ArticleStem cells translational medicine2021
TransSynW: A single-cell RNA-sequencing based web application to guide cell conversion experiments.
Article in Stem cells translational medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Computational blueprints for cell fate programming.Stem cell reports · 2026Review
- High-throughput proteomic profiling reveals dysregulated serum proteins in low fertility bulls linked to nutrient-autophagy-inflammation-extracellular matrix axis.Veterinary research communications · 2025Article
- SinCMat: A single-cell-based method for predicting functional maturation transcription factors.Stem cell reports · 2024Article
- ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data.Genome biology · 2023Article
- A single cell-based computational platform to identify chemical compounds targeting desired sets of transcription factors for cellular conversion.Stem cell reports · 2023Article
- Probabilistic boolean networks predict transcription factor targets to induce transdifferentiation.iScience · 2022Article
- Narrative engineering of the liver.Current opinion in genetics & development · 2022Review
- TransSynW: A single-cell RNA-sequencing based web application to guide cell conversion experiments.Stem cells translational medicine · 2021Article
- NEUBOrg: Artificially Induced Pluripotent Stem Cell-Derived Brain Organoid to Model and Study Genetics of Alzheimer's Disease Progression.Frontiers in aging neuroscience · 2021Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Generation of desired cell types by cell conversion remains a challenge. In particular, derivation of novel cell subtypes identified by single-cell technologies will open up new strategies for cell therapies. The recent increase in the generation of single-cell RNA-sequencing (scRNA-seq) data and the concomitant increase in the interest expressed by researchers in generating a wide range of functional cells prompted us to develop a computational tool for tackling this challenge. Here we introduce a web application, TransSynW, which uses scRNA-seq data for predicting cell conversion transcription factors (TFs) for user-specified cell populations. TransSynW prioritizes pioneer factors among predicted conversion TFs to facilitate chromatin opening often required for cell conversion. In addition, it predicts marker genes for assessing the performance of cell conversion experiments. Furthermore, TransSynW does not require users' knowledge of computer programming and computational resources. We applied TransSynW to different levels of cell conversion specificity, which recapitulated known conversion TFs at each level. We foresee that TransSynW will be a valuable tool for guiding experimentalists to design novel protocols for cell conversion in stem cell research and regenerative medicine.
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Registered trials
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