An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics

FOXQ1-mediated SIRT1 upregulation enhances stemness and radio-resistance of colorectal cancer cells and restores intestinal microbiota function by promoting β-catenin nuclear translocation

(2022) Mei Yang et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

A Deletion Upstream of SOX10 Causes Light Yellow Plumage Colour in Chicken

(2022) Tao Zhu et al.   Genes

HNF4A modulates glucocorticoid action in the liver

(2022) A. Louise Hunter et al.   Cell Reports

The crest phenotype in domestic chicken is caused by a 197 bp duplication in the intron of HOXC10

(2021) Jingyi Li et al.   G3-Genes Genomes Genetics

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research

(2021) Colin Kern et al.   Nature Communications

Effect of age at first egg on reproduction performance and characterization of the hypothalamo–pituitary–gonadal axis in chickens

(2021) Y.G. Tan et al.   POULTRY SCIENCE

Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy

(2021) Ruifei Yang et al.   GigaScience

Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens

(2021) Jingyi Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

(2021) Zhangyuan Pan et al.   Nature Communications

Incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets

(2021) Carla Márquez-Luna et al.   Nature Communications

Quantitative Proteomics of Clinically Relevant Drug-Metabolizing Enzymes and Drug Transporters and Their Inter-correlations in the Human Small Intestine

(2020) Narciso Couto et al.   DRUG METABOLISM AND DISPOSITION

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

(2020) Lingzhao Fang et al.   GENOME RESEARCH

Parallel Genetic Origin of Foot Feathering in Birds

(2020) Chiara Bortoluzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken

(2020) Jingyi Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues

(2020) M. M. Halstead et al.   Scientific Reports

From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases

(2020) Eddie Cano-Gamez et al.   Frontiers in Genetics

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human

(2020) Shuli Liu et al.   BMC BIOLOGY

863 genomes reveal the origin and domestication of chicken

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

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line

(2020) Ganrea Chanthavixay et al.   Frontiers in Genetics

Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits

(2020) Yuzhe Wang et al.   Communications Biology

The chicken model organism for epigenomic research

(2020) Tasnim H. BEACON et al.   GENOME

Dexamethasone downregulates expression of several genes encoding orphan nuclear receptors that are important to steroidogenesis in stallion testes

(2019) Raul Valdez et al.   JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

(2019) Marta Farré et al.   GENOME RESEARCH

Transcription factors IRF8 and PU.1 are required for follicular B cell development and BCL6-driven germinal center responses

(2019) Hongsheng Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetics of adaptation in modern chicken

(2019) Saber Qanbari et al.   PLoS Genetics

Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

(2019) Lingzhao Fang et al.   BMC BIOLOGY

A resource-efficient tool for mixed model association analysis of large-scale data

(2019) Longda Jiang et al.   NATURE GENETICS

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

(2019) Sylvain Foissac et al.   BMC BIOLOGY

The RNA-binding protein, ZC3H14, is required for proper poly(A) tail length control, expression of synaptic proteins, and brain function in mice

(2017) Jennifer Rha et al.   HUMAN MOLECULAR GENETICS

Neuroblastoma is composed of two super-enhancer-associated differentiation states

(2017) Tim van Groningen et al.   NATURE GENETICS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Factors affecting adipose tissue development in chickens: A review

(2017) Guoqing Wang et al.   POULTRY SCIENCE

Association of SNP rs80659072 in the ZRS with polydactyly in Beijing You chickens

(2017) Qin Chu et al.   PLoS One

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

(2016) Martin Oti et al.   BMC GENOMICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Functional annotation and biological interpretation of proteomics data

(2015) Carolina M. Carnielli et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens

(2015) Hongyan Sun et al.   BMC GENOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

ARID3B Directly Regulates Ovarian Cancer Promoting Genes

(2015) Alexander Bobbs et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

(2014) Chungang Feng et al.   PLoS Genetics

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Tissue-Specific Cadherin CDH17 Is a Useful Marker of Gastrointestinal Adenocarcinomas With Higher Sensitivity Than CDX2

(2012) Nicole C. Panarelli et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10

(2011) Ulrika Gunnarsson et al.   Pigment Cell & Melanoma Research

Genomic Regions Associated with Dermal Hyperpigmentation, Polydactyly and Other Morphological Traits in the Silkie Chicken

(2010) B. Dorshorst et al.   JOURNAL OF HEREDITY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

HIF-Prolyl Hydroxylases in the Rat Kidney

(2009) Johannes Schödel et al.   AMERICAN JOURNAL OF PATHOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Structure and function of KH domains

(2008) Roberto Valverde et al.   FEBS Journal

A polymorphism of the metabotropic glutamate receptor mGluR7 (GRM7) gene is associated with schizophrenia

(2008) Tsuyuka Ohtsuki et al.   SCHIZOPHRENIA RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY