ArticleNature communications2021
A computer-guided design tool to increase the efficiency of cellular conversions.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 37 citations in OpenAlex.
- Derivation of elephant induced pluripotent stem cells.Nature methods · 2026Article
- Protocol for identifying cellular reprogramming minimal networks using combinatorial transcription factor screening.STAR protocols · 2026Article
- Computational blueprints for cell fate programming.Stem cell reports · 2026Review
- Directing stem cell differentiation by chromatin state approximation.Nucleic acids research · 2026Article
- Navigating the landscape of direct cellular reprogramming with DiReG.NPJ systems biology and applications · 2026Article
- Computational methods for biofabrication in tissue engineering and regenerative medicine - a literature review.Computational and structural biotechnology journal · 2024Review
- Epigenome editing technologies for discovery and medicine.Nature biotechnology · 2024Review
- Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes.Nature communications · 2024Article
- DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion.Bioinformatics (Oxford, England) · 2024Article
- Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON.Nature communications · 2023Article
- Programming human cell fate: overcoming challenges and unlocking potential through technological breakthroughs.Development (Cambridge, England) · 2023Article
- Mechanisms and biotechnological applications of transcription factors.Synthetic and systems biotechnology · 2023Review
- Article
- An Optogenetic-Controlled Cell Reprogramming System for Driving Cell Fate and Light-Responsive Chimeric Mice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Human Blood Serum Inhibits Ductal Carcinoma Cells BT474 Growth and Modulates Effect of HER2 Inhibition.Biomedicines · 2022Article
- Narrative engineering of the liver.Current opinion in genetics & development · 2022Review
- Ranking reprogramming factors for cell differentiation.Nature methods · 2022Article
- NETISCE: a network-based tool for cell fate reprogramming.NPJ systems biology and applications · 2022Article
- Benchmarking of ATAC Sequencing Data From BGI's Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions.Frontiers in molecular biosciences · 2022Article
- An integrated pipeline for mammalian genetic screening.Cell reports methods · 2021Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human cell conversion technology has become an important tool for devising new cell transplantation therapies, generating disease models and testing gene therapies. However, while transcription factor over-expression-based methods have shown great promise in generating cell types in vitro, they often endure low conversion efficiency. In this context, great effort has been devoted to increasing the efficiency of current protocols and the development of computational approaches can be of great help in this endeavor. Here we introduce a computer-guided design tool that combines a computational framework for prioritizing more efficient combinations of instructive factors (IFs) of cellular conversions, called IRENE, with a transposon-based genomic integration system for efficient delivery. Particularly, IRENE relies on a stochastic gene regulatory network model that systematically prioritizes more efficient IFs by maximizing the agreement of the transcriptional and epigenetic landscapes between the converted and target cells. Our predictions substantially increased the efficiency of two established iPSC-differentiation protocols (natural killer cells and melanocytes) and established the first protocol for iPSC-derived mammary epithelial cells with high efficiency.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.