Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors

Tracking the Near Eastern origins and European dispersal of the western house mouse

(2020) Thomas Cucchi et al.   Scientific Reports

Retroviral Restriction Factors and Their Viral Targets: Restriction Strategies and Evolutionary Adaptations

(2020) Guney Boso et al.   Microorganisms

Distribution of endogenous gammaretroviruses and variants of the Fv1 restriction gene in individual mouse strains and strain subgroups

(2019) Matthew Skorski et al.   PLoS One

Ancient evolutionary origin and positive selection of the retroviral restriction factor Fv1 in muroid rodents

(2018) Guney Boso et al.   JOURNAL OF VIROLOGY

Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

(2018) Steven Weaver et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary journey of the retroviral restriction gene Fv1

(2018) George R. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recombinant Origins of Pathogenic and Nonpathogenic Mouse Gammaretroviruses with Polytropic Host Range

(2017) Devinka Bamunusinghe et al.   JOURNAL OF VIROLOGY

Sequence Diversity, Intersubgroup Relationships, and Origins of the Mouse Leukemia Gammaretroviruses of Laboratory and Wild Mice

(2016) Devinka Bamunusinghe et al.   JOURNAL OF VIROLOGY

Selective sweeps versus introgression - population genetic dynamics of the murine leukemia virus receptor Xpr1 in wild populations of the house mouse (Mus musculus)

(2015) Natascha Hasenkamp et al.   BMC EVOLUTIONARY BIOLOGY

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evolution of the Retroviral Restriction Gene Fv1: Inhibition of Non-MLV Retroviruses

(2014) Melvyn W. Yap et al.   PLoS Pathogens

Pushing the endogenous envelope

(2013) J. E. Henzy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Inorganic Phosphate Export by the Retrovirus Receptor XPR1 in Metazoans

(2013) Donatella Giovannini et al.   Cell Reports

Evolution of different antiviral strategies in wild mouse populations exposed to different gammaretroviruses

(2013) Christine A. Kozak   Current Opinion in Virology

Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents

(2013) Daniel L. Halligan 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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Profound Amplification of Pathogenic Murine Polytropic Retrovirus Release from Coinfected Cells

(2012) K. Rosenke et al.   JOURNAL OF VIROLOGY

Second site mutation in the virus envelope expands the host range of a cytopathic variant of Moloney murine leukemia virus

(2012) John Ferrarone et al.   VIROLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Subspecific origin and haplotype diversity in the laboratory mouse

(2011) Hyuna Yang et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Evolution of Functional and Sequence Variants of the Mammalian XPR1 Receptor for Mouse Xenotropic Gammaretroviruses and the Human-Derived Retrovirus XMRV

(2010) Y. Yan et al.   JOURNAL OF VIROLOGY

The mouse "xenotropic" gammaretroviruses and their XPR1 receptor

(2010) Christine A Kozak   Retrovirology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene Fv1 in the genus Mus

(2009) Y. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Six host range variants of the xenotropic/polytropic gammaretroviruses define determinants for entry in the XPR1 cell surface receptor

(2009) Yuhe Yan et al.   Retrovirology

Novel Postentry Resistance to AKV Ecotropic Mouse Gammaretroviruses in the African Pygmy Mouse, Mus minutoides

(2008) Y. Yan et al.   JOURNAL OF VIROLOGY

Mobilization of Endogenous Retroviruses in Mice after Infection with an Exogenous Retrovirus

(2008) L. H. Evans et al.   JOURNAL OF VIROLOGY