CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

Accurate analysis of genuine CRISPR editing events with ampliCan

(2019) Kornel Labun et al.   GENOME RESEARCH

Genetic compensation triggered by mutant mRNA degradation

(2019) Mohamed A. El-Brolosy et al.   NATURE

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

(2018) Silvana Konermann et al.   CELL

Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity

(2018) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

(2018) Tslil Gabrieli et al.   NUCLEIC ACIDS RESEARCH

CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window

(2018) Shakked O. Halperin et al.   NATURE

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

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

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Nucleic acid detection with CRISPR-Cas13a/C2c2

(2017) Jonathan S. Gootenberg et al.   SCIENCE

Establishment of expanded and streamlined pipeline of PITCh knock-in – a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO

(2017) Kazuki Nakamae et al.   Bioengineered

In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration

(2016) Keiichiro Suzuki et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

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

(2016) Omar O. Abudayyeh et al.   SCIENCE

Internal guide RNA interactions interfere with Cas9-mediated cleavage

(2016) Summer B. Thyme et al.   Nature Communications

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

The New State of the Art: Cas9 for Gene Activation and Repression

(2015) Marie F. La Russa et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

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

(2015) Raj Chari et al.   NATURE METHODS

MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems

(2015) Tetsushi Sakuma et al.   Nature Protocols

Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs

(2014) James A. Gagnon et al.   PLoS One

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

ViennaRNA Package 2.0

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