Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells

(2021) Takashi Imada et al.   GENES TO CELLS

Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes

(2021) Yuanlong Liu et al.   Nature Communications

Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

(2021) Kevin Michael Creamer et al.   MOLECULAR CELL

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Mechanisms and Functions of Chromosome Compartmentalization

(2020) Erica M. Hildebrand et al.   TRENDS IN BIOCHEMICAL SCIENCES

Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins

(2020) Joseph Dopie et al.   JOURNAL OF CELL BIOLOGY

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

The nucleolus as a multiphase liquid condensate

(2020) Denis L. J. Lafontaine et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

PML nuclear bodies and chromatin dynamics: catch me if you can!

(2020) Armelle Corpet et al.   NUCLEIC ACIDS RESEARCH

SON and SRRM2 are essential for nuclear speckle formation

(2020) İbrahim Avşar Ilik et al.   eLife

Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision

(2020) Jackson M Gordon et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

DEBrowser: interactive differential expression analysis and visualization tool for count data

(2019) Alper Kucukural et al.   BMC GENOMICS

The mRNA Export Receptor NXF1 Coordinates Transcriptional Dynamics, Alternative Polyadenylation, and mRNA Export

(2019) Suli Chen et al.   MOLECULAR CELL

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

WashU Epigenome Browser update 2019

(2019) Daofeng Li et al.   NUCLEIC ACIDS RESEARCH

Differential contribution of steady‐state RNA and active transcription in chromatin organization

(2019) A Rasim Barutcu et al.   EMBO REPORTS

Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

(2019) Alejandro Padrón et al.   MOLECULAR CELL

Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions

(2019) Kyle Xiong et al.   Nature Communications

Quack: A quality assurance tool for high throughput sequence data

(2018) Adam Thrash et al.   ANALYTICAL BIOCHEMISTRY

PML nuclear bodies: from architecture to function

(2018) Valérie Lallemand-Breitenbach et al.   CURRENT OPINION IN CELL BIOLOGY

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

(2018) Archa H. Fox et al.   TRENDS IN BIOCHEMICAL SCIENCES

Intronless mRNAs transit through nuclear speckles to gain export competence

(2018) Ke Wang et al.   JOURNAL OF CELL BIOLOGY

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments

(2018) Daniel Benhalevy et al.   NATURE METHODS

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

ProHits-viz: a suite of web tools for visualizing interaction proteomics data

(2017) James D R Knight et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Nuclear speckles: molecular organization, biological function and role in disease

(2017) Lukasz Galganski et al.   NUCLEIC ACIDS RESEARCH

Coordinating cell cycle-regulated histone gene expression through assembly and function of the Histone Locus Body

(2017) Robert J. Duronio et al.   RNA Biology

Birth and Death of Histone mRNAs

(2017) William F. Marzluff et al.   TRENDS IN GENETICS

The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL

(2016) Taro Mannen et al.   JOURNAL OF CELL BIOLOGY

Data Independent Acquisition analysis in ProHits 4.0

(2016) Guomin Liu et al.   Journal of Proteomics

Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2

(2016) Victoria Hung et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data

(2016) Guoci Teo et al.   PROTEOMICS

An extensive program of periodic alternative splicing linked to cell cycle progression

(2016) Daniel Dominguez et al.   eLife

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes

(2015) Jean-Philippe Lambert et al.   Journal of Proteomics

The ImageJ ecosystem: An open platform for biomedical image analysis

(2015) Johannes Schindelin et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

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

(2014) Suhas S.P. Rao et al.   CELL

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

RNA and dynamic nuclear organization

(2014) J. Rinn et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells

(2013) Xinyi Lu et al.   NATURE CELL BIOLOGY

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Cajal bodies: where form meets function

(2012) Martin Machyna et al.   Wiley Interdisciplinary Reviews-RNA

ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs

(2011) Liuqing Yang et al.   CELL

SON Controls Cell-Cycle Progression by Coordinated Regulation of RNA Splicing

(2011) Eun-Young Ahn et al.   MOLECULAR CELL

Son Is Essential for Nuclear Speckle Organization and Cell Cycle Progression

(2010) Alok Sharma et al.   MOLECULAR BIOLOGY OF THE CELL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

ProHits: integrated software for mass spectrometry–based interaction proteomics

(2010) Guomin Liu et al.   NATURE BIOTECHNOLOGY

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

The Cajal Body and Histone Locus Body

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

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

A role for TREX components in the release of spliced mRNA from nuclear speckle domains

(2010) Anusha P. Dias et al.   Nature Communications

WRAP53 Is Essential for Cajal Body Formation and for Targeting the Survival of Motor Neuron Complex to Cajal Bodies

(2010) Salah Mahmoudi et al.   PLOS BIOLOGY

Next generation software for functional trend analysis

(2009) G. F. Berriz et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

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

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

Differential dynamics of splicing factor SC35 during the cell cycle

(2008) Kaushlendra Tripathi et al.   JOURNAL OF BIOSCIENCES