Viruses are a dominant driver of protein adaptation in mammals

Recent Positive Selection Has Acted on Genes Encoding Proteins with More Interactions within the Whole Human Interactome

(2015) Pierre Luisi et al.   Genome Biology and Evolution

Identification of Owl Monkey CD4 Receptors Broadly Compatible with Early-Stage HIV-1 Isolates

(2015) Nicholas R. Meyerson et al.   JOURNAL OF VIROLOGY

Gene-Wide Identification of Episodic Selection

(2015) Ben Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Global Mapping of Herpesvirus-Host Protein Complexes Reveals a Transcription Strategy for Late Genes

(2015) Zoe H. Davis et al.   MOLECULAR CELL

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats

(2015) Melinda Ng et al.   eLife

Molecular principles of human virus protein–protein interactions

(2014) Rachita Ramachandra Halehalli et al.   BIOINFORMATICS

Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life

(2014) Ralf Weßling et al.   Cell Host & Microbe

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

(2014) Thibaut Guirimand et al.   NUCLEIC ACIDS RESEARCH

Positive selection of primate genes that promote HIV-1 replication

(2014) Nicholas R. Meyerson et al.   VIROLOGY

SLiM: Simulating Evolution with Selection and Linkage

(2013) Philipp W. Messer   GENETICS

An Evolutionary Screen Highlights Canonical and Noncanonical Candidate Antiviral Genes within the Primate TRIM Gene Family

(2013) Ray Malfavon-Borja et al.   Genome Biology and Evolution

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Minke whale genome and aquatic adaptation in cetaceans

(2013) Hyung-Soon Yim et al.   NATURE GENETICS

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Bats are a major natural reservoir for hepaciviruses and pegiviruses

(2013) P.-L. Quan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frequent adaptation and the McDonald-Kreitman test

(2013) P. W. Messer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual Host-Virus Arms Races Shape an Essential Housekeeping Protein

(2013) Ann Demogines et al.   PLOS BIOLOGY

Evidence for ACE2-Utilizing Coronaviruses (CoVs) Related to Severe Acute Respiratory Syndrome CoV in Bats

(2012) A. Demogines et al.   JOURNAL OF VIROLOGY

A Trans-Specific Polymorphism in ZC3HAV1 Is Maintained by Long-Standing Balancing Selection and May Confer Susceptibility to Multiple Sclerosis

(2012) R. Cagliani et al.   MOLECULAR BIOLOGY AND EVOLUTION

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Evolutionary Reconstructions of the Transferrin Receptor of Caniforms Supports Canine Parvovirus Being a Re-emerged and Not a Novel Pathogen in Dogs

(2012) Jason T. Kaelber et al.   PLoS Pathogens

Structural Bases of Coronavirus Attachment to Host Aminopeptidase N and Its Inhibition by Neutralizing Antibodies

(2012) Juan Reguera et al.   PLoS Pathogens

A POSITIVELY SELECTED APOBEC3H HAPLOTYPE IS ASSOCIATED WITH NATURAL RESISTANCE TO HIV-1 INFECTION

(2011) Rachele Cagliani et al.   EVOLUTION

The selective footprints of viral pressures at the human RIG-I-like receptor family

(2011) Estelle Vasseur et al.   HUMAN MOLECULAR GENETICS

A Common Polymorphism in TLR3 Confers Natural Resistance to HIV-1 Infection

(2011) M. Sironi et al.   JOURNAL OF IMMUNOLOGY

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Global landscape of HIV–human protein complexes

(2011) Stefanie Jäger et al.   NATURE

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

Two-stepping through time: mammals and viruses

(2011) Nicholas R. Meyerson et al.   TRENDS IN MICROBIOLOGY

HIV-1 Capsid-Cyclophilin Interactions Determine Nuclear Import Pathway, Integration Targeting and Replication Efficiency

(2011) Torsten Schaller et al.   PLoS Pathogens

HPIDB - a unified resource for host-pathogen interactions

(2010) Ranjit Kumar et al.   BMC BIOINFORMATICS

Population Genetics of IFIH1: Ancient Population Structure, Local Selection, and Implications for Susceptibility to Type 1 Diabetes

(2010) M. Fumagalli et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Trajectories of Primate Genes Involved in HIV Pathogenesis

(2009) M. Ortiz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

The McDonald-Kreitman Test and Slightly Deleterious Mutations

(2008) J. Charlesworth et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein kinase R reveals an evolutionary model for defeating viral mimicry

(2008) Nels C. Elde et al.   NATURE

A model of evolution and structure for multiple sequence alignment

(2008) A. Loytynoja et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Positive Selection and Increased Antiviral Activity Associated with the PARP-Containing Isoform of Human Zinc-Finger Antiviral Protein

(2008) Julie A. Kerns et al.   PLoS Genetics

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

(2008) Matthew D. Dyer et al.   PLoS Pathogens

The moonlighting enzyme CD13: old and new functions to target

(2008) Paola Mina-Osorio   TRENDS IN MOLECULAR MEDICINE