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1. CRISPR‐Cas Biochemistry and CRISPR‐Based Molecular Diagnostics

   https://doi.org/10.1002/anie.202214987  

   Weng, Zhengyan; You, Zheng; Yang, Jie; Mohammad, Noor; Lin, Mengshi; Wei, Qingshan; Gao, Xue; Zhang, Yi (January 2023, Angewandte Chemie International edition in English)
2. CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation

   https://doi.org/10.1021/acssynbio.4c00473  

   Graham, Joshua_P; Zhang, Yu; He, Lifang; Gonzalez-Fernandez, Tomas (October 2024, ACS Synthetic Biology)
3. Very fast CRISPR on demand

   https://doi.org/10.1126/science.aay8204  

   Liu, Yang; Zou, Roger S.; He, Shuaixin; Nihongaki, Yuta; Li, Xiaoguang; Razavi, Shiva; Wu, Bin; Ha, Taekjip (June 2020, Science)

   CRISPR-Cas systems provide versatile tools for programmable genome editing. Here, we developed a caged RNA strategy that allows Cas9 to bind DNA but not cleave until light-induced activation. This approach, referred to as very fast CRISPR (vfCRISPR), creates double-strand breaks (DSBs) at the submicrometer and second scales. Synchronized cleavage improved kinetic analysis of DNA repair, revealing that cells respond to Cas9-induced DSBs within minutes and can retain MRE11 after DNA ligation. Phosphorylation of H2AX after DNA damage propagated more than 100 kilobases per minute, reaching up to 30 megabases. Using single-cell fluorescence imaging, we characterized multiple cycles of 53BP1 repair foci formation and dissolution, with the first cycle taking longer than subsequent cycles and its duration modulated by inhibition of repair. Imaging-guided subcellular Cas9 activation further facilitated genomic manipulation with single-allele resolution. vfCRISPR enables DNA-repair studies at high resolution in space, time, and genomic coordinates. 

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4. Reproducibility metrics for CRISPR screens

   https://doi.org/10.1101/2022.02.19.480892  

   Billmann, Maximilian; Ward, Henry N.; Aregger, Michael; Costanzo, Michael; Andrews, Brenda J.; Boone, C; Moffat, J; Myers, Chad L. (February 2022, bioRxiv)

   CRISPR screens are used extensively to systematically interrogate the phenotype-to-genotype problem. In contrast to early CRISPR screens, which defined core cell fitness genes, most current efforts now aim to identify context-specific phenotypes that differentiate a cell line, genetic background or condition of interest, such as a drug treatment. While CRISPR-related technologies have shown great promise and a fast pace of innovation, a better understanding of standards and methods for quality assessment of CRISPR screen results is crucial to guide technology development and application. Specifically, many commonly used metrics for quantifying screen quality do not accurately measure the reproducibility of context-specific hits. We highlight the importance of reporting reproducibility statistics that directly relate to the purpose of the screen and suggest the use of metrics that are sensitive to context-specific signal. 

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5. Controlling and enhancing CRISPR systems

   https://doi.org/10.1038/s41589-020-00700-7  

   Shivram, Haridha; Cress, Brady F.; Knott, Gavin J.; Doudna, Jennifer A. (January 2021, Nature Chemical Biology)

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