An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

(2014) Priscilla Turelli et al.   GENOME RESEARCH

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Minimal Active Human SVA Retrotransposon Requires Only the 5'-Hexamer and Alu-Like Domains

(2012) D. C. Hancks et al.   MOLECULAR AND CELLULAR BIOLOGY

Latent Regulatory Potential of Human-Specific Repetitive Elements

(2012) Michelle C. Ward et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gene Isoform Specificity through Enhancer-Associated Antisense Transcription

(2012) Courtney S. Onodera et al.   PLoS One

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolution of retroelements and tandem zinc finger genes

(2011) J. H. Thomas et al.   GENOME RESEARCH

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Predicting DNA recognition by Cys2His2 zinc finger proteins

(2008) Anton V. Persikov et al.   BIOINFORMATICS

Enhanced apoptosis during early neuronal differentiation in mouse ES cells with autosomal imbalance

(2008) Yoshiteru Kai et al.   CELL RESEARCH

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY