Comparative genomics reveals insights into avian genome evolution and adaptation

Postcranial Pneumaticity and Bone Structure in Two Clades of Neognath Birds

(2014) Sarah C. Gutzwiller et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

Convergent transcriptional specializations in the brains of humans and song-learning birds

(2014) A. R. Pfenning et al.   SCIENCE

Evidence for a single loss of mineralized teeth in the common avian ancestor

(2014) R. W. Meredith et al.   SCIENCE

Core and region-enriched networks of behaviorally regulated genes and the singing genome

(2014) O. Whitney et al.   SCIENCE

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

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

(2014) E. D. Jarvis et al.   SCIENCE

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment

(2014) Cai Li et al.   GigaScience

Comparative genomic data of the Avian Phylogenomics Project

(2014) Guojie Zhang et al.   GigaScience

Digital atlas of the zebra finch (Taeniopygia guttata) brain: A high-resolution photo atlas

(2013) Harvey J. Karten et al.   JOURNAL OF COMPARATIVE NEUROLOGY

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

Preservation of ovarian follicles reveals early evolution of avian reproductive behaviour

(2013) Xiaoting Zheng et al.   NATURE

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

(2013) Xiangjiang Zhan et al.   NATURE GENETICS

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

(2013) Yinhua Huang et al.   NATURE GENETICS

Reference-assisted chromosome assembly

(2013) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

(2013) M. D. Shapiro et al.   SCIENCE

Genetics of colouration in birds

(2013) Alexandre Roulin et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Genome of the Chinese tree shrew

(2013) Yu Fan et al.   Nature Communications

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

(2013) John A St John et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

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

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

Gene Duplication and the Evolution of Hemoglobin Isoform Differentiation in Birds

(2012) Michael T. Grispo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular ecology and adaptation of visual photopigments in craniates

(2012) WAYNE I. L. DAVIES et al.   MOLECULAR ECOLOGY

Gene duplication, genome duplication, and the functional diversification of vertebrate globins

(2012) Jay F. Storz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

(2012) G. Zhang et al.   SCIENCE

An Update of Wallace's Zoogeographic Regions of the World

(2012) B. G. Holt et al.   SCIENCE

Evolution of ultraviolet vision in the largest avian radiation - the passerines

(2011) Anders Ödeen et al.   BMC EVOLUTIONARY BIOLOGY

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Radiation and Functional Diversification of Alpha Keratins during Early Vertebrate Evolution

(2011) W. Vandebergh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-Genome Duplications Spurred the Functional Diversification of the Globin Gene Superfamily in Vertebrates

(2011) Federico G. Hoffmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Ensembl 2012

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

Recent Loss of Vitamin C Biosynthesis Ability in Bats

(2011) Jie Cui et al.   PLoS One

Candidate genes for carotenoid coloration in vertebrates and their expression profiles in the carotenoid-containing plumage and bill of a wild bird

(2011) N. Walsh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

From snout to beak: the loss of teeth in birds

(2011) Antoine Louchart et al.   TRENDS IN ECOLOGY & EVOLUTION

Characterizing complex structural variation in germline and somatic genomes

(2011) Aaron R. Quinlan et al.   TRENDS IN GENETICS

Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

(2011) Alexander Suh et al.   Nature Communications

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

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

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

(2010) Christian Arnold et al.   Algorithms for Molecular Biology

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

Genomic organization and molecular phylogenies of the beta (β) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution

(2010) Matthew J Greenwold et al.   BMC EVOLUTIONARY BIOLOGY

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Progressive Pseudogenization: Vitamin C Synthesis and Its Loss in Bats

(2010) Jie Cui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lineage-Specific Patterns of Functional Diversification in the  - and  -Globin Gene Families of Tetrapod Vertebrates

(2010) F. G. Hoffmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Bone density and the lightweight skeletons of birds

(2010) E. R. Dumont   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

Vertebrate pigmentation: from underlying genes to adaptive function

(2010) Joanna K. Hubbard et al.   TRENDS IN GENETICS

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates

(2010) Noa Sela et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

(2009) Benoit Nabholz et al.   BMC EVOLUTIONARY BIOLOGY

A novel neural-specific BMP antagonist, Brorin-like, of the Chordin family

(2009) Hiroyuki Miwa et al.   FEBS LETTERS

Independent Mammalian Genome Contractions Following the KT Boundary

(2009) Mina Rho et al.   Genome Biology and Evolution

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

(2009) D. M. Larkin et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Forty keratin-associated β-proteins (β-keratins) form the hard layers of scales, claws, and adhesive pads in the green anole lizard, Anolis carolinensis

(2009) Luisa Dalla Valle et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

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

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

(2009) C. M. Wade et al.   SCIENCE

Speciation as an active force in promoting genetic evolution

(2009) Chris Venditti et al.   TRENDS IN ECOLOGY & EVOLUTION

A whole-genome assembly of the domestic cow, Bos taurus

(2009) Aleksey V Zimin et al.   GENOME BIOLOGY

Transposable elements as drivers of genomic and biological diversity in vertebrates

(2008) Astrid Böhne et al.   CHROMOSOME RESEARCH

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

Quantifying avian sexual dichromatism: a comparison of methods

(2008) J. K. Armenta et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Genome Size Reduction in the Chicken Has Involved Massive Loss of Ancestral Protein-Coding Genes

(2008) A. L. Hughes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid Rates of Lineage-Specific Gene Duplication and Deletion in the α-Globin Gene Family

(2008) Federico G. Hoffmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Molecular Mapping of Movement-Associated Areas in the Avian Brain: A Motor Theory for Vocal Learning Origin

(2008) Gesa Feenders et al.   PLoS One

Birdsong “Transcriptomics”: Neurochemical Specializations of the Oscine Song System

(2008) Peter V. Lovell et al.   PLoS One