Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes

RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

(2011) Vipin Singh et al.   BMC BIOINFORMATICS

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Next-Generation Sequencing Reveals Recent Horizontal Transfer of a DNA Transposon between Divergent Mosquitoes

(2011) Yupu Diao et al.   PLoS One

Will Computers Crash Genomics?

(2011) E. Pennisi   SCIENCE

On the Future of Genomic Data

(2011) S. D. Kahn   SCIENCE

TE Displayer for post-genomic analysis of transposable elements

(2010) Rebecca Rooke et al.   BIOINFORMATICS

ModuleOrganizer: detecting modules in families of transposable elements

(2010) Sebastien Tempel et al.   BMC BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

A novel web-based TinT application and the chronology of the Primate Alu retroposon activity

(2010) Gennady Churakov et al.   BMC EVOLUTIONARY BIOLOGY

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

(2010) Jianchang Du et al.   BMC GENOMICS

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Small RNA-Mediated Quiescence of Transposable Elements in Animals

(2010) Kuniaki Saito et al.   DEVELOPMENTAL CELL

Variable DNA methylation of transposable elements: The case study of mouse Early Transposons

(2010) Daphne Reiss et al.   Epigenetics

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

(2010) C. Biemont   GENETICS

piRNAs, transposon silencing, andDrosophilagermline development

(2010) Jaspreet S. Khurana et al.   JOURNAL OF CELL BIOLOGY

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

(2010) Clément Gilbert et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

Temperature controls nuclear import of Tam3 transposase in Antirrhinum

(2010) Kaien Fujino et al.   PLANT JOURNAL

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

All y’all need to know ‘bout retroelements in cancer

(2010) Victoria P. Belancio et al.   SEMINARS IN CANCER BIOLOGY

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary dynamics of transposable elements in a small RNA world

(2010) Justin P. Blumenstiel   TRENDS IN GENETICS

A triptych of the evolution of plant transposable elements

(2010) Maud I. Tenaillon et al.   TRENDS IN PLANT SCIENCE

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Transposition of the Tourist-MITE mPing in yeast: an assay that retains key features of catalysis by the class 2 PIF/Harbinger superfamily

(2010) C Nathan Hancock et al.   Mobile DNA

Epigenetic Regulation of Mammalian Genomes by Transposable Elements

(2009) Ahsan Huda et al.   Annals of the New York Academy of Sciences

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences

(2009) Göran Sperber et al.   BMC BIOINFORMATICS

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS

RepPop: a database for repetitive elements in Populus trichocarpa

(2009) Fengfeng Zhou et al.   BMC GENOMICS

MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi

(2009) Yong Chen et al.   GENE

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

(2009) Carla J. Cohen et al.   GENE

Mariner Mos1 transposase optimization by rational mutagenesis

(2009) Stéphanie Germon et al.   GENETICA

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

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

(2009) J. Lu et al.   GENOME RESEARCH

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

(2009) E Lerat   HEREDITY

The L1 retrotransposition assay: A retrospective and toolkit

(2009) S RANGWALA   METHODS

New Superfamilies of Eukaryotic DNA Transposons and Their Internal Divisions

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

A systematic search and classification of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis suggests the existence of recently active MITE subfamilies

(2009) Akira Hikosaka et al.   MOLECULAR GENETICS AND GENOMICS

Impact of transposable elements on the organization and function of allopolyploid genomes

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes

(2009) M. Rho et al.   NUCLEIC ACIDS RESEARCH

Pack-MULEs Carry Functionality

(2009) N. A. Eckardt   PLANT CELL

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

(2009) K. Hanada et al.   PLANT CELL

Structure-based discovery and description of plant and animal Helitrons

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The polychromatic Helitron landscape of the maize genome

(2009) C. Du et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE

(2009) G. Yang et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

LINE dancing in the human genome: transposable elements and disease

(2009) Victoria P Belancio et al.   Genome Medicine

Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes

(2009) Carolina Bartolomé et al.   GENOME BIOLOGY

Identification of repeat structure in large genomes using repeat probability clouds

(2008) Wanjun Gu et al.   ANALYTICAL BIOCHEMISTRY

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

VisualRepbase: an interface for the study of occurrences of transposable element families

(2008) Sébastien Tempel et al.   BMC BIOINFORMATICS

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)

(2008) Thomas D Otto et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Automated paleontology of repetitive DNA with REANNOTATE

(2008) Vini Pereira   BMC GENOMICS

Computational prediction and molecular confirmation of Helitron transposons in the maize genome

(2008) Chunguang Du et al.   BMC GENOMICS

Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species

(2008) Hernan Lorenzi et al.   BMC GENOMICS

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements

(2008) E. S. Dolgin et al.   GENETICS

Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health

(2008) V. P. Belancio et al.   GENOME RESEARCH

Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus

(2008) D. A. Ray et al.   GENOME RESEARCH

Revisiting horizontal transfer of transposable elements in Drosophila

(2008) E L S Loreto et al.   HEREDITY

A universal classification of eukaryotic transposable elements implemented in Repbase

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

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Empirical comparison of ab initio repeat finding programs

(2008) S. Saha et al.   NUCLEIC ACIDS RESEARCH

Dual coding of siRNAs and miRNAs by plant transposable elements

(2008) J. Piriyapongsa et al.   RNA

Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences

(2008) Surya Saha et al.   Tropical Plant Biology

Bov-B-mobilized SINEs in vertebrate genomes

(2007) Konstantin P. Gogolevsky et al.   GENE