Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success

(2018) Ralph S. Peters et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration

(2018) Jeff Nivala et al.   Nature Microbiology

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems

(2017) Mari Yamada et al.   MOLECULAR CELL

The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit

(2017) Karthik Murugan et al.   MOLECULAR CELL

C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism

(2017) Liang Liu et al.   MOLECULAR CELL

RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes

(2017) Alexandra East-Seletsky et al.   MOLECULAR CELL

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

Class 2 CRISPR–Cas RNA-guided endonucleases: Swiss Army knives of genome editing

(2017) Stefano Stella et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Class 2 CRISPR–Cas RNA-guided endonucleases: Swiss Army knives of genome editing

(2017) Stefano Stella et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A decade of discovery: CRISPR functions and applications

(2017) Rodolphe Barrangou et al.   Nature Microbiology

CRISPR/Cas9 in Genome Editing and Beyond

(2016) Haifeng Wang et al.   Annual Review of Biochemistry

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

(2016) Takashi Yamano et al.   CELL

Structure and Engineering of Francisella novicida Cas9

(2016) Hisato Hirano et al.   CELL

PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease

(2016) Hui Yang et al.   CELL

Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition

(2016) Pu Gao et al.   CELL RESEARCH

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

New CRISPR–Cas systems from uncultivated microbes

(2016) David Burstein et al.   NATURE

Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection

(2016) Alexandra East-Seletsky et al.   NATURE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas: biology, mechanisms and relevance

(2016) Frank Hille et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

(2016) Prarthana Mohanraju et al.   SCIENCE

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

(2016) Omar O. Abudayyeh et al.   SCIENCE

Crystal Structure of Staphylococcus aureus Cas9

(2015) Hiroshi Nishimasu et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

CRISPR-Cas immunity in prokaryotes

(2015) Luciano A. Marraffini   NATURE

Cas9 specifies functional viral targets during CRISPR–Cas adaptation

(2015) Robert Heler et al.   NATURE

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

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

(2014) Hiroshi Nishimasu et al.   CELL

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality

(2014) Alexandra E. Briner et al.   MOLECULAR CELL

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

(2014) John van der Oost et al.   NATURE REVIEWS MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Classification and evolution of type II CRISPR-Cas systems

(2014) Krzysztof Chylinski et al.   NUCLEIC ACIDS RESEARCH

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

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

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

Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis

(2013) Yan Zhang et al.   MOLECULAR CELL

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

(2013) Ines Fonfara et al.   NUCLEIC ACIDS RESEARCH

The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems

(2013) Krzysztof Chylinski et al.   RNA Biology

crRNA and tracrRNA guide Cas9-mediated DNA interference inStreptococcus thermophilus

(2013) Tautvydas Karvelis et al.   RNA Biology

CRISPR-Cas systems and RNA-guided interference

(2013) Rodolphe Barrangou   Wiley Interdisciplinary Reviews-RNA

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

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

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

(2011) N. Takeuchi et al.   JOURNAL OF BACTERIOLOGY

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

(2011) Elitza Deltcheva et al.   NATURE

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

The Deep Archaeal Roots of Eukaryotes

(2008) N. Yutin et al.   MOLECULAR BIOLOGY AND EVOLUTION