Immune genes are hotspots of shared positive selection across birds and mammals

A global analysis of selection at the avian MHC

(2018) Piotr Minias et al.   EVOLUTION

Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)

(2018) Joseph D Manthey et al.   Genome Biology and Evolution

Stress, cell senescence and organismal ageing

(2018) João Pedro de Magalhães et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Toll-Like Receptor Evolution in Birds: Gene Duplication, Pseudogenization, and Diversifying Selection

(2018) Hana Velová et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary history of vertebrate RNA viruses

(2018) Mang Shi et al.   NATURE

The rate of telomere loss is related to maximum lifespan in birds

(2018) Gianna M. Tricola et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transcriptome Analysis in Spleen Reveals Differential Regulation of Response to Newcastle Disease Virus in Two Chicken Lines

(2018) Jibin Zhang et al.   Scientific Reports

Multinucleotide mutations cause false inferences of lineage-specific positive selection

(2018) Aarti Venkat et al.   Nature Ecology & Evolution

Identification of generic and pathogen-specific cord blood monocyte transcriptomes reveals a largely conserved response in preterm and term newborn infants

(2017) Emma de Jong et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Immune Signaling Networks: Sources of Robustness and Constrained Evolvability during Coevolution

(2017) Edward C Schrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites

(2017) Emily R. Ebel et al.   PLoS Genetics

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

(2017) Jemma L. Geoghegan et al.   PLoS Pathogens

Avian Interferons and Their Antiviral Effectors

(2017) Diwakar Santhakumar et al.   Frontiers in Immunology

Transcriptional response to West Nile virus infection in the zebra finch ( Taeniopygia guttata )

(2017) Daniel J. Newhouse et al.   Royal Society Open Science

Comprehensive RNA-Seq Profiling to Evaluate the Sheep Mammary Gland Transcriptome in Response to Experimental Mycoplasma agalactiae Infection

(2017) Rohini Chopra-Dewasthaly et al.   PLoS One

Evolution of bird genomes-a transposon's-eye view

(2016) Aurélie Kapusta et al.   Annals of the New York Academy of Sciences

Survey of Global Genetic Diversity Within the Drosophila Immune System

(2016) Angela M. Early et al.   GENETICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Infection-specific phosphorylation of glutamyl-prolyl tRNA synthetase induces antiviral immunity

(2016) Eun-Young Lee et al.   NATURE IMMUNOLOGY

Thymus transcriptome reveals novel pathways in response to avian pathogenicEscherichia coliinfection

(2016) H. Sun et al.   POULTRY SCIENCE

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Viruses are a dominant driver of protein adaptation in mammals

(2016) David Enard et al.   eLife

Survey of Global Genetic Diversity Within the Drosophila Immune System

(2016) Angela M. Early et al.   GENETICS

Retinal transcriptome sequencing sheds light on the adaptation to nocturnal and diurnal lifestyles in raptors

(2016) Yonghua Wu et al.   Scientific Reports

Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria

(2016) Tuan M. Tran et al.   Scientific Reports

Long live FOXO: unraveling the role of FOXO proteins in aging and longevity

(2015) Rute Martins et al.   AGING CELL

Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens

(2015) Hongyan Sun et al.   BMC GENOMICS

A comparative analysis of host responses to avian influenza infection in ducks and chickens highlights a role for the interferon-induced transmembrane proteins in viral resistance

(2015) Jacqueline Smith et al.   BMC GENOMICS

Third Report on Chicken Genes and Chromosomes 2015

(2015) Michael Schmid et al.   CYTOGENETIC AND GENOME RESEARCH

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

The Avian Transcriptome Response to Malaria Infection

(2015) Elin Videvall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene-Wide Identification of Episodic Selection

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

PARP9-DTX3L ubiquitin ligase targets host histone H2BJ and viral 3C protease to enhance interferon signaling and control viral infection

(2015) Yong Zhang et al.   NATURE IMMUNOLOGY

Evolutionary insights into host–pathogen interactions from mammalian sequence data

(2015) Manuela Sironi et al.   NATURE REVIEWS GENETICS

Hidden costs of infection: Chronic malaria accelerates telomere degradation and senescence in wild birds

(2015) M. Asghar et al.   SCIENCE

Transcription Profiling of Malaria-Naïve and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge

(2015) Monica L. Rojas-Peña et al.   PLoS Neglected Tropical Diseases

Novel Pathways Revealed in Bursa of Fabricius Transcriptome in Response to Extraintestinal Pathogenic Escherichia coli (ExPEC) Infection

(2015) Hongyan Sun et al.   PLoS One

Integrative “Omic” Analysis of Experimental Bacteremia Identifies a Metabolic Signature That Distinguishes Human Sepsis from Systemic Inflammatory Response Syndromes

(2014) Raymond J. Langley et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Patterns of Positive Selection in Seven Ant Genomes

(2014) Julien Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Episodic Positive Selection in the Evolution of Avian Toll-Like Receptor Innate Immunity Genes

(2014) Catherine E. Grueber et al.   PLoS One

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Viruses and the DNA Damage Response: Activation and Antagonism

(2014) Micah A. Luftig   Annual Review of Virology

Comparative genomic data of the Avian Phylogenomics Project

(2014) Guojie Zhang et al.   GigaScience

The Evolutionary Genomics of Birds

(2013) Hans Ellegren   Annual Review of Ecology Evolution and Systematics

Molecular adaptation of telomere associated genes in mammals

(2013) Claire C Morgan et al.   BMC EVOLUTIONARY BIOLOGY

The phylogenetic distribution of ultraviolet sensitivity in birds

(2013) Anders Ödeen et al.   BMC EVOLUTIONARY BIOLOGY

Ambient temperature and nutritional stress influence fatty acid composition of structural and fuel lipids in Japanese quail (Coturnix japonica) tissues

(2013) Miriam Ben-Hamo et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Macroevolution of life-history traits in passerine birds: adaptation and phylogenetic inertia

(2013) Jason Pienaar et al.   ECOLOGY LETTERS

A Novel Recombinant Retrovirus in the Genomes of Modern Birds Combines Features of Avian and Mammalian Retroviruses

(2013) J. E. Henzy et al.   JOURNAL OF VIROLOGY

Evidence from a House Finch (Haemorhous mexicanus) Spleen Transcriptome for Adaptive Evolution and Biased Gene Conversion in Passerine Birds

(2013) Niclas Backström et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis

(2013) Feng Qian et al.   Viruses-Basel

Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross

(2013) Martin T. Ferris et al.   PLoS Pathogens

Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3

(2013) Miguel Alcaide et al.   PeerJ

Patterns of selection and polymorphism of innate immunity genes in bumblebees (Hymenoptera: Apidae)

(2012) J. S. Ellis et al.   GENETICA

The Evolution of Intron Size in Amniotes: A Role for Powered Flight?

(2012) Qu Zhang et al.   Genome Biology and Evolution

Viral immune modulators perturb the human molecular network by common and unique strategies

(2012) Andreas Pichlmair et al.   NATURE

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

Molecular Evolution of the Toll-Like Receptor Multigene Family in Birds

(2011) M. Alcaide 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

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

Advances in avian immunology—prospects for disease control: a review

(2010) Pete Kaiser   AVIAN PATHOLOGY

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Rad9 Is Required for B Cell Proliferation and Immunoglobulin Class Switch Recombination

(2010) Lili An et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Adaptive Divergence of Ancient Gene Duplicates in the Avian MHC Class II  

(2010) R. Burri et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Corticosterone, testosterone and life-history strategies of birds

(2010) M. Hau et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

Viral manipulation of DNA repair and cell cycle checkpoints

(2009) Mira S. Chaurushiya et al.   DNA REPAIR

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

From evolutionary genetics to human immunology: how selection shapes host defence genes

(2009) Luis B. Barreiro et al.   NATURE REVIEWS GENETICS

Energetics and longevity in birds

(2008) L. J. Furness et al.   AGE

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

Evolutionary Patterns of MHC Class II B in Owls and Their Implications for the Understanding of Avian MHC Evolution

(2008) Reto Burri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein kinase R reveals an evolutionary model for defeating viral mimicry

(2008) Nels C. Elde et al.   NATURE

Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors

(2008) Stefan Rothenburg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2008) A. Loytynoja et al.   SCIENCE

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics

Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures

(2007) R. E. Randall et al.   JOURNAL OF GENERAL VIROLOGY