Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems

The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases

(2020) Carl J Schiltz et al.   NUCLEIC ACIDS RESEARCH

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

It takes two (Las1 HEPN endoribonuclease domains) to cut RNA correctly

(2020) Monica C. Pillon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

(2020) Alec Vallota-Eastman et al.   BMC GENOMICS

Diverse enzymatic activities mediate antiviral immunity in prokaryotes

(2020) Linyi Gao et al.   SCIENCE

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

RNases H: Structure and mechanism

(2019) Malwina Hyjek et al.   DNA REPAIR

Multiple origins of reverse transcriptases linked to CRISPR-Cas systems

(2019) Nicolás Toro et al.   RNA Biology

Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR–Cas system in Vibrio vulnificus

(2019) Alejandro González-Delgado et al.   NUCLEIC ACIDS RESEARCH

Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage

(2019) Carl J Schiltz et al.   NUCLEIC ACIDS RESEARCH

Recruitment of Reverse Transcriptase-Cas1 Fusion Proteins by Type VI-A CRISPR-Cas Systems

(2019) Nicolás Toro et al.   Frontiers in Microbiology

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

(2019) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

Retrons and their applications in genome engineering

(2019) Anna J Simon et al.   NUCLEIC ACIDS RESEARCH

DALI and the persistence of protein shape

(2019) Liisa Holm   PROTEIN SCIENCE

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

On the Origin and Evolutionary Relationships of the Reverse Transcriptases Associated With Type III CRISPR-Cas Systems

(2018) Nicolás Toro et al.   Frontiers in Microbiology

Transcriptional recording by CRISPR spacer acquisition from RNA

(2018) Florian Schmidt et al.   NATURE

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

The first demonstration of the existence of reverse transcriptases in bacteria

(2017) Masayori Inouye   GENE

Multi-copy single-stranded DNA in Escherichia coli

(2017) Xianxing Xie et al.   MICROBIOLOGY-SGM

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

Genomic and transcriptomic landscape of Escherichia coli BL21(DE3)

(2017) Sinyeon Kim et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Zasha Weinberg et al.   NUCLEIC ACIDS RESEARCH

Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey

(2017) Li Wu et al.   NUCLEIC ACIDS RESEARCH

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Viral reverse transcriptases

(2017) Luis Menéndez-Arias et al.   VIRUS RESEARCH

Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity

(2016) Wenyan Jiang et al.   CELL

RaptorX-Property: a web server for protein structure property prediction

(2016) Sheng Wang et al.   NUCLEIC ACIDS RESEARCH

Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein

(2016) S. Silas et al.   SCIENCE

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

I-TASSER server: new development for protein structure and function predictions

(2015) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens

(2015) Johanna R. Elfenbein et al.   PLoS Genetics

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deciphering key features in protein structures with the new ENDscript server

(2014) Xavier Robert et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

(2014) Nicolás Toro et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

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

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

(2013) Vivek Anantharaman et al.   Biology Direct

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

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

Retrotransposons

(2012) David J. Finnegan   CURRENT BIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

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

Two novel retron elements are replaced with retron-Vc95 in Vibrio cholerae

(2011) Kumiko Inouye et al.   MICROBIOLOGY AND IMMUNOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Nucleases: diversity of structure, function and mechanism

(2010) Wei Yang   QUARTERLY REVIEWS OF BIOPHYSICS

Analysis of the DDE Motif in the Mutator Superfamily

(2008) Aurélie Hua-Van et al.   JOURNAL OF MOLECULAR EVOLUTION

Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture

(2008) K. K. Kojima et al.   MOLECULAR BIOLOGY AND EVOLUTION