Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life

(2016) Atma M. Ivancevic et al.   Genome Biology and Evolution

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

(2015) Hani Z. Girgis   BMC BIOINFORMATICS

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

DNA Transposons: Nature and Applications in Genomics

(2010) Martin Munoz-Lopez et al.   CURRENT GENOMICS

Molecular phylogeny and systematics of drosophila retrotransposons and retroviruses

(2009) L. N. Nefedova et al.   MOLECULAR BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

The opossum genome: Insights and opportunities from an alternative mammal

(2008) P. B. Samollow   GENOME RESEARCH