Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome

HiCRep.py: fast comparison of Hi-C contact matrices in Python

(2021) Dejun Lin et al.   BIOINFORMATICS

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

(2021) Yunxia Zhao et al.   Nature Communications

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

CoolBox: a flexible toolkit for visual analysis of genomics data

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Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

(2021) Hyun Jung Oh et al.   CELL

A single-cell atlas of chromatin accessibility in the human genome

(2021) Kai Zhang et al.   CELL

An SETD1A/Wnt/β-catenin feedback loop promotes NSCLC development

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Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA

(2021) Arpita Ghosh et al.   NUCLEIC ACIDS RESEARCH

Coolpup.py: versatile pile-up analysis of Hi-C data

(2020) Ilya M Flyamer et al.   BIOINFORMATICS

Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits

(2020) Virginie Tissières et al.   Cell Reports

The origin of domestication genes in goats

(2020) Zhuqing Zheng et al.   Science Advances

Tead1 is essential for mitochondrial function in cardiomyocytes

(2020) Ruya Liu et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

Cell-type-specific 3D epigenomes in the developing human cortex

(2020) Michael Song et al.   NATURE

Stress-induced RNA–chromatin interactions promote endothelial dysfunction

(2020) Riccardo Calandrelli et al.   Nature Communications

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model

(2020) Yuhua Fu et al.   Communications Biology

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

Fibroadipogenic progenitors are responsible for muscle loss in limb girdle muscular dystrophy 2B

(2019) Marshall W. Hogarth et al.   Nature Communications

Efficient base editing for multiple genes and loci in pigs using base editors

(2019) Jingke Xie et al.   Nature Communications

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

(2019) Alessandro Bertero et al.   Nature Communications

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

(2019) Sourya Bhattacharyya et al.   Nature Communications

A Huntingtin Knockin Pig Model Recapitulates Features of Selective Neurodegeneration in Huntington’s Disease

(2018) Sen Yan et al.   CELL

Consistent success in life-supporting porcine cardiac xenotransplantation

(2018) Matthias Längin et al.   NATURE

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

(2017) Justyna Horodyska et al.   PLoS One

IRF3 promotes adipose inflammation and insulin resistance and represses browning

(2016) Manju Kumari et al.   JOURNAL OF CLINICAL INVESTIGATION

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

(2016) Guipeng Li et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Glucose-induced expression of the homeotic transcription factor Prep1 is associated with histone post-translational modifications in skeletal muscle

(2015) Marco Ciccarelli et al.   DIABETOLOGIA

Sarcolipin Is a Key Determinant of the Basal Metabolic Rate, and Its Overexpression Enhances Energy Expenditure and Resistance against Diet-induced Obesity

(2015) Santosh K. Maurya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2015) Huashui Ai et al.   NATURE GENETICS

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

In search of the determinants of enhancer–promoter interaction specificity

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Pknox1/Prep1 Regulates Mitochondrial Oxidative Phosphorylation Components in Skeletal Muscle

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Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

(2013) Mingzhou Li et al.   NATURE GENETICS

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

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Permanent Neonatal Diabetes in INSC94Y Transgenic Pigs

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Sarcolipin is a newly identified regulator of muscle-based thermogenesis in mammals

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Strong signatures of selection in the domestic pig genome

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Muscle-fiber transdifferentiation in an experimental model of respiratory chain myopathy

(2012) Nils Venhoff et al.   ARTHRITIS RESEARCH & THERAPY

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR 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

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

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Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

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Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY