Plant developmental biologist with a key interest in vascular tissues, cell division orientation and single cell omics at VIB/UGent 🇧🇪🇪🇺🌱
Happy to share our combined views on the opportunities and challenges in single-cell and spatial biology; collaborative work now out in @theplantcell.bsky.social : track.smtpsendmail.com/9032119/c?p=...
Decoding plants cell by cell: opportunities and challenges in single-cell and spatial biologySingle-cell and spatial biology techniques present new opportunities for plant research, but also come with methodological considerations, technical limitatrack.smtpsendmail.comBig congrats to Shunji @plant-circle10.bsky.social for obtaining an FWO junior post doc grant @psb-vib.bsky.social! Excited to have him in the team for a few more years studying procambium activation. Thanks to @fwovlaanderen.bsky.social for funding our research.
Not sure which scRNA-seq platform to use for 🪴 plant samples? How well do doublet detection algorithms really work in 🌱? How can I optimise sample prep ? Find out in our benchmark study! Led by @carogro.bsky.social and @thomaseekhout.bsky.social. Open access at EMBO Journal: doi.org/10.1038/s443...
Benchmarking plant single cell RNA-sequencing sample processing strategies - The EMBO JournalThe isolation of single plant cells from complex tissues is prone to selective enrichment and sampling biases, which complicates accurate profiling of the large diversity in cell types. Optimizing methodologies for cell enrichment and single-cell transcriptomics is therefore critical for single-cell studies addressing plant cell heterogeneity. Here, we systematically compared protoplast enrichment technologies (including conventional and image-based flow cytometry, as well as magnetic cell sorting) and single-cell RNA sequencing (scRNA-seq) platforms (10X Genomics Chromium, BD Rhapsody) using Arabidopsis roots. Image-based flow cytometry offered increased precision due to customizable gating strategies, while magnetic sorting provided faster processing and enhanced representation of cell size heterogeneity. Both scRNA-seq platforms captured root cell heterogeneity and yielded reproducible gene expression profiles, but showed platform-associated differences in cell type composition. Notably, single-nucleotide polymorphism analysis of a mixed ecotype sample revealed that, among cells identified as doublets by computational algorithms, two-thirds were likely to have been misclassified. These insights identify key biases in plant cell purification and scRNA-seq workflows and provide practical guidance for improving data quality across plant species.doi.orgFull house at @psb-vib.bsky.social for the seminar of @dolfweijers.bsky.social showcasing amazing unpublished results! An absolute pleasure to have him over again.
Happy to present our latest: Evolutionary adaptations to the hormonal regulation of vascular tissue development | PNAS www.pnas.org/doi/10.1073/.... Work by Wei Xiao and funded by @erc.europa.eu
PNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...www.pnas.orgInspiring visit and exciting talk by @likeyoda1.bsky.social today in @psb-vib.bsky.social. Impressive progress after starting her lab only 2 years ago!