Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

Homologous Capsid Proteins Testify to the Common Ancestry of Retroviruses, Caulimoviruses, Pseudoviruses, and Metaviruses

(2017) Mart Krupovic et al.   JOURNAL OF VIROLOGY

Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres

(2017) Irina R. Arkhipova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications

(2017) Jennifer L. Stamos et al.   MOLECULAR CELL

Advances in the field of single-particle cryo-electron microscopy over the last decade

(2017) Joachim Frank   Nature Protocols

Multiple origins of viral capsid proteins from cellular ancestors

(2017) Mart Krupovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mobile Group II Introns as Ancestral Eukaryotic Elements

(2017) Olga Novikova et al.   TRENDS IN GENETICS

LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types

(2017) Fernando Rodriguez et al.   Viruses-Basel

Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish

(2017) Yusuke Inoue et al.   Nature Communications

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

Convergence of retrotransposons in oomycetes and plants

(2017) Kirill Ustyantsev et al.   Mobile DNA

DNA Transposition at Work

(2016) Alison B. Hickman et al.   CHEMICAL REVIEWS

Common Structural Core of Three-Dozen Residues Reveals Intersuperfamily Relationships

(2016) Heli A.M. Mönttinen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mechanism for DNA transposons to generate introns on genomic scales

(2016) Jason T. Huff et al.   NATURE

Structure of a group II intron in complex with its reverse transcriptase

(2016) Guosheng Qu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution

(2016) Chen Zhao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes

(2016) Ivana Grabundzija et al.   Nature Communications

Structure of a group II intron in complex with its reverse transcriptase

(2016) Guosheng Qu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution

(2016) Chen Zhao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

(2016) Chong Chu et al.   PLoS One

Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes

(2015) Mart Krupovic et al.   Annals of the New York Academy of Sciences

Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease

(2015) Mart Krupovic et al.   Biology Direct

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

(2015) Magali Lescot et al.   ISME Journal

Convergent Evolution of Ribonuclease H in LTR Retrotransposons and Retroviruses

(2015) Kirill Ustyantsev et al.   MOLECULAR BIOLOGY AND EVOLUTION

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

(2015) Benoît Piégu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Crystal structure of the V(D)J recombinase RAG1–RAG2

(2015) Min-Sung Kim et al.   NATURE

The casposon-encoded Cas1 protein fromAciduliprofundum booneiis a DNA integrase that generates target site duplications

(2015) Alison B. Hickman et al.   NUCLEIC ACIDS RESEARCH

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Origins and evolution of viruses of eukaryotes: The ultimate modularity

(2015) Eugene V. Koonin et al.   VIROLOGY

A call for benchmarking transposable element annotation methods

(2015) Douglas R. Hoen et al.   Mobile DNA

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Transposable element detection from whole genome sequence data

(2015) Adam D. Ewing   Mobile DNA

Recurrent DNA virus domestication leading to different parasite virulence strategies

(2015) A. Pichon et al.   Science Advances

Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia

(2015) Kenji K. Kojima et al.   PLoS One

Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses

(2014) Mart Krupovic et al.   Biology Direct

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

(2014) Mart Krupovic et al.   BMC BIOLOGY

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi

(2014) Raúl Castanera et al.   BMC GENOMICS

Automated Structural Comparisons Clarify the Phylogeny of the Right-Hand-Shaped Polymerases

(2014) Heli A. M. Mönttinen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis of Maverick/Polinton giant transposons across organisms

(2014) Saija Haapa-Paananen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution

(2014) Mart Krupovic et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

(2014) Nicolás Toro et al.   PLoS One

Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes

(2014) Lakshminarayan M. Iyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer and Evolution of Prokaryote Transposable Elements in Eukaryotes

(2013) Clément Gilbert et al.   Genome Biology and Evolution

Automatic comparison and classification of protein structures

(2013) Janne Ravantti et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

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

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

(2013) Jean-François Flot et al.   NATURE

Crystal structure of Prp8 reveals active site cavity of the spliceosome

(2013) Wojciech P. Galej et al.   NATURE

Breaking and joining single-stranded DNA: the HUH endonuclease superfamily

(2013) Michael Chandler et al.   NATURE REVIEWS MICROBIOLOGY

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution

(2013) G. Smyshlyaev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank

(2013) Michael Abebe et al.   Mobile DNA

A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons

(2012) Veronika Steinbauerová et al.   GENETICA

The Mu transpososome structure sheds light on DDE recombinase evolution

(2012) Sherwin P. Montaño et al.   NATURE

Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms

(2012) G. K. Taylor et al.   NUCLEIC ACIDS RESEARCH

Zisupton--A Novel Superfamily of DNA Transposable Elements Recently Active in Fish

(2011) A. Bohne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Database for bacterial group II introns

(2011) M. A. Candales et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

A widespread class of reverse transcriptase-related cellular genes

(2011) E. A. Gladyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies

(2011) Y.-W. Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase

(2011) M. Dlakic et al.   RNA

A Virophage at the Origin of Large DNA Transposons

(2011) M. G. Fischer et al.   SCIENCE

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

(2011) Alessandro M Varani et al.   GENOME BIOLOGY

Crystal Structure of the HumanHsmar1-Derived Transposase Domain in the DNA Repair Enzyme Metnase,

(2010) Kristie D. Goodwin et al.   BIOCHEMISTRY

Integrating prokaryotes and eukaryotes: DNA transposases in light of structure

(2010) Alison Burgess Hickman et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Transposases are the most abundant, most ubiquitous genes in nature

(2010) Ramy K. Aziz et al.   NUCLEIC ACIDS RESEARCH

Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences

(2009) Vladimir V. Kapitonov et al.   GENE

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

(2009) Cédric Feschotte et al.   Genome Biology and Evolution

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

(2009) E Lerat   HEREDITY

New Superfamilies of Eukaryotic DNA Transposons and Their Internal Divisions

(2009) W. Bao et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reply: A unified classification system for eukaryotic transposable elements should reflect their phylogeny

(2009) Thomas Wicker et al.   NATURE REVIEWS GENETICS

A unified classification system for eukaryotic transposable elements should reflect their phylogeny

(2009) Ole Seberg et al.   NATURE REVIEWS GENETICS

The Take and Give Between Retrotransposable Elements and their Hosts

(2008) Arthur Beauregard et al.   Annual Review of Genetics

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

Structure of the Tribolium castaneum telomerase catalytic subunit TERT

(2008) Andrew J. Gillis et al.   NATURE

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups

(2008) Eugene V. Koonin et al.   NATURE REVIEWS MICROBIOLOGY

A diversity of uncharacterized reverse transcriptases in bacteria

(2008) Dawn M. Simon et al.   NUCLEIC ACIDS RESEARCH

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity

(2008) G. S. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA