ArticleScientific reports2019
Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 47 citations in OpenAlex.
- CRISPR for cystic fibrosis: Advances and insights from a systematic review.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Pooled it
- OmniEdit: A unified CRISPR/Cas9 platform for precise genome engineering and strain optimization of theSynthetic and systems biotechnology · 2026Article
- From Design to Single-Cell Cloning: A Complete RNP-Based CRISPR-Cas9 Protocol for Precision Gene Correction in Human iPSCs.Stem cell reviews and reports · 2026Article
- High-throughput DNA engineering by mating bacteria.Cell systems · 2026Article
- High-efficiency homology-directed insertion into the genome using the engineered homing endonuclease ARCUS.Nucleic acids research · 2025Article
- Prime editing outperforms homology-directed repair as a tool for CRISPR-mediated variant knock-in in zebrafish.Lab animal · 2025Article
- Efficient in vivo labeling of endogenous proteins with SMART delineates retina cellular and synaptic organization.Nature communications · 2025Article
- Beyond a few bases: methods for large DNA insertion and gene targeting in plants.The Plant journal : for cell and molecular biology · 2025Review
- protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in.Nucleic acids research · 2024Article
- Immunity against Moraxella catarrhalis requires guanylate-binding proteins and caspase-11-NLRP3 inflammasomes.The EMBO journal · 2023Article
- New advances in CRISPR/Cas-mediated precise gene-editing techniques.Disease models & mechanisms · 2023Review
- Review
- In search of an ideal template for therapeutic genome editing: A review of current developments for structure optimization.Frontiers in genome editing · 2023Review
- PrimedSherlock: a tool for rapid design of highly specific CRISPR-Cas12 crRNAs.BMC bioinformatics · 2022Article
- Pathogen-selective killing by guanylate-binding proteins as a molecular mechanism leading to inflammasome signaling.Nature communications · 2022Article
- Ligation-assisted homologous recombination enables precise genome editing by deploying both MMEJ and HDR.Nucleic acids research · 2022Article
- CRISPR genome surgery in a novel humanized model for autosomal dominant retinitis pigmentosa.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Interferon-γ primes macrophages for pathogen ligand-induced killing via a caspase-8 and mitochondrial cell death pathway.Immunity · 2022Article
- Challenges of CRISPR-Based Gene Editing in Primary T Cells.International journal of molecular sciences · 2022Review
- Optimizing CRISPR/Cas9 Editing of Repetitive Single Nucleotide Variants.Frontiers in genome editing · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Editing individual nucleotides is a crucial component for validating genomic disease association. It is currently hampered by CRISPR-Cas-mediated "base editing" being limited to certain nucleotide changes, and only achievable within a small window around CRISPR-Cas target sites. The more versatile alternative, HDR (homology directed repair), has a 3-fold lower efficiency with known optimization factors being largely immutable in experiments. Here, we investigated the variable efficiency-governing factors on a novel mouse dataset using machine learning. We found the sequence composition of the single-stranded oligodeoxynucleotide (ssODN), i.e. the repair template, to be a governing factor. Furthermore, different regions of the ssODN have variable influence, which reflects the underlying mechanism of the repair process. Our model improves HDR efficiency by 83% compared to traditionally chosen targets. Using our findings, we developed CUNE (Computational Universal Nucleotide Editor), which enables users to identify and design the optimal targeting strategy using traditional base editing or - for-the-first-time - HDR-mediated nucleotide changes.
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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 OpenQuestion graph.