Selective TnsC recruitment enhances the fidelity of RNA-guided transposition

Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons

(2022) Sanne E. Klompe et al.   MOLECULAR CELL

Structural basis for DNA targeting by the Tn7 transposon

(2022) Yao Shen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dual modes of CRISPR-associated transposon homing

(2021) Makoto Saito et al.   CELL

Structural basis for target site selection in RNA-guided DNA transposition systems

(2021) Jung-Un Park et al.   SCIENCE

Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing

(2021) Phuc Leo H. Vo et al.   Mobile DNA

Target site selection and remodelling by type V CRISPR-transposon systems

(2021) Irma Querques et al.   NATURE

A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition

(2020) David M. Walker et al.   CELL

Structure–function insights into the initial step of DNA integration by a CRISPR–Cas–Transposon complex

(2020) Ning Jia et al.   CELL RESEARCH

Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1

(2020) Jasenko Zivanov et al.   IUCrJ

Localized reconstruction in scipion expedites the analysis of symmetry mismatches in Cryo-EM data

(2020) Vahid Abrishami et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering

(2020) Phuc Leo H. Vo et al.   NATURE BIOTECHNOLOGY

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

(2019) Guilhem Faure et al.   NATURE REVIEWS MICROBIOLOGY

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond

(2019) Joseph E. Peters   MOLECULAR MICROBIOLOGY

The molecular principles governing the activity and functional diversity of AAA+ proteins

(2019) Cristina Puchades et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Current Developments in Coot for Macromolecular Model Building of Electron Cryo‐microscopy and Crystallographic Data

(2019) Ana Casañal et al.   PROTEIN SCIENCE

Jump ahead with a twist: DNA acrobatics drive transposition forward

(2019) Vladimir Arinkin et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural basis of DNA targeting by a transposon-encoded CRISPR–Cas system

(2019) Tyler S. Halpin-Healy et al.   NATURE

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

(2019) Michael G. Prisant et al.   PROTEIN SCIENCE

Improved design and analysis of CRISPR knockout screens

(2018) Chen-Hao Chen et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Quantitative mass imaging of single biological macromolecules

(2018) Gavin Young et al.   SCIENCE

Determining the Specificity of Cascade Binding, Interference, and Primed Adaptation In Vivo in the Escherichia coli Type I-E CRISPR-Cas System

(2018) Lauren A. Cooper et al.   mBio

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis

(2018) Jasenko Zivanov et al.   IUCrJ

Deciphering, Communicating, and Engineering the CRISPR PAM

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

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Viruses and mobile elements as drivers of evolutionary transitions

(2016) Eugene V. Koonin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

The Cas6e ribonuclease is not required for interference and adaptation by theE. colitype I-E CRISPR-Cas system

(2015) Ekaterina Semenova et al.   NUCLEIC ACIDS RESEARCH

A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture

(2015) Henriette O'Geen et al.   NUCLEIC ACIDS RESEARCH

Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection

(2015) Marius Rutkauskas et al.   Cell Reports

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

(2015) Alan Brown et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

(2014) Cem Kuscu et al.   NATURE BIOTECHNOLOGY

Ultrastable gold substrates for electron cryomicroscopy

(2014) C. J. Russo et al.   SCIENCE

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

(2013) Lei S. Qi et al.   CELL

MuB is an AAA+ ATPase that forms helical filaments to control target selection for DNA transposition

(2013) N. Mizuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Architecture of the Tn7 Posttransposition Complex: An Elaborate Nucleoprotein Structure

(2010) Jason W. Holder et al.   JOURNAL OF MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

A Temporal Threshold for Formaldehyde Crosslinking and Fixation

(2009) Lars Schmiedeberg et al.   PLoS One

The AAA+ superfamily of functionally diverse proteins

(2008) Jamie Snider et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY