Avian diversity: Speciation, macroevolution, and ecological function

JA Tobias, J Ottenburghs… - Annual Review of Ecology …, 2020 - annualreviews.org
The origin, distribution, and function of biological diversity are fundamental themes of
ecology and evolutionary biology. Research on birds has played a major role in the history …

Genetic variation and the de novo assembly of human genomes

MJP Chaisson, RK Wilson, EE Eichler - Nature Reviews Genetics, 2015 - nature.com
The discovery of genetic variation and the assembly of genome sequences are both
inextricably linked to advances in DNA-sequencing technology. Short-read massively …

[HTML][HTML] Towards complete and error-free genome assemblies of all vertebrate species

A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti… - Nature, 2021 - nature.com
High-quality and complete reference genome assemblies are fundamental for the
application of genomics to biology, disease, and biodiversity conservation. However, such …

Dense sampling of bird diversity increases power of comparative genomics

S Feng, J Stiller, Y Deng, J Armstrong, QI Fang… - Nature, 2020 - nature.com
Whole-genome sequencing projects are increasingly populating the tree of life and
characterizing biodiversity–. Sparse taxon sampling has previously been proposed to …

[HTML][HTML] Progressive Cactus is a multiple-genome aligner for the thousand-genome era

J Armstrong, G Hickey, M Diekhans, IT Fiddes… - Nature, 2020 - nature.com
New genome assemblies have been arriving at a rapidly increasing pace, thanks to
decreases in sequencing costs and improvements in third-generation sequencing …

A cortex-like canonical circuit in the avian forebrain

M Stacho, C Herold, N Rook, H Wagner, M Axer… - Science, 2020 - science.org
INTRODUCTION For more than a century, the avian forebrain has been a riddle for
neuroscientists. Birds demonstrate exceptional cognitive abilities comparable to those of …

[HTML][HTML] Platypus and echidna genomes reveal mammalian biology and evolution

Y Zhou, L Shearwin-Whyatt, J Li, Z Song, T Hayakawa… - Nature, 2021 - nature.com
Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians
(marsupial and eutherian animals) and provide key insights into mammalian evolution 1, 2 …

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

NA O'Leary, MW Wright, JR Brister, S Ciufo… - Nucleic acids …, 2016 - academic.oup.com
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains
and curates a publicly available database of annotated genomic, transcript, and protein …

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

ED Jarvis, S Mirarab, AJ Aberer, B Li, P Houde, C Li… - Science, 2014 - science.org
To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …

Uniclust databases of clustered and deeply annotated protein sequences and alignments

M Mirdita, L Von Den Driesch, C Galiez… - Nucleic acids …, 2017 - academic.oup.com
We present three clustered protein sequence databases, Uniclust90, Uniclust50, Uniclust30
and three databases of multiple sequence alignments (MSAs), Uniboost10, Uniboost20 and …