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

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

(2016) Ming-Shan Wang et al.   CELL RESEARCH

Genome-wide association study of growth traits in Jinghai Yellow chicken hens using SLAF-seq technology

(2015) W. H. Wang et al.   ANIMAL GENETICS

The frequent evolutionary birth and death of functional promoters in mouse and human

(2015) Robert S. Young et al.   GENOME RESEARCH

Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens

(2015) Ming-Shan Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Genetic studies of body mass index yield new insights for obesity biology

(2015) Adam E. Locke et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

(2014) Guoqiang Yi et al.   BMC GENOMICS

Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia

(2014) Xiao Gou et al.   GENOME RESEARCH

Dnmt3a in Sim1 Neurons Is Necessary for Normal Energy Homeostasis

(2014) D. Kohno et al.   JOURNAL OF NEUROSCIENCE

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

(2014) M. Carneiro et al.   SCIENCE

Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

(2014) Saber Qanbari et al.   PLoS Genetics

The Role of Gastrokine 1 in Gastric Cancer

(2014) Jung Hwan Yoon et al.   Journal of Gastric Cancer

Teratogenic Factors Affect Transcription Factor Expression

(2013) Takuya KOJIMA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Glypican-5 is a novel metastasis suppressor gene in non-small cell lung cancer

(2013) Xin Yang et al.   CANCER LETTERS

Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant

(2013) Yana G. Kamberov et al.   CELL

Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens

(2013) Wen-Lang Fan et al.   Genome Biology and Evolution

Derived variants at six genes explain nearly half of size reduction in dog breeds

(2013) M. Rimbault et al.   GENOME RESEARCH

GKN2 Contributes to the Homeostasis of Gastric Mucosa by Inhibiting GKN1 Activity

(2013) Olga Kim et al.   JOURNAL OF CELLULAR PHYSIOLOGY

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

(2013) M. D. Shapiro et al.   SCIENCE

Gastrokines: stomach-specific proteins with putative homeostatic and tumor suppressor roles

(2012) Trevelyan R. Menheniott et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Chicken domestication: an updated perspective based on mitochondrial genomes

(2012) Y-W Miao et al.   HEREDITY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome-Wide Association Study Identified a Narrow Chromosome 1 Region Associated with Chicken Growth Traits

(2012) Liang Xie et al.   PLoS One

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

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

Four Loci Explain 83% of Size Variation in the Horse

(2012) Shokouh Makvandi-Nejad et al.   PLoS One

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Association Study of Body Weight in Chicken F2 Resource Population

(2011) Xiaorong Gu et al.   PLoS One

Abnormal behavior in mice mutant for the Disc1 binding partner, Dixdc1

(2011) S Kivimäe et al.   Translational Psychiatry

GCTA: A Tool for Genome-wide Complex Trait Analysis

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

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

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

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

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

Identification of chromosomal regions associated with growth and carcass traits in an F3full sib intercross line originating from a cross of chicken lines divergently selected on body weight

(2009) D. Terčič et al.   ANIMAL GENETICS

Sall genes regulate region-specific morphogenesis in the mouse limb by modulating Hox activities

(2009) Y. Kawakami et al.   DEVELOPMENT

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Regulation and function of Spalt proteins during animal development

(2009) Jose F. de Celis et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

SALL3 Interacts with DNMT3A and Shows the Ability To Inhibit CpG Island Methylation in Hepatocellular Carcinoma

(2009) Y. Shikauchi et al.   MOLECULAR AND CELLULAR BIOLOGY

Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (Oncorhynchus kisutch)

(2009) R. H. Devlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Many sequence variants affecting diversity of adult human height

(2008) Daniel F Gudbjartsson et al.   NATURE GENETICS

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

(2008) Jonas Eriksson et al.   PLoS Genetics