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

Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice

(2021) G. W. K. Moore et al.   Nature Communications

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

Systematic identification of silencers in human cells

(2020) Baoxu Pang et al.   NATURE GENETICS

Re-epithelialization and immune cell behaviour in an ex vivo human skin model

(2020) Ana Rakita et al.   Scientific Reports

Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs

(2020) Hao Chen et al.   GigaScience

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

(2020) Lingzhao Fang et al.   GENOME RESEARCH

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

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

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

(2020) Yupeng He et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

(2020) Michelle M. Halstead et al.   BMC GENOMICS

Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs

(2019) Deborah Velez-Irizarry et al.   BMC GENOMICS

Author Correction: A compendium of geochemical information from the Saanich Inlet water column

(2019) Mónica Torres-Beltrán et al.   Scientific Data

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

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

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

(2019) Ruidong Xiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HNF4 Regulates Fatty Acid Oxidation and is Required for Renewal of Intestinal Stem Cells in Mice

(2019) Lei Chen et al.   GASTROENTEROLOGY

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

(2019) Sylvain Foissac et al.   BMC BIOLOGY

Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq

(2019) N. B. Kingsley et al.   Genes

Villin-1 and Gelsolin Regulate Changes in Actin Dynamics That Affect Cell Survival Signaling Pathways and Intestinal Inflammation

(2018) Swati Roy et al.   GASTROENTEROLOGY

Integrative multi‐omics analysis of intestinal organoid differentiation

(2018) Rik GH Lindeboom et al.   Molecular Systems Biology

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

(2018) E. N. Burns et al.   ANIMAL GENETICS

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

(2018) Siyang Liu et al.   CELL

Behavioural genetic differences between Chinese and European pigs

(2017) Qingpo Chu et al.   JOURNAL OF GENETICS

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

(2017) M Ryan Corces et al.   NATURE METHODS

Production of transgenic pig as an Alzheimer’s disease model using a multi-cistronic vector system

(2017) Seung-Eun Lee et al.   PLoS One

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

(2017) Camille Berthelot et al.   Nature Ecology & Evolution

Identification of genes in longissimus dorsi muscle differentially expressed between Wannanhua and Yorkshire pigs using RNA-sequencing

(2016) X.-J. Li et al.   ANIMAL GENETICS

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

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

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

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Extensive Expression Differences along Porcine Small Intestine Evidenced by Transcriptome Sequencing

(2014) Núria Mach et al.   PLoS One

The pig as an animal model for human pathologies: A proteomics perspective

(2014) Anna Bassols et al.   Proteomics Clinical Applications

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

(2014) James R Wagner et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Enterocyte Microvillus-Derived Vesicles Detoxify Bacterial Products and Regulate Epithelial-Microbial Interactions

(2012) David A. Shifrin et al.   CURRENT BIOLOGY

Pig proteomics: A review of a species in the crossroad between biomedical and food sciences

(2012) André Martinho de Almeida et al.   Journal of Proteomics

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

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

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

The pig: a model for human infectious diseases

(2011) François Meurens et al.   TRENDS IN MICROBIOLOGY

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Hemizygous minipigs produced by random gene insertion and handmade cloning express the Alzheimer’s disease-causing dominant mutation APPsw

(2009) Peter M. Kragh et al.   TRANSGENIC RESEARCH

Erhualian and Pietrain pigs exhibit distinct behavioral, endocrine and biochemical responses during transport

(2007) Liu-An Li et al.   Livestock Science