Chromatin accessibility and guide sequence secondary structure affect CRISPR ‐Cas9 gene editing efficiency

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

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Multiplex Genome Engineering Using CRISPR/Cas Systems

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Genome engineering using the CRISPR-Cas9 system

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High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells

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Rationally engineered Cas9 nucleases with improved specificity

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Easy quantitative assessment of genome editing by sequence trace decomposition

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Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation

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CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

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Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

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Sequence determinants of improved CRISPR sgRNA design

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Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes

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Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems

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Nucleosomes impede Cas9 access to DNA in vivo and in vitro

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Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

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WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system

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Surrogate reporters for enrichment of cells with nuclease-induced mutations

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The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells

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Internal guide RNA interactions interfere with Cas9-mediated cleavage

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Probing the impact of chromatin conformation on genome editing tools

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Dual-reporter surrogate systems for efficient enrichment of genetically modified cells

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Enhanced genome editing in mammalian cells with a modified dual-fluorescent surrogate system

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Minimum-free-energy distribution of RNA secondary structures: Entropic and thermodynamic properties of rare events

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Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

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First report of CRISPR/cas9 mediated dna-free editing of 4cl and rve7 genes in chickpea protoplasts

Badhan, S., Ball, A. S., & Mantri, N. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22010396 · Cited by 193 · see citing works

Genome-wide profiling of adenine base editor specificity by EndoV-seq

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DIG-Seq: A genome-wide CRISPR off-target profiling method using chromatin DNA

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Single and multiple gene knockouts by CRISPR–Cas9 in maize

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Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects

Naeem, M., & Alkhnbashi, O. S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076261 · Cited by 70 · see citing works

Massively targeted evaluation of therapeutic CRISPR off-targets in cells

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Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing

Li, J., Wu, P., Cao, Z., Huang, G., Lu, Z., Yan, J., Zhang, H., Zhou, Y., Liu, R., Chen, H., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113765 · Cited by 26 · see citing works

Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9

Okada, K., Aoki, K., Tabei, T., Sugio, K., Imai, K., Bonkohara, Y., & Kamachi, Y. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac100 · Cited by 14 · see citing works

Rescue of the disease-associated phenotype in CRISPR-corrected hiPSCs as a therapeutic approach for inherited retinal dystrophies

Siles, L., & Pomares, E. (2025) · Molecular Therapy Nucleic Acids · doi:10.1016/j.omtn.2025.102482 · Cited by 4 · see citing works

Adenine base editor for knockout of proteins: A practical guide from design to analysis with updated MultiEditRbatch

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Variations in length and area in human Y chromosome: an ultrastructural analysis.

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Reviewer #1 (Public Review): Alternative end-joining results in smaller deletions in heterochromatin relative to euchromatin

(2023) · doi:10.7554/elife.91851.1.sa2

Faculty Opinions recommendation of Heterochromatin drives compartmentalization of inverted and conventional nuclei.

Xie, W. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735906976.793572893

The consequences of differential origin licensing dynamics in distinct chromatin environmentsPreprint

Liu, M., Kedziora, K. M., Song, E. C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.28.450210 · Cited by 5 · see citing works

Alternative end-joining results in smaller deletions in heterochromatin relative to euchromatinPreprint

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