Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

BLAST+: architecture and applications

(2009) Christiam Camacho 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

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

(2009) E Lerat   HEREDITY

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Empirical comparison of ab initio repeat finding programs

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