Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3

(2014) Derrick J. Zwickl et al.   SYSTEMATIC BIOLOGY

Role of DNA secondary structures in fragile site breakage along human chromosome 10

(2013) Laura W. Dillon et al.   HUMAN MOLECULAR GENETICS

Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion

(2013) Julie Jacquemin et al.   Molecular Plant

Multilocus estimation of divergence times and ancestral effective population sizes ofOryzaspecies and implications for the rapid diversification of the genus

(2013) Xin-Hui Zou et al.   NEW PHYTOLOGIST

Molecular and Fossil Evidence on the Origin of Angiosperms

(2012) James A. Doyle   Annual Review of Earth and Planetary Sciences

Complete nucleotide sequence of rose yellow vein virus, a member of the family Caulimoviridae having a novel genome organization

(2012) Dimitre Mollov et al.   ARCHIVES OF VIROLOGY

Endogenous retroviruses in mammals: An emerging picture of how ERVs modify expression of adjacent genes

(2012) Luke Isbel et al.   BIOESSAYS

Phylogeny and biogeography in Solanaceae, Verbenaceae and Bignoniaceae: a comparison of continental and intercontinental diversification patterns

(2012) Richard G. Olmstead   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance

(2012) J. Li et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Endogenous viruses: insights into viral evolution and impact on host biology

(2012) Cédric Feschotte et al.   NATURE REVIEWS GENETICS

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

(2012) Grégory Carrier et al.   PLoS One

Paleovirology and virally derived immunity

(2012) Amr Aswad et al.   TRENDS IN ECOLOGY & EVOLUTION

Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A

(2011) Todd S. Macfarlan et al.   GENES & DEVELOPMENT

Biogeography of Nicotiana section Suaveolentes (Solanaceae) reveals geographical tracks in arid Australia

(2011) Pauline Y. Ladiges et al.   JOURNAL OF BIOGEOGRAPHY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Oldest Known Eucalyptus Macrofossils Are from South America

(2011) María A. Gandolfo et al.   PLoS One

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

(2011) Matthias Zytnicki et al.   PLoS One

Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes

(2011) Sotaro Chiba et al.   PLoS Pathogens

Taming of the shrewd: novel eukaryotic genes from RNA viruses

(2010) Eugene V Koonin   BMC BIOLOGY

Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes

(2010) H. Liu et al.   JOURNAL OF VIROLOGY

Evolution of Endogenous Sequences of Banana Streak Virus: What Can We Learn from Banana (Musa sp.) Evolution?

(2010) P. Gayral et al.   JOURNAL OF VIROLOGY

DNA resection in eukaryotes: deciding how to fix the break

(2010) Pablo Huertas   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The classification and nomenclature of endogenous viruses of the family Caulimoviridae

(2009) Andrew D. W. Geering et al.   ARCHIVES OF VIROLOGY

Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance

(2009) Christophe Bertsch et al.   Biology Direct

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

(2009) Carla J. Cohen et al.   GENE

Classification and nomenclature of endogenous retroviral sequences (ERVs)

(2009) Jonas Blomberg et al.   GENE

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

(2009) Liang Tang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene

(2009) A. Dupressoir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

(2009) Eduard Kejnovsky et al.   TRENDS IN ECOLOGY & EVOLUTION

Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

(2009) Jan F. Kreuze et al.   VIROLOGY

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution

(2008) R. J. Gifford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA