbial systems | |
| 10:15 –10:45 | Coffee break | ||
| 10:45 - 11:10 | Contributed talk: David Dreifuss | Estimating growth advantages of SARS-CoV-2 variants through Bayesian hierarchical modeling of wastewater sequencing data across space and time | |
| 11:10 – 11:35 | Contributed talk: Ben Raphael | Alignment and Integration of Spatial Transcriptomics Data | |
| 11:35 - 12:00 | Contributed talk: Mark Robinson | OPTASO: Optimal annotation of spatial omics data | |
| 12:15 | Lunch | ||
| 13:30 | Excursion | Hike in the Verzasca Valley | |
| 18:30 | Conference Dinner | Grotto Broggini restaurant | |
| Sept 12 | 9:00 – 9:50 | Keynote talk: Anna Kreshuk | |
| 9:50 - 10:15 | Contributed talk: Valeriya Rogovchenko | Clustering Spatial Transcriptomics Data with Dirichlet Process Mixture of Random Spanning Trees | |
| 10:15 – 10:45 | Coffee break | ||
| 10:45 – 11:35 | Keynote talk: Virginie Uhlmann | ||
| 11:35 - 12:00 | Contributed talk: MIng Yu | Spatial transcriptomics analysis of human colon adenomas reveals distinct features of precancer microenvironment associated with tumor progression | |
| 12:15 | Lunch | ||
| Unstructured time | |||
| 15:30 - 16:00 | Coffee and cake | ||
| 16:00 – 16:50 | Keynote talk: Maria Christina Gambetta | ||
| 16:50 – 17:15 | Contributed talk: Eloise Withnell | SpottedPy uncovers new environmental cues of epithelial-mesenchymal plasticity in cancer | |
| 19:00 | Dinner | ||
| Sept 13 | 9:00 – 9:50 | Keynote talk: Emma Schymanski | |
| 9:50 – 10:15 | Contributed talk: Shadi Shafighi | Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues | |
| 10:15 –10:45 | Coffee break | ||
| 10:45 - 11:10 | Contributed talk: Philipp Weiler | CellRank 2: Unified fate mapping in multiview single-cell data | |
| 11:10 – 11:35 | Contributed talk: Daniela Corbetta | Conformal inference for cell type prediction leveraging the cell ontology | |
| 11:35 - 12:00 | Contributed talk: Charlotte Bunne | Modeling Cellular Behavior in Space and Time using the Virtual Cell and Artificial Intelligence | |
| 12:15 | Lunch | ||
| Departure |
Sponsors
