The long-range interaction map of ribosomal DNA arrays

A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome

(2016) Shoukai Yu et al.   Genome Biology and Evolution

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

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

Grabbing the genome by the NADs

(2015) Timothy D. Matheson et al.   CHROMOSOMA

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes

(2015) John G. Gibbons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization

(2014) Jonas Paulsen et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

A Sequence-Specific Interaction between the Saccharomyces cerevisiae rRNA Gene Repeats and a Locus Encoding an RNA Polymerase I Subunit Affects Ribosomal DNA Stability

(2014) Inswasti Cahyani et al.   MOLECULAR AND CELLULAR BIOLOGY

A separable domain of the p150 subunit of human chromatin assembly factor-1 promotes protein and chromosome associations with nucleoli

(2014) Corey L. Smith et al.   MOLECULAR BIOLOGY OF THE CELL

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans

(2014) John G. Gibbons et al.   Nature Communications

Plant rDNA database: update and new features

(2014) S. Garcia et al.   Database-The Journal of Biological Databases and Curation

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae

(2013) John L. Woolford et al.   GENETICS

ABH2 Couples Regulation of Ribosomal DNA Transcription with DNA Alkylation Repair

(2013) Pishun Li et al.   Cell Reports

Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses

(2012) Yang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization

(2012) Jesse D. Ziebarth et al.   NUCLEIC ACIDS RESEARCH

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

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

Nucleolar Association and Transcriptional Inhibition through 5S rDNA in Mammals

(2012) Andrew M. Fedoriw et al.   PLoS Genetics

Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18

(2011) A. Smirnov et al.   GENES & DEVELOPMENT

Restless 5S: The re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants

(2011) Susann Wicke et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome organization in and around the nucleolus

(2011) Attila Németh et al.   TRENDS IN GENETICS

Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: “rDNA–Sensitive” Genes and Natural Variation

(2011) Silvana Paredes et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Nucleolus

(2010) T. Pederson   Cold Spring Harbor Perspectives in Biology

CTCF regulates the local epigenetic state of ribosomal DNA repeats

(2010) Suzanne van de Nobelen et al.   Epigenetics & Chromatin

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

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

(2009) Da Wei Huang et al.   Nature Protocols

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

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