Discovery and characterization of the evolution, variation and functions of diversity-generating retroelements using thousands of genomes and metagenomes

Template-assisted synthesis of adenine-mutagenized cDNA by a retroelement protein complex

(2018) Sumit Handa 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

DGR mutagenic transposition occurs via hypermutagenic reverse transcription primed by nicked template RNA

(2017) Santa S. Naorem et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea

(2017) Blair G. Paul et al.   Nature Microbiology

A Distinct Type of Pilus from the Human Microbiome

(2016) Qingping Xu et al.   CELL

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

Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements

(2016) Sumit Handa et al.   BMC STRUCTURAL BIOLOGY

Identification of Diversity-Generating Retroelements in Human Microbiomes

(2014) Yuzhen Ye   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

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

Widespread horizontal transfer of retrotransposons

(2013) A. M. Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF

(2012) Thomas Schillinger et al.   BMC GENOMICS

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structure of the Essential Diversity-Generating Retroelement Protein bAvd and Its Functionally Important Interaction with Reverse Transcriptase

(2012) Maher Alayyoubi et al.   STRUCTURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Three-dimensional structure of tropism-switching Bordetella bacteriophage

(2010) W. Dai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Diversity-Generating Retroelement Homing Regenerates Target Sequences for Repeated Rounds of Codon Rewriting and Protein Diversification

(2008) Huatao Guo et al.   MOLECULAR CELL