Spatial transcriptomics and cell-cell communication modeling: new opportunities to study the cellular dynamics of biological systems

Workshop details
  • Date: Tuesday, September 13th
  • Time: 17:00 to 20:00 CEST
  • Format: Virtual
  • Giacomo Baruzzo, Department of Information Engineering, University of Padova, Padova (Italy)
  • Enrica Calura, Department of Biology, University of Padova, Padova (Italy)
  • Davide Risso, Department of Statistical Sciences, University of Padova, Padova (Italy)
  • Chiara Romualdi, Department of Biology, University of Padova, Padova (Italy)
  • Gabriele Sales, Department of Biology, University of Padova, Padova (Italy)
  • Luz García-Alonso, Wellcome Sanger Institute, Cambridge (UK)
  • Roser Vento-Tormo, Wellcome Sanger Institute, Cambridge (UK)
  • Julio Saez-Rodriguez, Heidelberg University, Heidelberg (Germany)
  • Yvan Saeys, VIB, Ghent University, Ghent (Belgium)

In this workshop we will focus on the new opportunities to study the cellular dynamics of biological systems, aided by the advent of spatial transcriptomics and cell-cell communication modelling.

Spatial transcriptomics adds a new layer of knowledge providing, for the first time, transcriptomic measurements in 2D/3D to estimate the location of cells and characterise tissue structure. This offers new venues to model cell-cell communication and understand tissue functioning.

Together, these next-generation microscopes yield unprecedented opportunities to go beyond a mere description of cell types and states, allowing us to study the dynamics of the cells in a tissue and understand how tissues are spatially and temporally organized as a system of multiple interacting cells.


Advances in single-cell and spatial omics have drastically increased the resolution at which we can study biological systems.

Recently, spatial transcriptomics has emerged as a disruptive technological advancement in the field of gene expression measurements. Its ability to uncover dynamic responses at the cellular and subcellular levels offers an unprecedented perspective on the cellular location and organization of tissues. Since the identification of “spatially resolved transcriptomics” as “Method of the Year” in 2020 by Nature Methods, an increasing number of experimental protocols has been proposed differing in throughput, cost, resolution, and complexity.

While a number of methodological issues are still being debated, the advantages of spatial transcriptomics have already been highlighted by studies improving our knowledge of cellular dynamics of tissues, an important aspect of which is defined by how cells communicate with each other in space and time to establish tissue physiology.

To address this important aspect, the field of computational biology has witnessed a steep increase in the number of tools available to study cell-cell communication. This new field of computational models of cell-cell communication has been rapidly taken up by (computational) biologists, who recognized the power of these models to yield drastically new biological insights that could not have been previously gained at high throughput scale. Important applications of these models include, for example, uncovering the role of immune cells in different tissues and diseases, functional characterization of niche environments and the tumor microenvironment, identification of novel targets for therapeutic intervention (e.g. prioritizing surface receptors), or guiding in vitro differentiation by mimicking the niche environment (e.g. informing culturing conditions).

Together, spatial transcriptomics and cell-cell communication modelling provide a powerful framework to study the dynamics of biological systems and represent an unprecedented opportunity to understand how tissues are spatially and temporally organized as a system of multiple interacting cells.

This workshop aims to provide a view on recent development on both spatial transcriptomics and cell-cell communication modelling, as well as how to combine them, with a particular focus on:

  • Spatial information: technologies and data integration (e.g. co-registration of spatially-resolved transcriptomics and imaging, deconvolution of cell mixtures for multi-cell pixel-resolution data)
  • Spatially enabled bioinformatics analyses: tools and resources to unveil cellular dynamics in biological systems (e.g. BioConductor environment, platforms to store, share and annotate spatial data, signaling databases, spatially resolved cell-to-cell communication, combining transcriptomic profiling and morphology to infer cell types, alignment of spatial features over multiple samples)
  • Cellular communication bioinformatics: from cell-cell communication models to spatially-enhanced analyses (e.g. intercellular and intracellular signaling databases, paracrine/endocrine/physics-based models for cell-cell communication modeling, temporal and/or spatial aspects of cell-cell communication, multi-omics data integration approaches for cell-cell communication models, visualization of cellular communication analysis results)
  • Assessment and benchmarking of computational method to infer cell-cell communication (e.g. developing of benchmarking framework, ensemble approaches, novel biological assays and experimental validation of cell-cell communication models)
  • Biological, medical, and environmental applications and case studies

The final goal is to stimulate novel developments in the field, raise awareness about these technologies/methods, and inform researchers about the high potential of using them in their studies.

Target Audience

Researchers and students in the field of molecular biology, developmental biology, cancer biology, medicine, biotechnology, computational biology and bioinformatics.

The target audience is kept broad to stimulate discussion between researchers with different backgrounds.

First, we aim to target researchers who are working on developing novel approaches in the broad area of spatial transcriptomics and cell-cell communication modeling. For them, we would like the workshop to be a forum to discuss novel ideas and approaches, thinking on how to shape and improve the field towards the future.

Second, we aim to target researchers who are not experts on the topics, but who are rather interested in seeing what currently exists in terms of methods and opportunities, thus fulfilling a more educational objective to inform them on what is currently possible.

The workshop will provide the necessary background on both spatial transcriptomics and cell-cell communication, so no specific knowledge on these topics will be required.

Call for abstracts

The workshop will include talks from call for submissions. Please submit your one page abstract (11 pt, pdf file) before August 7, 2022 using the following EasyChair link: https://easychair.org/conferences/?conf=ntbw04eccb2022

17:00 – 18:00Spatial transcriptomics – invited talks
Elisabetta Mereu, Josep Carreras Research Institute
Lukas Weber, Johns Hopkins Bloomberg School of Public Health
Giovanni Palla, Helmholtz Zentrum München
18:00 – 18:15“Young women in single cell” (invited talk)
Helena Crowell, University of Zurich
18:15 – 18:30Talks from call for submissions
Eva Viesi, University of Verona
Giulia Cesaro, University of Padova
18:30 – 19:30Cell-cell communication – invited talks
Robin Browaeys, Ghent University
Luz Garcia-Alonso / Kevin Troule, Wellcome Sanger Institute
Daniel Dimitrov, Heidelberg University
19:30 – 19:45Talks from call for submissions
Alice Chiodi, Institute of biomedical Technologies, National Research Council (Italy)
James Shiniti Nagai, RWTH University Hospital
19:45 – 20:00Q&A, discussion, and final remarks talk