A5045565587- Pluripotent Stem Cells Research
- 3D Printing in Biomedical Research
- Computational Physics and Python Applications
- CRISPR and Genetic Engineering
- Arctic and Russian Policy Studies
- Developmental Biology and Gene Regulation
- Data Analysis with R
- Gene Regulatory Network Analysis
- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Cell Image Analysis Techniques
- Cellular Mechanics and Interactions
- Simulation Techniques and Applications
- Neuroscience and Neural Engineering
- Cancer Cells and Metastasis
- Tissue Engineering and Regenerative Medicine
- Online Learning and Analytics
- Statistics Education and Methodologies
- Manufacturing Process and Optimization
- Single-cell and spatial transcriptomics
- Face and Expression Recognition
- Data Visualization and Analytics
- Teaching and Learning Programming
- Cruise Tourism Development and Management
- Food Industry and Aquatic Biology
University of Toronto
2013-2022
University of British Columbia
2019-2022
Canada's Michael Smith Genome Sciences Centre
2019
Occupational Cancer Research Centre
2019
Karolinska Institutet
2012
How position-dependent cell fate acquisition occurs during embryogenesis is a central question in developmental biology. To study this process, we developed defined, high-throughput assay to induce peri-gastrulation-associated patterning geometrically-confined human pluripotent stem (hPSC) colonies. We observed that, upon BMP4 treatment, phosphorylated SMAD1 (pSMAD1) activity the colonies organized into radial gradient. Reaction-Diffusion (RD) based computational model and that...
Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The mechanisms that maintain pluripotency, or cause its destabilization to initiate development, are complex incompletely understood. We have developed a model predict stabilized PSC gene regulatory network (GRN) states response input signals. Our strategy used random asynchronous Boolean simulations (R-ABS) simulate single-cell fate transitions strongly connected...
Abstract To accelerate the cardiac drug discovery pipeline, we set out to develop a platform that would be capable of quantifying tissue-level functions such as contractile force and amenable standard multiwell-plate manipulations. We report 96-well-based array 3D human pluripotent stem cell (hPSC)-derived microtissues - termed Cardiac MicroRings (CaMiRi) in custom 3D-print-molded multiwell plates measurement. Within each well, two elastomeric microcantilevers are situated above...
In vitro models of postimplantation human development are valuable to the fields regenerative medicine and developmental biology. Here, we report characterization a robust in platform that enabled high-content screening multiple pluripotent stem cell (hPSC) lines for their ability undergo peri-gastrulation–like fate patterning upon bone morphogenetic protein 4 (BMP4) treatment geometrically confined colonies observed significant heterogeneity differentiation propensities along gastrulation...
Abstract Low differentiation propensity towards a targeted lineage can significantly hamper the utility of individual human pluripotent stem cell (hPSC) lines in biomedical applications. Here, we use monolayer and micropatterned cultures, as well transcriptomic profiling, to investigate how variability signalling pathway activity between embryonic affects their efficiency definitive endoderm (DE). We show that endogenous suppression WNT hPSCs at onset prevents switch from self-renewal DE...
In the data science courses at University of British Columbia, we define as study, development and practice reproducible auditable processes to obtain insight from data. While reproducibility is core our definition, most learners enter field with other aspects in mind, for example predictive modelling, which often one interesting topic novices. This fact, along highly technical nature industry standard tools currently employed science, present out-of-the gate challenges teaching classroom....
A growing body of evidence highlights the importance cellular microenvironment as a regulator phenotypic and functional responses to perturbations. We have previously developed cell patterning techniques control population context parameters, here we demonstrate context-explorer (CE), software tool improve investigation fate acquisitions through community level analyses. capabilities CE in analysis human mouse pluripotent stem cells (hPSCs, mPSCs) patterned colonies defined geometries...
Johnston et al., (2019). A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching. Journal of Open Source Education, 2(16), 49, https://doi.org/10.21105/jose.00049
Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The process by which pluripotency is either maintained or destabilized to initiate developmental programs poorly understood. We have developed a model predict stabilized PSC gene regulatory network (GRN) states response combinations of input signals. While previous attempts fate been limited static cell compositions, our approach enables simulations dynamic...
ABSTRACT To accelerate the cardiac drug discovery pipeline, we set out to develop a platform that would be amenable standard multiwell-plate manipulations and capable of quantifying tissue-level functions such as contractile force. We report 96-well-based array 3D human pluripotent stem cell (hPSC)-derived microtissues - termed Cardiac MicroRings (CaMiRi) in custom printed multiwell plates force measurement. Within each well, two elastomeric microcantilevers are situated above ramp. The...
Abstract In vitro models of post-implantation human development are valuable to the fields regenerative medicine and developmental biology. Here, we report characterization a robust in platform that enabled high-content screening multiple pluripotent stem cell (hPSC) lines for their ability undergo peri-gastrulation-like fate patterning upon BMP4 treatment geometrically-confined colonies observed significant heterogeneity differentiation propensities along gastrulation associable...
Abstract A growing body of evidence highlights the importance cellular microenvironment as a regulator phenotypic and functional responses to perturbations. We have previously developed cell patterning techniques control population context parameters, here we demonstrate Context-explorer (CE), software tool improve investigation microenvironmental variables through colony level analyses. capabilities CE in analysis human mouse pluripotent stem cells (hPSCs, mPSCs) patterned colonies defined...