RNA-Oligo

I. siRNA/ASO

Our papers: NAR 2008a, 2008b, 2008c
2018 BMC Genomics, SiRNA silencing efficacy prediction based on a deep architecture
2008 Bioinformatics, siDRM: an effective and generally applicable online siRNA design tool
2007 NAR - Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
2006 BMC Bioinformatics - Computational models with thermodynamic and composition features improve siRNA design
2006 BMC Bioinformatics - An accurate and interpretable model for siRNA efficacy prediction
2005 Nature Biotech. - Design of a genome-wide siRNA library using an artificial neural network

✅ 2024 Bioinformatics - SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments
✅ 2017 Cell Systems - Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results
2013 Biomed Res Int. - SeedSeq: Off-Target Transcriptome Database

2023 Advanced Drug Delivery Reviews - A holistic analysis of the intrinsic and delivery-mediated toxicity of siRNA therapeutics
2020 Signal Transduction and Targeted Therapy - Therapeutic siRNA: state of the art
2016 Scientific Reports - siRNAmod: A database of experimentally validated chemically modified siRNAs

✅ 2018 Nature Biotech. - Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity
more sgRNA papers

[Benchmark] 2023 BIB - Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities
[review] 2023 BIB - Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review
2023 Nature Communications - Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints
✅ [off-target] 2016 Nature Biotech. -Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

2024 Nat. Biotech. - Tracking-seq reveals the heterogeneity of off-target effects in CRISPR–Cas9-mediated genome editing
2023 Nat. Methods - Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+
2019 Science - Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq