A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii’s Last Remaining Crow Species

The importance of non-academic coauthors in bridging the conservation genetics gap

(2018) Meghan Britt et al.   BIOLOGICAL CONSERVATION

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

(2017) Matthias H. Weissensteiner et al.   GENOME RESEARCH

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

(2017) Jonas Korlach et al.   GigaScience

Bridging the conservation genetics gap by identifying barriers to implementation for conservation practitioners

(2017) Helen R. Taylor et al.   Global Ecology and Conservation

Roles of Toll-like receptors 2 and 6 in the inflammatory response to Mycoplasma gallisepticum infection in DF-1 cells and in chicken embryos

(2016) Wei Tian et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Genomics advances the study of inbreeding depression in the wild

(2016) Marty Kardos et al.   Evolutionary Applications

TLR4 and TLR21 expression, MIF, IFN-β, MD-2, CD14 activation, and sIgA production in chickens administered with EFAL41 strain challenged with Campylobacter jejuni

(2016) Karaffová V. et al.   FOLIA MICROBIOLOGICA

Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs

(2016) Jamie A. Ivy et al.   JOURNAL OF HEREDITY

Discovery of species-wide tool use in the Hawaiian crow

(2016) Christian Rutz et al.   NATURE

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Inbreeding depression across the lifespan in a wild mammal population

(2016) Jisca Huisman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

(2016) Brittany A. Garner et al.   TRENDS IN ECOLOGY & EVOLUTION

Understanding Inbreeding Depression, Purging, and Genetic Rescue

(2016) Philip W. Hedrick et al.   TRENDS IN ECOLOGY & EVOLUTION

Early Duplication of a Single MHC IIB Locus Prior to the Passerine Radiations

(2016) John A. Eimes et al.   PLoS One

Splenic gene expression profiling in White Leghorn layer inoculated with theSalmonella entericaserovar Enteritidis

(2015) Guixian Wu et al.   ANIMAL GENETICS

Activation of Toll-like receptor 3 inhibits Marek’s disease virus infection in chicken embryo fibroblast cells

(2015) Xuming Hu et al.   ARCHIVES OF VIROLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Effects of inbreeding and parental incubation on captive breeding success in Hawaiian crows

(2015) Paquita E.A. Hoeck et al.   BIOLOGICAL CONSERVATION

The influence of captive breeding management on founder representation and inbreeding in the ‘Alalā, the Hawaiian crow

(2015) Philip W. Hedrick et al.   CONSERVATION GENETICS

Toll-like receptor diversity in 10 threatened bird species: relationship with microsatellite heterozygosity

(2015) Catherine E. Grueber et al.   CONSERVATION GENETICS

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

Patterns of evolution of MHC class II genes of crows (Corvus) suggest trans-species polymorphism

(2015) John A. Eimes et al.   PeerJ

Comparative genomics for biodiversity conservation

(2015) Catherine E. Grueber   Computational and Structural Biotechnology Journal

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

First evidence of independent pseudogenization of Toll-like receptor 5 in passerine birds

(2014) Hana Bainová et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Genetic depletion at adaptive but not neutral loci in an endangered bird species

(2014) Stefanie A. Hartmann et al.   MOLECULAR ECOLOGY

Technology: The $1,000 genome

(2014) Erika Check Hayden   NATURE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

Upregulation of chicken TLR4, TLR15 and MyD88 in heterophils and monocyte-derived macrophages stimulated with Eimeria tenella in vitro

(2013) Zuoyong Zhou et al.   EXPERIMENTAL PARASITOLOGY

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

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

A comparison of pedigree- and DNA-based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie-chicken

(2013) Susan C. Hammerly et al.   MOLECULAR ECOLOGY

Conservation Genomics of Threatened Animal Species

(2013) Cynthia C. Steiner et al.   Annual Review of Animal Biosciences

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

(2012) M. Kearse et al.   BIOINFORMATICS

Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

(2012) Irem Sepil et al.   BMC EVOLUTIONARY BIOLOGY

Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)

(2012) Muhammad L Aslam et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Seed dispersal by a captive corvid: the role of the ‘Alalā (Corvus hawaiiensis) in shaping Hawai‘i's plant communities

(2012) Susan Culliney et al.   ECOLOGICAL APPLICATIONS

Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations

(2012) M. Ferenčaković et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Treatment with Ligands for Toll-Like Receptors 2 and 5 Induces a Mixed T-helper 1- and 2-Like Response in Chicken Splenocytes

(2012) Michael St. Paul et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Variation at Innate Immunity Toll-Like Receptor Genes in a Bottlenecked Population of a New Zealand Robin

(2012) Catherine E. Grueber et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

(2011) Magdalena Zagalska-Neubauer et al.   BMC EVOLUTIONARY BIOLOGY

Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

(2011) Daniel P Howrigan et al.   BMC GENOMICS

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

(2011) M. Alcaide et al.   MOLECULAR BIOLOGY AND EVOLUTION

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Toll-like receptor 2 type 1 and type 2 polymorphisms in different chicken breeds

(2011) W. K. Ruan et al.   POULTRY SCIENCE

Challenges and opportunities of genetic approaches to biological conservation

(2010) Richard Frankham   BIOLOGICAL CONSERVATION

Gene duplication and fragmentation in the zebra finch major histocompatibility complex

(2010) Christopher N Balakrishnan et al.   BMC BIOLOGY

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Genomic Runs of Homozygosity Record Population History and Consanguinity

(2010) Mirna Kirin et al.   PLoS One

Conservation genetics in transition to conservation genomics

(2010) N. Joop Ouborg et al.   TRENDS IN GENETICS

Evolution of primate orphan proteins

(2009) Macarena Toll-Riera et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The value of avian genomics to the conservation of wildlife

(2009) Michael N Romanov et al.   BMC GENOMICS

The avian Toll-Like receptor pathway—Subtle differences amidst general conformity

(2009) Paul Cormican et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Runs of Homozygosity in European Populations

(2008) Ruth McQuillan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Evolution of the chicken Toll-like receptor gene family: A story of gene gain and gene loss

(2008) Nicholas D Temperley et al.   BMC GENOMICS

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