Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens

Glucagon-like peptide-1 receptor agonists and diabetic retinopathy: nationwide cohort and Mendelian randomization studies

(2023) Deqiang Zheng et al.   BMC Medicine

Integrated metabolomics and lipidomics evaluate the alterations of flavor precursors in chicken breast muscle with white striping symptom

(2023) Fuli Kong et al.   Frontiers in Physiology

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

(2022) Tianliu Zhang et al.   BMC BIOLOGY

Assessment the effect of genomic selection and detection of selective signature in broilers

(2022) Xiaodong Tan et al.   POULTRY SCIENCE

Dominant changes in the breast muscle lipid profiles of broiler chickens with wooden breast syndrome revealed by lipidomics analyses

(2022) Ranran Liu et al.   Journal of Animal Science and Biotechnology

Meat quality of broiler chickens processed using electrical and controlled atmosphere stunning systems

(2022) Montana R. Riggs et al.   POULTRY SCIENCE

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait

(2021) Yun-Mei Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens

(2021) Juniper A. Lake et al.   Scientific Reports

Large-scale genomic analysis reveals the genetic cost of chicken domestication

(2021) Ming-Shan Wang et al.   BMC BIOLOGY

The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size

(2021) Kejun Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Serum Creatine Kinase as a Biomarker to Predict Wooden Breast in vivo for Chicken Breeding

(2021) Fuli Kong et al.   Frontiers in Physiology

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken

(2021) Siyuan Xing et al.   Frontiers in Genetics

Autoimmmune hepatitis

(2021) Benedetta Terziroli Beretta-Piccoli et al.   Cellular & Molecular Immunology

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

(2021) Xiaodong Tan et al.   Genes

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

(2020) Xunhe Huang et al.   BMC GENOMICS

863 genomes reveal the origin and domestication of chicken

(2020) Ming-Shan Wang et al.   CELL RESEARCH

miRNA–mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome

(2020) Yifan Liu et al.   Scientific Reports

New insights into the associations among feed efficiency, metabolizable efficiency traits and related QTL regions in broiler chickens

(2020) Wei Li et al.   Journal of Animal Science and Biotechnology

Genetics of adaptation in modern chicken

(2019) Saber Qanbari et al.   PLoS Genetics

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

(2019) Qiong Wang et al.   BMC GENOMICS

Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing

(2018) Muhammad L Aslam et al.   BMC GENETICS

Mapping QTL for white striping in relation to breast muscle yield and meat quality traits in broiler chickens

(2018) Eva Pampouille et al.   BMC GENOMICS

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils

(2018) Marcella Sabino et al.   BMC GENOMICS

Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals

(2018) Fabio Morgante et al.   HEREDITY

An intercross population study reveals genes associated with body size and plumage color in ducks

(2018) Zhengkui Zhou et al.   Nature Communications

Copy Number Variation in SOX6 Contributes to Chicken Muscle Development

(2018) Shudai Lin et al.   Genes

Accumulation of deleterious mutations in the domestic yak genome

(2018) X. Xie et al.   ANIMAL GENETICS

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

High doses of phytase on growth performance and apparent ileal amino acid digestibility of broilers fed diets with graded concentrations of digestible lysine

(2018) Carrie L Walk et al.   JOURNAL OF ANIMAL SCIENCE

A novel stopgain mutation c.G992A (p.W331X) in TACR3 gene was identified in nonobstructive azoospermia by targeted next-generation sequencing

(2018) Dongfeng Geng et al.   JOURNAL OF CLINICAL LABORATORY ANALYSIS

The optimum valine: lysine ratios on performance and carcass traits of male broilers based on different regression approaches

(2018) P S Agostini et al.   POULTRY SCIENCE

Phenotypic characteristic of junglefowl and chicken

(2018) T.T. DESTA   WORLDS POULTRY SCIENCE JOURNAL

An Evolutionary Genomic Perspective on the Breeding of Dwarf Chickens

(2017) Ming-Shan Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detection of genomic signatures of recent selection in commercial broiler chickens

(2016) Weixuan Fu et al.   BMC GENETICS

Genetic features of red and green junglefowls and relationship with Indonesian native chickens Sumatera and Kedu Hitam

(2016) Maria Ulfah et al.   BMC GENOMICS

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Genome-Wide Detection of Selective Signatures in Chicken through High Density SNPs

(2016) Zhuang Liu et al.   PLoS One

Expression and methylation of microsomal triglyceride transfer protein and acetyl-CoA carboxylase are associated with fatty liver syndrome in chicken

(2016) Zhen Liu et al.   POULTRY SCIENCE

Comparative population genomics reveals genetic basis underlying body size of domestic chickens

(2016) Ming-Shan Wang et al.   Journal of Molecular Cell Biology

Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression

(2015) J. Bowden et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

The Evolution of Animal Domestication

(2014) Greger Larson et al.   Annual Review of Ecology Evolution and Systematics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Growth, efficiency, and yield of commercial broilers from 1957, 1978, and 20051

(2014) M. J. Zuidhof et al.   POULTRY SCIENCE

Missense Mutations in SLC26A8, Encoding a Sperm-Specific Activator of CFTR, Are Associated with Human Asthenozoospermia

(2013) Thassadite Dirami et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A population genetics view of animal domestication

(2013) Greger Larson et al.   TRENDS IN GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6

(2011) Chung-Il An et al.   BMC DEVELOPMENTAL BIOLOGY

Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6

(2011) D. Quiat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

Definition, conservation and epigenetics of housekeeping and tissue-enriched genes

(2009) Xinwei She et al.   BMC GENOMICS

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

(2008) S. Kumar et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

(2008) W. M. Muir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken

(2008) Jonas Eriksson et al.   PLoS Genetics