Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens

Copy number variation in the genomes of domestic animals

(2012) A. Clop et al.   ANIMAL GENETICS

A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method

(2012) Y. Wang et al.   ANIMAL GENETICS

Copy number variations identified in the chicken using a 60K SNP BeadChip

(2012) X. Jia et al.   ANIMAL GENETICS

NELL-1 increases pre-osteoblast mineralization using both phosphate transporter Pit1 and Pit2

(2012) Catherine M. Cowan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Disease gene identification strategies for exome sequencing

(2012) Christian Gilissen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Gastrocnemius transcriptome analysis reveals domestication induced gene expression changes between wild and domestic chickens

(2012) Qinghe Li et al.   GENOMICS

Chicken domestication: an updated perspective based on mitochondrial genomes

(2012) Y-W Miao et al.   HEREDITY

Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders

(2012) Bahareh Rabbani et al.   JOURNAL OF HUMAN GENETICS

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

(2012) K. A. Dittmar et al.   MOLECULAR AND CELLULAR BIOLOGY

Polymorphisms of the pro-opiomelanocortin and agouti-related protein genes and their association with chicken production traits

(2012) Yichun Bai et al.   MOLECULAR BIOLOGY REPORTS

Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in the silkworm, Bombyx mori

(2012) Xiaodong Xie et al.   MOLECULAR BIOLOGY REPORTS

Analyses of pig genomes provide insight into porcine demography and evolution

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

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

(2012) Martin G. Elferink et al.   PLoS One

The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin

(2012) Yanqiang Wang et al.   PLoS One

Selection Signature Analysis Implicates the PC1/PCSK1 Region for Chicken Abdominal Fat Content

(2012) Hui Zhang et al.   PLoS One

Differential Gene Expression from Genome-Wide Microarray Analyses Distinguishes Lohmann Selected Leghorn and Lohmann Brown Layers

(2012) Christin Habig et al.   PLoS One

Allelic Variation and Differential Expression of the mSIN3A Histone Deacetylase Complex Gene Arid4b Promote Mammary Tumor Growth and Metastasis

(2012) Scott F. Winter et al.   PLoS Genetics

The Chicken Frizzle Feather Is Due to an α-Keratin (KRT75) Mutation That Causes a Defective Rachis

(2012) Chen Siang Ng et al.   PLoS Genetics

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility

(2012) Freyja Imsland et al.   PLoS Genetics

A Sexual Ornament in Chickens Is Affected by Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication

(2012) Martin Johnsson et al.   PLoS Genetics

Human Genome Sequencing in Health and Disease

(2011) Claudia Gonzaga-Jauregui et al.   Annual Review of Medicine

Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

(2011) Hindrik HD Kerstens et al.   BMC GENOMICS

Targeted enrichment of genomic DNA regions for next-generation sequencing

(2011) F. Mertes et al.   Briefings in Functional Genomics

NELL-1 binds to APR3 affecting human osteoblast proliferation and differentiation

(2011) Xuan Zou et al.   FEBS LETTERS

Gene Duplication of endothelin 3 Is Closely Correlated with the Hyperpigmentation of the Internal Organs ( Fibromelanosis ) in Silky Chickens

(2011) Ai Shinomiya et al.   GENETICS

Revisiting Mendelian disorders through exome sequencing

(2011) Chee-Seng Ku et al.   HUMAN GENETICS

Association of Mx1 Asn631 variant alleles with reductions in morbidity, early mortality, viral shedding, and cytokine responses in chickens infected with a highly pathogenic avian influenza virus

(2011) Sandra J. Ewald et al.   IMMUNOGENETICS

What can exome sequencing do for you?

(2011) J. Majewski et al.   JOURNAL OF MEDICAL GENETICS

Novel SNPs in the PRDM16 gene and their associations with performance traits in chickens

(2011) Ruili Han et al.   MOLECULAR BIOLOGY REPORTS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

NELL-1, an Osteoinductive Factor, Is a Direct Transcriptional Target of Osterix

(2011) Feng Chen et al.   PLoS One

The Nell-1 Growth Factor Stimulates Bone Formation by Purified Human Perivascular Cells

(2011) Xinli Zhang et al.   TISSUE ENGINEERING PART A

NELL-1 Promotes Cartilage Regeneration in an In Vivo Rabbit Model

(2011) Ronald K. Siu et al.   TISSUE ENGINEERING PART A

Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering

(2011) Chunyan Mou et al.   PLOS BIOLOGY

A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken

(2011) Ben Dorshorst et al.   PLoS Genetics

Unlocking Mendelian disease using exome sequencing

(2011) Christian Gilissen et al.   GENOME BIOLOGY

Evaluation of theIGFs(IGF1andIGF2) Genes as Candidates for Growth, Body Measurement, Carcass, and Reproduction Traits in Beijing You and Silkie Chickens

(2010) Shaoqing Tang et al.   ANIMAL BIOTECHNOLOGY

Evaluation of SNPs in the chicken HMGA2 gene as markers for body weight gain

(2010) C. Song et al.   ANIMAL GENETICS

Association between ovocalyxin-32 gene haplotypes and eggshell quality traits in an F2 intercross between two chicken lines divergently selected for eggshell strength

(2010) H. Takahashi et al.   ANIMAL GENETICS

Across-Line SNP Association Study for Direct and Associative Effects on Feather Damage in Laying Hens

(2010) F. Biscarini et al.   BEHAVIOR GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

An initial map of chromosomal segmental copy number variations in the chicken

(2010) Xiaofei Wang et al.   BMC GENOMICS

An ESRP-regulated splicing programme is abrogated during the epithelial–mesenchymal transition

(2010) Claude C Warzecha et al.   EMBO JOURNAL

Exome sequencing: the sweet spot before whole genomes

(2010) J. K. Teer et al.   HUMAN MOLECULAR GENETICS

The Role of NELL-1, a Growth Factor Associated with Craniosynostosis, in Promoting Bone Regeneration

(2010) X. Zhang et al.   JOURNAL OF DENTAL RESEARCH

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

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

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius

(2010) Hiromi Sawai et al.   PLoS One

The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events

(2010) Claude C. Warzecha et al.   RNA Biology

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Cardiac ankyrins in health and disease

(2009) Seyed M. Hashemi et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

ESRP1 and ESRP2 Are Epithelial Cell-Type-Specific Regulators of FGFR2 Splicing

(2009) Claude C. Warzecha et al.   MOLECULAR CELL

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens

(2009) Dominic Wright et al.   PLoS Genetics

Genetic analyses ofRoundabout(ROBO) axon guidance receptors in autism

(2008) A. Anitha et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken

(2008) Martin G Elferink et al.   BMC GENOMICS

Mannan-binding lectin (MBL) in two chicken breeds and the correlation with experimental Pasteurella multocida infection

(2008) T.W. Schou et al.   COMPARATIVE IMMUNOLOGY MICROBIOLOGY AND INFECTIOUS DISEASES

Ancestral TSH Mechanism Signals Summer in a Photoperiodic Mammal

(2008) Elodie A. Hanon et al.   CURRENT BIOLOGY

Thyrotrophin in the pars tuberalis triggers photoperiodic response

(2008) Nobuhiro Nakao et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Polymorphisms in Uncoupling Protein, Melanocortin 3 Receptor, Melanocortin 4 Receptor, and Pro-Opiomelanocortin Genes and Association with Production Traits in a Commercial Broiler Line

(2008) P. Sharma et al.   POULTRY SCIENCE

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

(2008) Jonas Eriksson et al.   PLoS Genetics