Regulated splicing of large exons is linked to phase‐separation of vertebrate transcription factors

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tRIP‐seq reveals repression of premature polyadenylation by co‐transcriptional FUS‐U1 snRNP assembly

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The SWI/SNF complex in cancer — biology, biomarkers and therapy

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Interplay between coding and exonic splicing regulatory sequences

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Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites

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The emerging roles of hnRNPK

(2019) Ziyi Wang et al.   JOURNAL OF CELLULAR PHYSIOLOGY

A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells

(2019) Byung Ran So et al.   MOLECULAR CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

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Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

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Human long intrinsically disordered protein regions are frequent targets of positive selection

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Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

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Advances in CLIP Technologies for Studies of Protein-RNA Interactions

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IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

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Imaging dynamic and selective low-complexity domain interactions that control gene transcription

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Coactivator condensation at super-enhancers links phase separation and gene control

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Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

(2018) Yoav Lubelsky et al.   NATURE

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

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Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

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Defining the Transcriptional Ecosystem

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Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

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The UCSC Genome Browser database: 2019 update

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STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

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TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein intrinsic disorder negatively associates with gene age in different eukaryotic lineages

(2017) Sanghita Banerjee et al.   Molecular BioSystems

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

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The Encyclopedia of DNA elements (ENCODE): data portal update

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Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR

(2016) Andrey Damianov et al.   CELL

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

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Control of the heat stress-induced alternative splicing of a subset of genes by hnRNP K

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Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide

(2016) Takayuki Nojima et al.   Nature Protocols

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

Position-specific binding of FUS to nascent RNA regulates mRNA length

(2015) Akio Masuda et al.   GENES & DEVELOPMENT

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Splice junctions are constrained by protein disorder

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The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Repbase Update, a database of repetitive elements in eukaryotic genomes

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Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions

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

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CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

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Context-dependent control of alternative splicing by RNA-binding proteins

(2014) Xiang-Dong Fu et al.   NATURE REVIEWS GENETICS

SRp20: An overview of its role in human diseases

(2013) Claudia Corbo et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

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STAR: ultrafast universal RNA-seq aligner

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Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

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Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

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

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Splicing of internal large exons is defined by novel cis -acting sequence elements

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The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

MEME-ChIP: motif analysis of large DNA datasets

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SpliceAid 2: A database of human splicing factors expression data and RNA target motifs

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Evolution of SR protein and hnRNP splicing regulatory factors

(2011) Anke Busch et al.   Wiley Interdisciplinary Reviews-RNA

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

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Model-based Analysis of ChIP-Seq (MACS)

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