RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus

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

(2018) Sofia A. Quinodoz et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

COMRADES determines in vivo RNA structures and interactions

(2018) Omer Ziv et al.   NATURE METHODS

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Neuroblastoma is composed of two super-enhancer-associated differentiation states

(2017) Tim van Groningen et al.   NATURE GENETICS

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

(2017) Sofia Battaglia et al.   eLife

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

(2016) Nikolay Tsanov et al.   NUCLEIC ACIDS RESEARCH

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox

(2016) Chase A. Weidmann et al.   TRENDS IN BIOCHEMICAL SCIENCES

Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

(2016) Tri C. Nguyen et al.   Nature Communications

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

(2015) Jonathan Neve et al.   GENOME RESEARCH

Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed

(2015) Agnieszka Rybak-Wolf et al.   MOLECULAR CELL

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

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

(2015) Borbala Mifsud et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

(2015) Marie Trussart et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz 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

Nucleolus and nuclear periphery: Velcro for heterochromatin

(2014) Jan Padeken et al.   CURRENT OPINION IN CELL BIOLOGY

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2012) Tom Sexton et al.   CELL

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

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

HEXEvent: a database of Human EXon splicing Events

(2012) Anke Busch et al.   NUCLEIC ACIDS RESEARCH

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

(2010) V. Kaimal et al.   NUCLEIC ACIDS RESEARCH

Nuclear neighborhoods and gene expression

(2009) Rui Zhao et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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