Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues

Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle

(2021) Renqiang Yuan et al.   DNA RESEARCH

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

(2021) Yunxia Zhao et al.   Nature Communications

A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription

(2021) Long Jin et al.   Nature Communications

Nuclear Magnetic Resonance-Based Metabolomic Analysis Reveals Physiological Stage, Breed, and Diet Effects on the Intramuscular Metabolism of Amino Acids and Related Nutrients in Pigs

(2021) Yingying Liu et al.   Frontiers in Veterinary Science

Major Reorganization of Chromosome Conformation During Muscle Development in Pig

(2021) Maria Marti-Marimon et al.   Frontiers in Genetics

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

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

(2019) Sylvain Foissac et al.   BMC BIOLOGY

Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells

(2019) Changya Chen et al.   Cell Reports

p53 Functions in Adipose Tissue Metabolism and Homeostasis

(2018) Jelena Krstic et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Reconstitution ofUCP1using CRISPR/Cas9 in the white adipose tissue of pigs decreases fat deposition and improves thermogenic capacity

(2017) Qiantao Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains

(2017) Gil Ron et al.   Nature Communications

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

Analysis of carcass and meat quality traits and nutritional values of hybrid wild boars under different crossing systems

(2015) S.-H. Zhang et al.   GENETICS AND MOLECULAR RESEARCH

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

(2015) Paul Martin et al.   Nature Communications

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Role of p53 in preadipocyte differentiation

(2014) Qiong Huang et al.   CELL BIOLOGY INTERNATIONAL

GATA3: a master of many trades in immune regulation

(2014) Yisong Y. Wan   TRENDS IN IMMUNOLOGY

Adipose depots differ in cellularity, adipokines produced, gene expression, and cell systems

(2014) Michael V Dodson et al.   Adipocyte

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

(2012) E. Josephine Clowney et al.   CELL

The Chemokine Superfamily Revisited

(2012) Albert Zlotnik et al.   IMMUNITY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

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

(2010) Heng Li et al.   BIOINFORMATICS

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

Subcutaneous and visceral adipose tissue: structural and functional differences

(2009) M. Mohsen Ibrahim   Obesity Reviews

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE