Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

(2018) G. P. Tiley et al.   BMC GENOMICS

Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

(2018) Chien-Yueh Lee et al.   GigaScience

Population genomic data reveal genes related to important traits of quail

(2018) Yan Wu et al.   GigaScience

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

What makes the Sino-Himalayan mountains the major diversity hotspots for pheasants?

(2017) Tianlong Cai et al.   JOURNAL OF BIOGEOGRAPHY

Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data

(2017) Ning Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts

(2017) Robin van der Lee et al.   NUCLEIC ACIDS RESEARCH

How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

(2017) Peter A. Hosner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

(2017) Sushma Reddy et al.   SYSTEMATIC BIOLOGY

Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes

(2016) Matthieu Deschamps et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling

(2016) Ning Wang et al.   JOURNAL OF BIOGEOGRAPHY

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Structural basis of complement membrane attack complex formation

(2016) Marina Serna et al.   Nature Communications

AGOUTI: improving genome assembly and annotation using transcriptome data

(2016) Simo V. Zhang et al.   GigaScience

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

(2015) Krystyna Nadachowska-Brzyska et al.   CURRENT BIOLOGY

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution

(2015) Alison E. Wright et al.   MOLECULAR ECOLOGY

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Sexual selection drives evolution and rapid turnover of male gene expression

(2015) Peter W. Harrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

(2015) J. Cracraft et al.   SCIENCE

A new time tree reveals Earth historys imprint on the evolution of modern birds

(2015) S. Claramunt et al.   Science Advances

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

NLRC3, a Member of the NLR Family of Proteins, Is a Negative Regulator of Innate Immune Signaling Induced by the DNA Sensor STING

(2014) Lu Zhang et al.   IMMUNITY

Testing the Hamilton-Zuk Hypothesis: Past, Present, and Future

(2014) S. L. Balenger et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection

(2014) Benjamin Redelings   MOLECULAR BIOLOGY AND EVOLUTION

Incongruence among different mitochondrial regions: A case study using complete mitogenomes

(2014) Kelly A. Meiklejohn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

(2014) K. Sun et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

(2014) Rebecca T. Kimball et al.   PeerJ

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

(2013) Yinhua Huang et al.   NATURE GENETICS

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

(2013) Ning Wang et al.   PLoS One

Regulation of bone and cartilage development by network between BMP signalling and transcription factors

(2012) R. Nishimura et al.   JOURNAL OF BIOCHEMISTRY

Wnt Signaling in Skin Development, Homeostasis, and Disease

(2012) X. Lim et al.   Cold Spring Harbor Perspectives in Biology

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

(2012) Ruibang Luo et al.   GigaScience

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the phasianidae

(2010) Yong-Yi Shen et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes

(2010) X.-Z. Kan et al.   GENETICS AND MOLECULAR RESEARCH

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

(2010) Robert Ekblom et al.   Genome Biology and Evolution

Metaves, Mirandornithes, Strisores and other novelties - a critical review of the higher-level phylogeny of neornithine birds

(2010) Gerald Mayr   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes

(2010) Amber J. Bonilla et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Genome-Wide Identification of Susceptibility Alleles for Viral Infections through a Population Genetics Approach

(2010) Matteo Fumagalli et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

North American ice-sheet dynamics and the onset of 100,000-year glacial cycles

(2008) R. Bintanja et al.   NATURE

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics