Gene architecture directs splicing outcome in separate nuclear spatial regions

The upstream 5′ splice site remains associated to the transcription machinery during intron synthesis

(2021) Yodfat Leader et al.   Nature Communications

Exon definition facilitates reliable control of alternative splicing in the RON proto-oncogene

(2020) Mihaela Enculescu et al.   BIOPHYSICAL JOURNAL

Radial Organization in the Mammalian Nucleus

(2020) Nicola Crosetto et al.   Frontiers in Genetics

Ancient genomic regulatory blocks are a source for regulatory gene deserts in vertebrates after whole genome duplications

(2020) María Touceda-Suárez et al.   MOLECULAR BIOLOGY AND EVOLUTION

GPSeq reveals the radial organization of chromatin in the cell nucleus

(2020) Gabriele Girelli et al.   NATURE BIOTECHNOLOGY

FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention

(2020) Jack Humphrey et al.   NUCLEIC ACIDS RESEARCH

Exploring chromosomal structural heterogeneity across multiple cell lines

(2020) Ryan R Cheng et al.   eLife

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

A unified mechanism for intron and exon definition and back-splicing

(2019) Xueni Li et al.   NATURE

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

(2019) Jernej Ule et al.   MOLECULAR CELL

DNA sequence-dependent chromatin architecture and nuclear hubs formation

(2019) Kamel Jabbari et al.   Scientific Reports

HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo

(2018) Jonathan M. Howard et al.   GENOME RESEARCH

A comprehensive characterization ofcis-acting splicing-associated variants in human cancer

(2018) Yuichi Shiraishi et al.   GENOME RESEARCH

Advances in CLIP Technologies for Studies of Protein-RNA Interactions

(2018) Flora C.Y. Lee et al.   MOLECULAR CELL

Computational 3D genome modeling using Chrom3D

(2018) Jonas Paulsen et al.   Nature Protocols

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

(2018) Reyka G. Jayasinghe et al.   Cell Reports

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

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

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

Obtaining estimates for the ages of all the protein-coding genes and most of the ontology-identified noncoding genes of the human genome, assigned to 19 phylostrata

(2018) Thomas Litman et al.   SEMINARS IN ONCOLOGY

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

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

(2017) Hong Han et al.   MOLECULAR CELL

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2017) Lukasz Galganski et al.   NUCLEIC ACIDS RESEARCH

Advances and challenges in the detection of transcriptome-wide protein-RNA interactions

(2017) Emily C. Wheeler et al.   Wiley Interdisciplinary Reviews-RNA

Towards Consensus Gene Ages

(2016) Benjamin J. Liebeskind et al.   Genome Biology and Evolution

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

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

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

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

The alternative role of DNA methylation in splicing regulation

(2015) Galit Lev Maor et al.   TRENDS IN GENETICS

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia 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

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

(2014) Eivind Lund et al.   NUCLEIC ACIDS RESEARCH

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

(2014) Yao-Cheng Lin et al.   Nature Communications

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

When epigenetics meets alternative splicing: the roles of DNA methylation and GC architecture

(2013) Sahar Gelfman et al.   Epigenomics

HiCNorm: removing biases in Hi-C data via Poisson regression

(2012) Ming Hu et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

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

(2012) Maayan Amit et al.   Cell Reports

Exon and intron definition in pre-mRNA splicing

(2012) Laura De Conti et al.   Wiley Interdisciplinary Reviews-RNA

GC content around splice sites affects splicing through pre-mRNA secondary structures

(2011) Jing Zhang et al.   BMC GENOMICS

A U1-U2 snRNP Interaction Network during Intron Definition

(2011) W. Shao et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks

(2011) N. Yosef et al.   Science Signaling

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

(2011) Yehuda Brody et al.   PLOS BIOLOGY

Lamin A and lamin C form homodimers and coexist in higher complex forms both in the nucleoplasmic fraction and in the lamina of cultured human cells

(2011) Thorsten Kolb et al.   Nucleus

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Exon Definition Complexes Contain the Tri-snRNP and Can Be Directly Converted into B-like Precatalytic Splicing Complexes

(2010) Marc Schneider et al.   MOLECULAR CELL

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nuclear Speckles

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

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Cooperative-Binding and Splicing-Repressive Properties of hnRNP A1

(2009) H. L. Okunola et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2009) Da Wei Huang et al.   Nature Protocols

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SROOGLE: webserver for integrative, user-friendly visualization of splicing signals

(2009) S. Schwartz et al.   NUCLEIC ACIDS RESEARCH

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome

(2008) Shalini Sharma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH