Major Reorganization of Chromosome Conformation During Muscle Development in Pig

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals

(2020) Yana Feodorova et al.   TRENDS IN CELL BIOLOGY

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

(2020) Nan Zhang et al.   Nature Communications

The maturity in fetal pigs using a multi-fluid metabolomic approach

(2020) Gaëlle Lefort et al.   Scientific Reports

A TAD Skeptic: Is 3D Genome Topology Conserved?

(2020) Ittai E. Eres et al.   TRENDS IN GENETICS

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

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

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

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

(2019) Sylvain Foissac et al.   BMC BIOLOGY

Integrated Analysis of Proteomic and Transcriptomic Data Highlights Late Fetal Muscle Maturation Process

(2018) Valentin Voillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis

(2018) Mengnan He et al.   International Journal of Biological Sciences

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation

(2018) M. Marti-Marimon et al.   Scientific Reports

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

(2018) Elisabetta Giuffra et al.   Annual Review of Animal Biosciences

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

(2017) Tao Yang et al.   GENOME RESEARCH

Evolution of peroxisomal trans-2-enoyl-CoA reductase ( PECR ) as candidate gene for meat quality

(2017) K. Piórkowska et al.   Livestock Science

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment

(2017) Ravi Boya et al.   NUCLEIC ACIDS RESEARCH

A critical assessment of topologically associating domain prediction tools

(2017) Rola Dali et al.   NUCLEIC ACIDS RESEARCH

Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro

(2017) Malina D. Doynova et al.   Skeletal Muscle

Expressed alleles of imprinted IGF2, DLK1 and MEG3 colocalize in 3D-preserved nuclei of porcine fetal cells

(2016) Yvette Lahbib-Mansais et al.   BMC CELL BIOLOGY

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

(2016) A. Rasim Barutcu et al.   GENOME RESEARCH

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

(2015) Aaron T.L. Lun et al.   BMC BIOINFORMATICS

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

(2015) Darío G. Lupiáñez et al.   CELL

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems Biology

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Spatial re-organization of myogenic regulatory sequences temporally controls gene expression

(2015) Akihito Harada et al.   NUCLEIC ACIDS RESEARCH

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Topologically Associating Domains: An invariant framework or a dynamic scaffold?

(2015) Caelin Cubeñas-Potts et al.   Nucleus

Topologically Associating Domains: An invariant framework or a dynamic scaffold?

(2015) Caelin Cubeñas-Potts et al.   Nucleus

Muscle transcriptomic investigation of late fetal development identifies candidate genes for piglet maturity

(2014) Valentin Voillet et al.   BMC GENOMICS

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

(2014) Suhas S.P. Rao et al.   CELL

Gathering up meiotic telomeres: a novel function of the microtubule-organizing center

(2014) Ayumu Yamamoto   CELLULAR AND MOLECULAR LIFE SCIENCES

A mechanistic link between gene regulation and genome architecture in mammalian development

(2014) Giancarlo Bonora et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Telomere position effect: regulation of gene expression with progressive telomere shortening over long distances

(2014) Jérôme D. Robin et al.   GENES & DEVELOPMENT

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

3D organization of telomeres in porcine neutrophils and analysis of LPS-activation effect

(2013) Florence Mompart et al.   BMC CELL BIOLOGY

Spatial telomere organization and clustering in yeast Saccharomyces cerevisiae nucleus is generated by a random dynamics of aggregation–dissociation

(2013) Nathanaël Hozé et al.   MOLECULAR BIOLOGY OF THE CELL

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Growth Associated Protein 43 Is Expressed in Skeletal Muscle Fibers and Is Localized in Proximity of Mitochondria and Calcium Release Units

(2013) Simone Guarnieri et al.   PLoS One

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

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

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

(2012) Yin C Lin et al.   NATURE IMMUNOLOGY

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

The pig: a model for human infectious diseases

(2011) François Meurens et al.   TRENDS IN MICROBIOLOGY

NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments

(2010) E. Iannuccelli et al.   BIOINFORMATICS

Human Muscle Economy Myoblast Differentiation and Excitation-Contraction Coupling Use the Same Molecular Partners, STIM1 and STIM2

(2010) Basile Darbellay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Nuclear architecture of resting and LPS-stimulated porcine neutrophils by 3D FISH

(2009) Martine Yerle-Bouissou et al.   CHROMOSOME RESEARCH

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

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

Rapid telomere motions in live human cells analyzed by highly time-resolved microscopy

(2008) Xueying Wang et al.   Epigenetics & Chromatin