Computational Stem Cell Biology

15 March, 31 March, and 12 April 2021

Groundbreaking advances in RNA- and DNA-sequencing and bioinformatic technologies have presented stem cell biologists with new insights into complex biological, developmental, and disease processes. It has also catalyzed a relatively new field of computational stem cell biology. This program focuses on the latest developments in this rapidly advancing field.


Part 1: Exploring Stem Cells with Single Cell and Combinatorial Analyses
15 March, 2021
02:00 EDT (view your time zone)

With the ability to perturb and molecularly characterise cells at the single-cell resolution comes a new ability to combinatorially explore cell fate at a completely different scale. We will discuss how the evolving single-cell tool-kit and the associated computational tools allow us to understand and control cell fate in new ways, from the emergence of previously uncovered cell-states to the high-throughput screening of transcriptional and genetic perturbations. The session will include presentations from experts in the field and an open discussion on future directions and opportunities. 

Part 1 Co-Organizers

Owen Rackham Square
Owen Rackham, PhD
Duke-NUS, Singapore
Jay Shin Square
Jay Shin, D. Sci.
RIKEN Center for Integrative Medical Sciences, Japan


Grace YeoSquare
Hui Ting (Grace) Yeo, PhD
Genome Institute of Singapore, Singapore
Sarah Pierce Square
Sarah Pierce, BS
Stanford University, USA
Jay Shin Square
Jay Shin, D. Sci.
RIKEN Center for Integrative Medical Sciences, Japan


Jose M. Polo, PhD
Monash University, Australia

Part 2: Reference Maps for Stem Cell Biology
31 March, 2021
02:30 EDT (view your time zone)

How closely do organoids resemble developing tissues? How comparable are organoids derived from different methods? There are a dizzying number of single cell profiling approaches, computational tools to classify cell types, and an ever-increasing number of 'reference' single cell atlases. Hear from Barbara Treutlein from the organoid cell atlas project, Melissa Little, who is using single cell technologies to benchmark kidney organoids, and statistician Shila Ghazanfar on key analytical considerations for those using reference cell maps. Join hosts Samantha Morris and Christine Wells on a discussion of cell classification challenges for computational and stem cell researchers using reference maps.

Part 2 Co-Organizers

Sam Morris Square
Samantha Morris, PhD
Washington University in St. Louis, USA
Christine Wells Square
Christine Wells, PhD
University of Melbourne, Australia


Melissa Little, PhD
GAI, Murdoch Childrens Research Institute, Australia
Barbara Treutlein Squarev2
Barbara Treutlein, PhD
ETH Zürich, Germany
Shila Ghazanfar Square
Shila Ghazanfar, PhD
Cancer Research UK Cambridge Institute, UK

Part 3: Computational Models in Stem Cells and Development
12 April, 2021
14:30 EDT (view your time zone)

The advent of big data in biology has created major bottlenecks in translating it into knowledge. Computational modeling can alleviate this problem by providing a platform to explore, in silico, mechanistic models that explain a set of observations and that yield specific, testable hypotheses. In this webinar, three speakers will guide us through different classes and applications of computational models ranging from intra-cellular regulatory networks to multi-scale cell-based models of stem cells.

Part 3 Co-Organizers

Patrick Cahan Square
Patrick Cahan, PhD
Johns Hopkins University, USA
Peter Zandstra Square
Peter Zandstra, PhD
The University of British Columbia


Sarah Dunn Square
Sara-Jane Dunn, DPhil
DeepMind, UK
Kaul Himanshu Squarev2
Himanshu Kaul, DPhil
University of Leicester, UK
Xiling Shen Square
Xiling Shen, PhD
Duke University, USA