Prediction of on-target and off-target activity of CRISPR–Cas13d guide RNAs using deep learning

Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches

(2023) Xiaolong Cheng et al.   Nature Communications

CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression

(2023) Gemma Noviello et al.   Nature Communications

Collateral activity of the CRISPR/RfxCas13d system in human cells

(2023) Peiguo Shi et al.   Communications Biology

Targeted gene silencing in the nervous system with CRISPR-Cas13

(2022) Jackson E. Powell et al.   Science Advances

Designing sensitive viral diagnostics with machine learning

(2022) Hayden C. Metsky et al.   NATURE BIOTECHNOLOGY

Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells

(2022) Sarah Lensch et al.   eLife

Specific knockdown of Htra2 by CRISPR-CasRx prevents acquired sensorineural hearing loss in mice

(2022) Yang Guo et al.   Molecular Therapy-Nucleic Acids

Hierarchical self-uncloaking CRISPR-Cas13a–customized RNA nanococoons for spatial-controlled genome editing and precise cancer therapy

(2022) Ningke Fan et al.   Science Advances

A cross-disorder dosage sensitivity map of the human genome

(2022) Ryan L. Collins et al.   CELL

Negative autoregulation mitigates collateral RNase activity of repeat-targeting CRISPR-Cas13d in mammalian cells

(2022) Chase P. Kelley et al.   Cell Reports

Species-agnostic polymeric formulations for inhalable messenger RNA delivery to the lung

(2022) Laura Rotolo et al.   NATURE MATERIALS

An RNA-targeting CRISPR–Cas13d system alleviates disease-related phenotypes in Huntington’s disease models

(2022) Kathryn H. Morelli et al.   NATURE NEUROSCIENCE

Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing

(2021) Jeremy Charlier et al.   BIOINFORMATICS

Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks

(2021) Guishan Zhang et al.   Computational and Structural Biotechnology Journal

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

(2021) Xi Xiang et al.   Nature Communications

R-CRISPR: A Deep Learning Network to Predict Off-Target Activities with Mismatch, Insertion and Deletion in CRISPR-Cas9 System

(2021) Rui Niu et al.   Genes

Deep learning improves the ability of sgRNA off-target propensity prediction

(2020) Qiaoyue Liu et al.   BMC BIOINFORMATICS

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs

(2020) Marco Jost et al.   NATURE BIOTECHNOLOGY

RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering

(2020) Aaron A. Smargon et al.   NATURE CELL BIOLOGY

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells

(2020) Hui Kwon Kim et al.   Nature Biomedical Engineering

Massively parallel Cas13 screens reveal principles for guide RNA design

(2020) Hans-Hermann Wessels et al.   NATURE BIOTECHNOLOGY

CRISPR‐Net: A Recurrent Convolutional Network Quantifies CRISPR Off‐Target Activities with Mismatches and Indels

(2020) Jiecong Lin et al.   Advanced Science

Prediction of the sequence-specific cleavage activity of Cas9 variants

(2020) Nahye Kim et al.   NATURE BIOTECHNOLOGY

Precise tuning of gene expression levels in mammalian cells

(2019) Yale S. Michaels et al.   Nature Communications

Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks

(2019) Jiesi Luo et al.   BMC BIOINFORMATICS

SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance

(2019) Hui Kwon Kim et al.   Science Advances

OUP accepted manuscript

(2018)   BIOINFORMATICS

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein

(2018) Winston X. Yan et al.   MOLECULAR CELL

Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d

(2018) Cheng Zhang et al.   CELL

RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a

(2018) Akshay Tambe et al.   Cell Reports

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

(2017) Aaron A. Smargon et al.   MOLECULAR CELL

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

Passive Noise Filtering by Cellular Compartmentalization

(2016) Thomas Stoeger et al.   CELL

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

(2016) Omar O. Abudayyeh et al.   SCIENCE

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

Sources of Error in Mammalian Genetic Screens

(2016) Laura Magill Sack et al.   G3-Genes Genomes Genetics

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

(2015) Sidi Chen et al.   CELL

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Gene expression analysis identifies global gene dosage sensitivity in cancer

(2015) Rudolf S N Fehrmann et al.   NATURE GENETICS

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Fast Implementation of DeLong’s Algorithm for Comparing the Areas Under Correlated Receiver Operating Characteristic Curves

(2014) Xu Sun et al.   IEEE SIGNAL PROCESSING LETTERS

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Stoichiometric imbalance in the receptor complex contributes to dysfunctional BMPR-II mediated signalling in pulmonary arterial hypertension

(2008) M. Talat Nasim et al.   HUMAN MOLECULAR GENETICS