Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR–Cas12a gRNA switch

Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs

(2020) Thomas Jacobsen et al.   NUCLEIC ACIDS RESEARCH

Nucleic Acid Detection Using CRISPR/Cas Biosensing Technologies

(2020) Rashid Aman et al.   ACS Synthetic Biology

Conditional guide RNA through two intermediate hairpins for programmable CRISPR/Cas9 function: building regulatory connections between endogenous RNA expressions

(2020) Jiao Lin et al.   NUCLEIC ACIDS RESEARCH

A deep learning approach to programmable RNA switches

(2020) Nicolaas M. Angenent-Mari et al.   Nature Communications

Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics

(2020) Roberto Galizi et al.   CRISPR Journal

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

(2019) Alexandra Westbrook et al.   BIOTECHNOLOGY AND BIOENGINEERING

A microRNA-inducible CRISPR–Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool

(2019) Xi-Wen Wang et al.   NATURE CELL BIOLOGY

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas

(2019) Adam E. Dolan et al.   MOLECULAR CELL

Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis

(2019) Chunyu Liao et al.   Nature Communications

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

(2019) Kale Kundert et al.   Nature Communications

Switching the activity of Cas12a using guide RNA strand displacement circuits

(2019) Lukas Oesinghaus et al.   Nature Communications

Programmable CRISPR-Cas Repression, Activation, and Computation with Sequence-Independent Targets and Triggers

(2019) Mike Jin et al.   ACS Synthetic Biology

Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology

(2019) Mikhail H. Hanewich-Hollatz et al.   ACS Central Science

Targeted transcriptional modulation with type I CRISPR–Cas systems in human cells

(2019) Adrian Pickar-Oliver et al.   NATURE BIOTECHNOLOGY

CRISPR-TSKO: A Technique for Efficient Mutagenesis in Specific Cell Types, Tissues, or Organs in Arabidopsis

(2019) Ward Decaestecker et al.   PLANT CELL

Point-of-care biomarker quantification enabled by sample-specific calibration

(2019) Monica P. McNerney et al.   Science Advances

Harnessing type I CRISPR–Cas systems for genome engineering in human cells

(2019) Peter Cameron et al.   NATURE BIOTECHNOLOGY

De novo-designed translation-repressing riboregulators for multi-input cellular logic

(2019) Jongmin Kim et al.   Nature Chemical Biology

In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller

(2019) Deepak K. Agrawal et al.   Nature Communications

CRISPR-Cas3 induces broad and unidirectional genome editing in human cells

(2019) Hiroyuki Morisaka et al.   Nature Communications

Design of a Transcriptional Biosensor for the Portable, On-Demand Detection of Cyanuric Acid

(2019) Xiangyang Liu et al.   ACS Synthetic Biology

Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

(2018) Ryan Marshall et al.   MOLECULAR CELL

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

(2018) Janice S. Chen et al.   SCIENCE

CRISPR-Based Gene Drives for Pest Control

(2018) Gus R. McFarlane et al.   TRENDS IN BIOTECHNOLOGY

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

(2018) Lun Cui et al.   Nature Communications

High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli

(2018) Suhyung Cho et al.   ACS Synthetic Biology

The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays

(2018) Chunyu Liao et al.   RNA Biology

High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites

(2018) Mia K. Mihailovic et al.   Nature Communications

Riboregulated toehold-gated gRNA for programmable CRISPR–Cas9 function

(2018) Ka-Hei Siu et al.   Nature Chemical Biology

Tuning the Performance of Synthetic Riboswitches using Machine Learning

(2018) Ann-Christin Groher et al.   ACS Synthetic Biology

Deciphering, Communicating, and Engineering the CRISPR PAM

(2017) Ryan T. Leenay et al.   JOURNAL OF MOLECULAR BIOLOGY

Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering

(2017) Brian R. Wolfe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Computational design of small transcription activating RNAs for versatile and dynamic gene regulation

(2017) James Chappell et al.   Nature Communications

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

(2016) Takashi Yamano et al.   CELL

Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems

(2016) Ryan T. Leenay et al.   MOLECULAR CELL

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

(2016) Ines Fonfara et al.   NATURE

Applications of CRISPR technologies in research and beyond

(2016) Rodolphe Barrangou et al.   NATURE BIOTECHNOLOGY

Directing cellular information flow via CRISPR signal conductors

(2016) Yuchen Liu et al.   NATURE METHODS

Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases

(2016) Shengdar Q. Tsai et al.   NATURE REVIEWS GENETICS

Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system

(2016) Young Je Lee et al.   NUCLEIC ACIDS RESEARCH

The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology

(2016) Jonathan Garamella et al.   ACS Synthetic Biology

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly

(2015) Michael E. Lee et al.   ACS Synthetic Biology

Toehold Switches: De-Novo-Designed Regulators of Gene Expression

(2014) Alexander A. Green et al.   CELL

Efficient programmable gene silencing by Cascade

(2014) Devashish Rath et al.   NUCLEIC ACIDS RESEARCH

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

(2014) Michelle L. Luo et al.   NUCLEIC ACIDS RESEARCH

Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems

(2014) A. A. Gomaa et al.   mBio

Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”

(2014) Dan Siegal-Gaskins et al.   ACS Synthetic Biology

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

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

An E. coli Cell-Free Expression Toolbox: Application to Synthetic Gene Circuits and Artificial Cells

(2011) Jonghyeon Shin et al.   ACS Synthetic Biology

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Measuring the activity of BioBrick promoters using an in vivo reference standard

(2009) Jason R Kelly et al.   Journal of Biological Engineering