DDX54 regulates transcriptome dynamics during DNA damage response

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

(2016) Endre Sebestyén et al.   GENOME RESEARCH

The mRNA-bound proteome of the early fly embryo

(2016) Hans-Hermann Wessels et al.   GENOME RESEARCH

Roles of RNA-Binding Proteins in DNA Damage Response

(2016) Mihoko Kai   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A

(2016) Rei Yoshimoto et al.   RNA

Sec16 alternative splicing dynamically controls COPII transport efficiency

(2016) Ilka Wilhelmi et al.   Nature Communications

SRSF10 Connects DNA Damage to the Alternative Splicing of Transcripts Encoding Apoptosis, Cell-Cycle Control, and DNA Repair Factors

(2016) Lulzim Shkreta et al.   Cell Reports

Multiomic Analysis of the UV-Induced DNA Damage Response

(2016) Stefan Boeing et al.   Cell Reports

INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments

(2015) Stefano de Pretis et al.   BIOINFORMATICS

Cell cycle regulation of human DNA repair and chromatin remodeling genes

(2015) Robin Mjelle et al.   DNA REPAIR

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

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

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

A novel role for the mono-ADP-ribosyltransferase PARP14/ARTD8 in promoting homologous recombination and protecting against replication stress

(2015) Claudia M. Nicolae et al.   NUCLEIC ACIDS RESEARCH

Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1

(2015) Amelia F. Alessi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

SF3B1 Association with Chromatin Determines Splicing Outcomes

(2015) Nir Kfir et al.   Cell Reports

Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression

(2015) Jorge Boucas et al.   PLoS One

Schlafen-11 sensitizes colorectal carcinoma cells to irinotecan

(2014) Li Tian et al.   ANTI-CANCER DRUGS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response

(2014) Melanie Blasius et al.   GENES & DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects

(2014) Haiyan Qiu et al.   JOURNAL OF CLINICAL INVESTIGATION

FUS is Phosphorylated by DNA-PK and Accumulates in the Cytoplasm after DNA Damage

(2014) Q. Deng et al.   JOURNAL OF NEUROSCIENCE

MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs

(2014) Lea H. Gregersen et al.   MOLECULAR CELL

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

(2014) Eliezer Calo et al.   NATURE

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Mechanisms for U2AF to define 3′ splice sites and regulate alternative splicing in the human genome

(2014) Changwei Shao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA damage: RNA-binding proteins protect from near and far

(2014) Martin Dutertre et al.   TRENDS IN BIOCHEMICAL SCIENCES

The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa

(2014) Linda Lauinger et al.   Nature Communications

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

Separation of long RNA by agarose–formaldehyde gel electrophoresis

(2013) Farrah H. Mansour et al.   ANALYTICAL BIOCHEMISTRY

CHD4 in the DNA-damage response and cell cycle progression: not so NuRDy now

(2013) Aoife O’Shaughnessy et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

DDX3 regulates DNA damage-induced apoptosis and p53 stabilization

(2013) Mianen Sun et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

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

(2013) Kathi Zarnack et al.   CELL

The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors

(2013) Lionel Tafforeau et al.   MOLECULAR CELL

Proteome-wide Identification of Poly(ADP-Ribosyl)ation Targets in Different Genotoxic Stress Responses

(2013) Stephanie Jungmichel et al.   MOLECULAR CELL

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

(2013) Shatakshi Pandit et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Interaction of FUS and HDAC1 regulates DNA damage response and repair in neurons

(2013) Wen-Yuan Wang et al.   NATURE NEUROSCIENCE

Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells

(2013) Daniel Menendez et al.   NUCLEIC ACIDS RESEARCH

YB-1 disrupts mismatch repair complex formation, interferes with MutSα recruitment on mismatch and inhibits mismatch repair through interacting with PCNA

(2013) Y-W Chang et al.   ONCOGENE

Requirement of Heterogeneous Nuclear Ribonucleoprotein C for BRCA Gene Expression and Homologous Recombination

(2013) Rachel W. Anantha et al.   PLoS One

RNA Helicase DDX3 Is a Regulatory Subunit of Casein Kinase 1 in Wnt- -Catenin Signaling

(2013) C.-M. Cruciat et al.   SCIENCE

Protein Interaction Network of the Mammalian Hippo Pathway Reveals Mechanisms of Kinase-Phosphatase Interactions

(2013) A. L. Couzens et al.   Science Signaling

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

(2013) Bernd Rädle et al.   Jove-Journal of Visualized Experiments

DP97, a DEAD box DNA/RNA helicase, is a target gene-selective co-regulator of the constitutive androstane receptor

(2012) Yuichiro Kanno et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis

(2012) F Nikulenkov et al.   CELL DEATH AND DIFFERENTIATION

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

(2012) L. Windhager et al.   GENOME RESEARCH

Dynamic Protein-Protein Interaction Wiring of the Human Spliceosome

(2012) Anna Hegele et al.   MOLECULAR CELL

Regulation of DNA-End Resection by hnRNPU-like Proteins Promotes DNA Double-Strand Break Signaling and Repair

(2012) Sophie E. Polo et al.   MOLECULAR CELL

Proteomic Investigations Reveal a Role for RNA Processing Factor THRAP3 in the DNA Damage Response

(2012) Petra Beli et al.   MOLECULAR CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response

(2012) Britt Adamson et al.   NATURE CELL BIOLOGY

PARP activation regulates the RNA-binding protein NONO in the DNA damage response to DNA double-strand breaks

(2012) Jana Krietsch et al.   NUCLEIC ACIDS RESEARCH

The RNA helicase p68 (DDX5) is selectively required for the induction of p53-dependent p21 expression and cell-cycle arrest after DNA damage

(2012) S M Nicol et al.   ONCOGENE

Putative DNA/RNA helicase Schlafen-11 (SLFN11) sensitizes cancer cells to DNA-damaging agents

(2012) G. Zoppoli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Is post-transcriptional stabilization, splicing and translation of selective mRNAs a key to the DNA damage response?

(2011) H. Christian Reinhardt et al.   CELL CYCLE

Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications

(2011) S. E. Polo et al.   GENES & DEVELOPMENT

Quantitative Proteomics and Dynamic Imaging of the Nucleolus Reveal Distinct Responses to UV and Ionizing Radiation

(2011) Henna M. Moore et al.   MOLECULAR & CELLULAR PROTEOMICS

The Ewing Sarcoma Protein Regulates DNA Damage-Induced Alternative Splicing

(2011) Maria Paola Paronetto et al.   MOLECULAR CELL

DNA Unwinding by ASCC3 Helicase Is Coupled to ALKBH3-Dependent DNA Alkylation Repair and Cancer Cell Proliferation

(2011) Sebastian Dango et al.   MOLECULAR CELL

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

The involvement of human RECQL4 in DNA double-strand break repair

(2010) Dharmendra Kumar Singh et al.   AGING CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Phosphorylation of RIG-I by Casein Kinase II Inhibits Its Antiviral Response

(2010) Z. Sun et al.   JOURNAL OF VIROLOGY

Site-specific Phosphorylation Dynamics of the Nuclear Proteome during the DNA Damage Response

(2010) Martin V. Bennetzen et al.   MOLECULAR & CELLULAR PROTEOMICS

The Nucleolus under Stress

(2010) Séverine Boulon et al.   MOLECULAR CELL

The DNA Damage Response: Making It Safe to Play with Knives

(2010) Alberto Ciccia et al.   MOLECULAR CELL

The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion

(2010) Changanamkandath Rajesh et al.   NUCLEIC ACIDS RESEARCH

REPAIRtoire--a database of DNA repair pathways

(2010) K. Milanowska et al.   NUCLEIC ACIDS RESEARCH

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

(2010) A. Bensimon et al.   Science Signaling

Genome-Wide Association between Branch Point Properties and Alternative Splicing

(2010) André Corvelo et al.   PLoS Computational Biology

A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

(2009) Renee D. Paulsen et al.   MOLECULAR CELL

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Automatic detection of exonic splicing enhancers (ESEs) using SVMs

(2008) Britta Mersch et al.   BMC BIOINFORMATICS

A Role for DEAD Box 1 at DNA Double-Strand Breaks

(2008) L. Li et al.   MOLECULAR AND CELLULAR BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Transcriptional control of human p53-regulated genes

(2008) Todd Riley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Global analysis of cellular protein translation by pulsed SILAC

(2008) Björn Schwanhäusser et al.   PROTEOMICS