crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays

Störtz, Florian; Mináry, Péter

doi:10.1093/nar/gkaa885

Cited by 24 publications

(26 citation statements)

References 49 publications

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“…The utilization of MGE may increase the effect of off-target occurrence as the number of targets increased (McCarty et al, 2020). Several online toolboxes for off-target detection and expectations have been developed and updated for eliminating the percentage of offtarget occurrence (Cradick et al, 2014;Kang et al, 2020;Naeem et al, 2020;Störtz and Minary, 2021).…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Multiplex Genome-Editing Technologies for Revolutionizing Plant Biology and Crop Improvement

et al. 2021

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Multiplex genome-editing (MGE) technologies are recently developed versatile bioengineering tools for modifying two or more specific DNA loci in a genome with high precision. These genome-editing tools have greatly increased the feasibility of introducing desired changes at multiple nucleotide levels into a target genome. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) [CRISPR/Cas] system-based MGE tools allow the simultaneous generation of direct mutations precisely at multiple loci in a gene or multiple genes. MGE is enhancing the field of plant molecular biology and providing capabilities for revolutionizing modern crop-breeding methods as it was virtually impossible to edit genomes so precisely at the single base-pair level with prior genome-editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Recently, researchers have not only started using MGE tools to advance genome-editing applications in certain plant science fields but also have attempted to decipher and answer basic questions related to plant biology. In this review, we discuss the current progress that has been made toward the development and utilization of MGE tools with an emphasis on the improvements in plant biology after the discovery of CRISPR/Cas9. Furthermore, the most recent advancements involving CRISPR/Cas applications for editing multiple loci or genes are described. Finally, insights into the strengths and importance of MGE technology in advancing crop-improvement programs are presented.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Multiplex Genome-Editing Technologies for Revolutionizing Plant Biology and Crop Improvement

et al. 2021

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“…For instance, CRISPR-Local [ 51 ], GuideScan [ 52 ] and GPP sgRNA Designer [ 53 ] were developed based on CFD (computational fluid dynamics) technology [ 54 ] for quantifying off-target activity and are used to guide the design of sgRNAs. Additionally, crisprSQL [ 55 ] and OffScan [ 56 ] are used to detect off-target sites.…”

Section: Description Of Crispr-cas Systemsmentioning

confidence: 99%

Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections

Battalapalli

Hakeem

et al. 2021

J Nanobiotechnol

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Antibiotic resistance is spreading rapidly around the world and seriously impeding efforts to control microbial infections. Although nucleic acid testing is widely deployed for the detection of antibiotic resistant bacteria, the current techniques—mainly based on polymerase chain reaction (PCR)—are time-consuming and laborious. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance (AMR). The CRISPR-Cas system is an adaptive immune system found in many prokaryotes that presents attractive opportunities to target and edit nucleic acids with high precision and reliability. Engineered CRISPR-Cas systems are reported to effectively kill bacteria or even revert bacterial resistance to antibiotics (resensitizing bacterial cells to antibiotics). Strategies for combating antimicrobial resistance using CRISPR (i.e., Cas9, Cas12, Cas13, and Cas14) can be of great significance in detecting bacteria and their resistance to antibiotics. This review discusses the structures, mechanisms, and detection methods of CRISPR-Cas systems and how these systems can be engineered for the rapid and reliable detection of bacteria using various approaches, with a particular focus on nanoparticles. In addition, we summarize the most recent advances in applying the CRISPR-Cas system for virulence modulation of bacterial infections and combating antimicrobial resistance. Graphical Abstract

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“… 204 http://drugcombdb.denglab.org/ CRISPR on-target Leenay et al. 205 https://tdcommons.ai/single_pred_tasks/CRISPROutcome/ CRISPR off-target Störtz and Minary 206 http://www.CRISPRsql.com/ virus vector design Bryant et al. 156 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA673640/ Clinical study (“ machine learning for genomics in clinical studies ”) cross-species translation Poussin et al.…”

Section: A Primer On Genomics Data and Machine Learning Modelsmentioning

confidence: 99%

Machine learning applications for therapeutic tasks with genomics data

Huang

Xiao²,

Glass

et al. 2021

Patterns

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Summary Thanks to the increasing availability of genomics and other biomedical data, many machine learning algorithms have been proposed for a wide range of therapeutic discovery and development tasks. In this survey, we review the literature on machine learning applications for genomics through the lens of therapeutic development. We investigate the interplay among genomics, compounds, proteins, electronic health records, cellular images, and clinical texts. We identify 22 machine learning in genomics applications that span the whole therapeutics pipeline, from discovering novel targets, personalizing medicine, developing gene-editing tools, all the way to facilitating clinical trials and post-market studies. We also pinpoint seven key challenges in this field with potentials for expansion and impact. This survey examines recent research at the intersection of machine learning, genomics, and therapeutic development.

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crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays

Cited by 24 publications

References 49 publications

Multiplex Genome-Editing Technologies for Revolutionizing Plant Biology and Crop Improvement

Multiplex Genome-Editing Technologies for Revolutionizing Plant Biology and Crop Improvement

Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections

Machine learning applications for therapeutic tasks with genomics data

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