A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity
de Jong et al. 2025
CV
Education
- PhD in Biological Sciences, University of Cambridge, 2025
- MSc in Genome Science and Technology, University of British Columbia, 2019
- BSc (Honours) in Genome Biology and Evolutionary Biology, University of Toronto, 2015
Work experience
- 2026: Bioinformatician, Sanger Institute
- Developed workflows for the integration and analysis of subcellular spatial transcriptomics data
- Assisted with collaborator analyses, focusing on multimodal data integration and analysis of spatial tran- scriptomics data
- 2021–2025: Postgraduate researcher, Sanger Institute
- Led data analysis for the GBMspace project using the latest computational methods for integrative analysis of single nucleus multiome sequencing, spatial transcriptomics, and spatial genomics data (see Publica- tions)
- Assisted with experimental design, including LCM sampling strategies for spatial genomics data generation
- Assisted with data quality control during data generation phase of GBMspace
- Assisted collaborators with subsequent analyses and in a consultatory context for biological interpretation of data
- 2020-2021: Bioinformatician at Canexia Health
- Helped develop a plasma-based oncogenomic panel targeting low-VAF mutations from cfDNA
- Assisted with longitudinal cancer studies
- Optimized FFPE-based cancer screen
- 2016-2019: Graduate Researcher (Adams Lab)
- Generated lab pipelines forthe analysis of duplicate gene expression
- Developed a pipeline forthe detection and quantitative comparison of alternative splicing events
- Supervised an undergraduate research project with the goal of familiarizing the student with HPC best practices using Compute Canada resources
- Performed the role of lab server administrator
- Completed two projects pertaining to evolutionary plant transcriptomics (see below for more detail)
Skills
- Programming
- Python, R, Bash, NextFlow
- Omics expertise
- Spatial transcriptomics (Visium, Xenium), conventional transcriptomics (single cell RNA-seq, bulk RNA-seq), genomics (single cell DNA-seq, bulk WGS), ATAC (multiome-derived single cell ATAC-seq)
- Common analysis pipelines
- Atlas-level single cell data integration (e.g. scvi-tools), cell type deconvolution of spatial transcriptomics data, atlas-level label transfer or ”surgery” pipelines, RNA velocity inference, WGS variant detection, cell-cell communication inference.
- Machine learning
- PyTorch-based probabilistic models (e.g. scvi-tools), scikit-learn models (e.g. for classification, clustering, dimensionality reduction, matrix decomposition (NMF), parameter optimisation).
- Technical
- HPC best practices, Pipeline development, Git and GitHub, Microsoft Azure, AWS, Server administration
- Molecular Biology
- Sequencing library preparation, RNA/DNA extractions, RT-PCR, basic protein identification (e.g.GC-MS)
Publications
Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics
Saraswat et al. 2025
Talks
A multi-modal spatiotemporal map of glioblastoma heterogeneity
Talk at 16th International Conference on Genomics and Systems Biology of Human Disease and Aging, Sisi, Greece
A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity
Talk at Wellcome Genome Campus, Omics approach to Engineering Biology, Wellcome Genome Campus, UK
Recurrent spatial tissue microenvironments in GBM
Talk at Campus Biotech, delta Tissue, Geneva, Switzerland
Exploring the cellular circuits of glioblastoma.
Talk at University of California San Diego, delta Tissue, San Diego, California, USA
Transcriptomic response of multiple Brassica species to Sclerotinia sclerotiorum infection
Talk at University of Guelph, Plant Canada Conference, Guelph, ON, Canada
Evolution of paralog gene expression patterns among paleopolyploid and cytogenetically polyploid plants
Exit seminar at University of British Columbia, Department of Botany, Vancouver BC, Canada
A survey of ancient paralog alternative splicing patterns in Arabidopsis thaliana root cell-types
Lightning talk at University of British Columbia, Department of Botany, Vancouver BC, Canada
Introduction to RNA-Seq informatics
Tutorial at University of British Columbia, BIOL430, Vancouver, British Columbia