The widespread IS200/605 transposon family encodes diverse programmable RNA-guided endonucleases

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

(2020) Annie M. Sriramachandran et al.   MOLECULAR CELL

A short history of guide RNAs

(2020) André Schneider   EMBO REPORTS

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

(2020) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

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

(2019) Sanne E. Klompe et al.   NATURE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

(2019) Suha Naser-Khdour et al.   Genome Biology and Evolution

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis

(2018) Sergey A. Shmakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

(2017) Zasha Weinberg et al.   NUCLEIC ACIDS RESEARCH

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae

(2017) Monique Turmel et al.   Scientific Reports

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

(2016) Elena Rivas et al.   NATURE METHODS

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

(2015) Bernd Zetsche et al.   CELL

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs

(2015) Vladimir V. Kapitonov et al.   JOURNAL OF BACTERIOLOGY

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

(2015) José Vicente Gomes-Filho et al.   RNA Biology

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity

(2014) Mart Krupovic et al.   BMC BIOLOGY

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

A new set of highly efficient, tag-cleaving proteases for purifying recombinant proteins

(2014) Steffen Frey et al.   JOURNAL OF CHROMATOGRAPHY A

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

(2014) Karolina A. Majorek et al.   NUCLEIC ACIDS RESEARCH

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

(2014) M. Jinek et al.   SCIENCE

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

(2013) Weidong Bao et al.   Mobile DNA

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

ViennaRNA Package 2.0

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

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

(2011) Zasha Weinberg et al.   BMC BIOINFORMATICS

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

(2009) Zasha Weinberg et al.   NATURE