ArticleScience advances2019
SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance.
Article in Science advances, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers, 1 of them a synthesis that pooled it.
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Who cites it
140 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- Towards efficient perturbation for the noncoding genome.Nature communications · 2026Article
- High-throughput evaluation of in vitro CRISPR activities enables optimized large-scale multiplex enrichment of rare variants.Nature biomedical engineering · 2026Article
- Comprehensive resistance profiling of chronic myeloid leukaemia associated ABL1 variants against five tyrosine kinase inhibitors using prime editing.Nature biomedical engineering · 2026Article
- Harnessing Deep Learning Models for Guide RNA Optimization and Off-Target Prediction in CRISPR Systems.Biotechnology journal · 2026Review
- Balancing off-target and on-target considerations for optimized CRISPR-Cas9 knockout library design.Cell genomics · 2026Article
- CRISPR-MBTF: a multi-branch transformer fusion framework for CRISPR-Cas9 off-target prediction.Briefings in bioinformatics · 2026Article
- Deep learning-driven prediction of on-target activity, off-target risk, and repair outcomes in CRISPR/Cas9: current landscape and multi-scale perspectives.Journal of translational medicine · 2026Review
- Application of extracellular vesicles in the CRISPR-based diagnosis and treatment: possibilities and challenges.Journal of biological engineering · 2026Review
- Systematic pegRNA design with PRIDICT2.0 and ePRIDICT for efficient prime editing.Nature protocols · 2026Review
- Viral genome editing methods and applications in the CRISPR era.Journal of virology · 2026Review
- Enhancement of prime editing by recruiting engineered or evolved components and implementing novel strategies.Biochemistry and biophysics reports · 2026Review
- CasMiner: a deep-learning tool for high-throughput mining and rational design of efficient Cas9.National science review · 2026Article
- Harnessing artificial intelligence to advance CRISPR-based genome editing technologies.Nature reviews. Genetics · 2026Review
- Mechanistic machine learning enables interpretable and generalizable prediction of prime editing outcomes.bioRxiv : the preprint server for biology · 2026Article
- AI-driven CRISPR screening: optimizing gene editing through automation and intelligent decision support.Journal of translational medicine · 2026Review
- Optimization of functional genetics tools for a model tetraploid Capsella bursa-pastoris, with focus on homoeolog-aware gene editing.Transgenic research · 2026Article
- Computation and deep-learning-driven advances in CRISPR genome editing.Nature structural & molecular biology · 2026Review
- Decoding thebioRxiv : the preprint server for biology · 2026Article
- Empirical optimization of dual-sgRNA design for in vivo CRISPR/Cas9-mediated exon deletion in mice.Computational and structural biotechnology journal · 2026Article
80 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing single-guide RNA-encoding and target sequence pairs. Deep learning-based training on this large dataset of SpCas9-induced indel frequencies led to the development of a SpCas9 activity-predicting model named DeepSpCas9. When tested against independently generated datasets (our own and those published by other groups), DeepSpCas9 showed high generalization performance. DeepSpCas9 is available at http://deepcrispr.info/DeepSpCas9.
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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.