Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode of Caulimoviridae

The paradox of HBV evolution as revealed from a 16th century mummy

(2018) Zoe Patterson Ross et al.   PLoS Pathogens

Marine origin of retroviruses in the early Palaeozoic Era

(2017) Pakorn Aiewsakun et al.   Nature Communications

Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences

(2017) Sunlu Chen et al.   PLoS Pathogens

Phylogenetic rooting using minimal ancestor deviation

(2017) Fernando Domingues Kümmel Tria et al.   Nature Ecology & Evolution

Field Guide to Plant Model Systems

(2016) Caren Chang et al.   CELL

Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses

(2016) Jennifer A. Dill et al.   JOURNAL OF VIROLOGY

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Draft genome of the living fossil Ginkgo biloba

(2016) Rui Guan et al.   GigaScience

An Exploration into Fern Genome Space

(2015) Paul G. Wolf et al.   Genome Biology and Evolution

Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes

(2015) Arcady R. Mushegian et al.   VIROLOGY

Endogenous viruses: Connecting recent and ancient viral evolution

(2015) Pakorn Aiewsakun et al.   VIROLOGY

Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

(2014) K. Brown et al.   JOURNAL OF VIROLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus

(2014) Ryosuke Yasaka et al.   PLoS One

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

(2014) C. Gilbert et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2014) Andrew D. W. Geering et al.   Nature Communications

Early Mesozoic Coexistence of Amniotes and Hepadnaviridae

(2014) Alexander Suh et al.   PLoS Genetics

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

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

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

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Broad-scale phylogenomics provides insights into retrovirus-host evolution

(2013) A. Hayward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation

(2013) Cécile Esnault et al.   PLoS Genetics

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

(2012) Cédric Feschotte et al.   NATURE REVIEWS GENETICS

Hemisphere-scale differences in conifer evolutionary dynamics

(2012) A. B. Leslie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Extreme Case of Plant–Insect Codiversification: Figs and Fig-Pollinating Wasps

(2012) Astrid Cruaud et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Paleovirology and virally derived immunity

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

LINE-1 Elements in Structural Variation and Disease

(2011) Christine R. Beck et al.   Annual Review of Genomics and Human Genetics

Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

(2010) Clément Gilbert et al.   PLOS BIOLOGY

Paleovirology—Modern Consequences of Ancient Viruses

(2010) Michael Emerman et al.   PLOS BIOLOGY

Endogenous Viral Elements in Animal Genomes

(2010) Aris Katzourakis et al.   PLoS Genetics

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

(2009) Carlos Llorens et al.   Biology Direct

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

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

A Single Banana Streak Virus Integration Event in the Banana Genome as the Origin of Infectious Endogenous Pararetrovirus

(2008) P. Gayral et al.   JOURNAL OF VIROLOGY