AIMC Topic: CRISPR-Cas Systems

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Predictable and precise template-free CRISPR editing of pathogenic variants.

Nature Nov 7, 2018
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a pre...
Hermanski-Pudlak Syndrome Reproducibility of Results Substrate Specificity Menkes Kinky Hair Syndrome Fibroblasts Templates, Genetic DNA Repair CRISPR-Cas Systems Humans CRISPR-Associated Protein 9 Base Sequence Machine Learning Gene Editing Alleles K562 Cells HCT116 Cells HEK293 Cells
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A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action.

PLoS computational biology Oct 16, 2017
The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated much excitement in recent years owing to its ability to manipulate targeted genes and genomic regions that are complementary to a programmed single guide RNA (sgRNA)...
RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Gene Editing Algorithms Humans Machine Learning ROC Curve Computational Biology
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GuideScan software for improved single and paired CRISPR guide RNA design.

Nature biotechnology Mar 6, 2017
We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We a...
RNA, Small Interfering Clustered Regularly Interspaced Short Palindromic Repeats Chromosome Mapping Gene Silencing Machine Learning Algorithms Software Sequence Analysis, RNA CRISPR-Cas Systems
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Prediction of potent shRNAs with a sequential classification algorithm.

Nature biotechnology Mar 6, 2017
We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel data sets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a give...
RNA, Small Interfering Clustered Regularly Interspaced Short Palindromic Repeats Chromosome Mapping Algorithms Machine Learning Sequence Analysis, RNA Software CRISPR-Cas Systems Gene Silencing
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Accurate Diagnosis of Colorectal Cancer Using a Combination of Lectin-Induced Recombinase Polymerase Amplification and CRISPR/Cas12a Assay on a Point-of-Care Testing Platform with Deep Learning Assistant.

Analytical chemistry Jul 1, 2025
Specific glycosylation patterns on exosome surfaces represent novel diagnostic biomarkers for cancer liquid biopsy. Lectins can induce exosome aggregation through multiple bindings with exosomal glycoproteins. In this work, we developed a one-pot lec...
Limit of Detection CRISPR-Cas Systems Humans Bacterial Proteins Exosomes Colorectal Neoplasms Endodeoxyribonucleases Lectins Cell Line, Tumor Animals CRISPR-Associated Proteins Recombinases Mice Deep Learning Point-of-Care Testing Nucleic Acid Amplification Techniques
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Machine learning and statistical classification in CRISPR-Cas12a diagnostic assays.

Biosensors & bioelectronics Jul 1, 2025
CRISPR-based diagnostics have gained increasing attention as biosensing tools able to address limitations in contemporary molecular diagnostic tests. To maximize the performance of CRISPR-based assays, much effort has focused on optimizing the chemis...
Bacterial Proteins Endodeoxyribonucleases CRISPR-Associated Proteins Biosensing Techniques CRISPR-Cas Systems Humans Neural Networks, Computer Machine Learning
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High-throughput robotic isolation of human iPS cell clones reveals frequent homozygous induction of identical genetic manipulations by CRISPR-Cas9.

Stem cell research & therapy Jun 7, 2025
BACKGROUND: Genome editing in human iPS cells is a powerful approach in regenerative medicine. CRISPR-Cas9 is the most common genome editing tool, but it often induces byproduct insertions and deletions in addition to the desired edits. Therefore, ge...
Homozygote Induced Pluripotent Stem Cells CRISPR-Cas Systems Clone Cells Gene Editing Humans Robotics
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Learning to utilize internal protein 3D nanoenvironment descriptors in predicting CRISPR-Cas9 off-target activity.

NAR genomics and bioinformatics Jun 1, 2025
Despite advances in determining the factors influencing cleavage activity of a CRISPR-Cas9 single guide RNA (sgRNA) at an (off-)target DNA sequence, a comprehensive assessment of pertinent physico-chemical/structural descriptors is missing. In partic...
Gene Editing RNA, Guide, CRISPR-Cas Systems CRISPR-Associated Protein 9 Machine Learning CRISPR-Cas Systems Mutation
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Precise genome editing process and its applications in plants driven by AI.

Functional & integrative genomics May 24, 2025
Genome editing technologies have emerged as the keystone of biotechnological research, enabling precise gene modification. The field has evolved rapidly through revolutionary advancements, transitioning from early explorations to the breakthrough of ...
Gene Editing Genome, Plant Plant Breeding Artificial Intelligence CRISPR-Cas Systems Plants
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Deep Learning-Based Classification of CRISPR Loci Using Repeat Sequences.

ACS synthetic biology May 16, 2025
With the widespread application of the CRISPR-Cas system in gene editing and related fields, along with the increasing availability of metagenomic data, the demand for detecting and classifying CRISPR-Cas systems in metagenomic data sets has grown si...
Neural Networks, Computer Deep Learning CRISPR-Cas Systems Clustered Regularly Interspaced Short Palindromic Repeats Gene Editing Repetitive Sequences, Nucleic Acid
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