High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

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Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

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Identifying Nuclear Matrix-Attached DNA Across the Genome

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Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Spatial organization of chromatin domains and compartments in single chromosomes

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Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains

(2015) Vuthy Ea et al.   BMC GENOMICS

Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells

(2015) M. Amendola et al.   EMBO REPORTS

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

(2015) Vishnu Dileep et al.   GENOME RESEARCH

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

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

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dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

The 3D folding of metazoan genomes correlates with the association of similar repetitive elements

(2015) Axel Cournac et al.   NUCLEIC ACIDS RESEARCH

Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization

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

(2014) Suhas S.P. Rao et al.   CELL

Nucleolus and nuclear periphery: Velcro for heterochromatin

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Nuclear bodies: new insights into assembly/dynamics and disease relevance

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ASox2distal enhancer cluster regulates embryonic stem cell differentiation potential

(2014) Harry Y. Zhou et al.   GENES & DEVELOPMENT

The Quantitative Nuclear Matrix Proteome as a Biochemical Snapshot of Nuclear Organization

(2014) Rudolf Engelke et al.   JOURNAL OF PROTEOME RESEARCH

The Hierarchy of the 3D Genome

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

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

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Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

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(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

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

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Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

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(2011) Anton Valouev et al.   NATURE

Long-range chromatin interactions at the mouse Igf2/H19 locus reveal a novel paternally expressed long non-coding RNA

(2011) Franck Court et al.   NUCLEIC ACIDS RESEARCH

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Impaired minor tri-snRNP assembly generates differential splicing defects of U12-type introns in lymphoblasts derived from a type I SMA patient

(2010) Nawal Boulisfane et al.   HUMAN MOLECULAR GENETICS

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

The Cajal Body and Histone Locus Body

(2010) Z. Nizami et al.   Cold Spring Harbor Perspectives in Biology

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

A Model for all Genomes: The Role of Transcription Factories

(2009) Peter R. Cook   JOURNAL OF MOLECULAR BIOLOGY

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

Generation of cortical neurons from mouse embryonic stem cells

(2009) Nicolas Gaspard et al.   Nature Protocols

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Transcription factories: gene expression in unions?

(2009) Heidi Sutherland et al.   NATURE REVIEWS GENETICS

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

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

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

(2009) Gary Hon et al.   PLoS Computational Biology

Genome-wide profiling of salt fractions maps physical properties of chromatin

(2008) S. Henikoff et al.   GENOME RESEARCH

Differential nuclear scaffold/matrix attachment marks expressed genes†

(2008) Amelia K. Linnemann et al.   HUMAN MOLECULAR GENETICS

Genomic Matrix Attachment Region and Chromosome Conformation Capture Quantitative Real Time PCR Assays Identify Novel Putative Regulatory Elements at the ImprintedDlk1/Gtl2Locus

(2008) Caroline Braem et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An intrinsic mechanism of corticogenesis from embryonic stem cells

(2008) Nicolas Gaspard et al.   NATURE