Aberrant RNA methylation triggers recruitment of an alkylation repair complex

The roles of RNA in DNA double-strand break repair

(2020) Aldo S. Bader et al.   BRITISH JOURNAL OF CANCER

RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1

(2020) Yoshitaka Matsuo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The ASC-1 Complex Disassembles Collided Ribosomes

(2020) Szymon Juszkiewicz et al.   MOLECULAR CELL

TDP-43 dysfunction results in R-loop accumulation and DNA replication defects

(2020) Matthew Wood et al.   JOURNAL OF CELL SCIENCE

Mitotic regulators TPX2 and Aurora A protect DNA forks during replication stress by counteracting 53BP1 function

(2019) Andrea K. Byrum et al.   JOURNAL OF CELL BIOLOGY

Post-translational regulation of ubiquitin signaling

(2019) Lei Song et al.   JOURNAL OF CELL BIOLOGY

Transcriptome-wide Mapping of Internal N7-Methylguanosine Methylome in Mammalian mRNA

(2019) Li-Sheng Zhang et al.   MOLECULAR CELL

Intersections between transcription-coupled repair and alkylation damage reversal

(2019) Joshua R. Brickner et al.   DNA REPAIR

Oxidation and alkylation stresses activate ribosome-quality control

(2019) Liewei L. Yan et al.   Nature Communications

Structure and Conformational Dynamics of the Human Spliceosomal B act Complex

(2018) David Haselbach et al.   CELL

Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds

(2018) Constantin Cretu et al.   MOLECULAR CELL

OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling

(2018) Yu Zhao et al.   MOLECULAR CELL

Three distinct 3-methylcytidine (m 3 C) methyltransferases modify tRNA and mRNA in mice and humans

(2017) Luang Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair

(2017) Olga M. Mazina et al.   MOLECULAR CELL

A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair

(2017) Joshua R. Brickner et al.   NATURE

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Regulation of DNA Alkylation Damage Repair: Lessons and Therapeutic Opportunities

(2017) Jennifer M. Soll et al.   TRENDS IN BIOCHEMICAL SCIENCES

AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis in cancer cells

(2017) Yuko Ueda et al.   Scientific Reports

ALKBH1-Mediated tRNA Demethylation Regulates Translation

(2016) Fange Liu et al.   CELL

Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers

(2016) Petra Schwertman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure of a yeast activated spliceosome at 3.5 A resolution

(2016) C. Yan et al.   SCIENCE

EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test

(2016) Alexander Marx et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond

(2015) Bogdan I. Fedeles et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

(2015) Ruijie Liu et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The p53 mRNA-Mdm2 Interaction Controls Mdm2 Nuclear Trafficking and Is Required for p53 Activation following DNA Damage

(2012) Madhavsai Gajjar et al.   CANCER CELL

Methylation damage to RNA induced in vivo in Escherichia coli is repaired by endogenous AlkB as part of the adaptive response

(2012) Cathrine Broberg Vågbø et al.   DNA REPAIR

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

(2011) Sebastian Dango et al.   MOLECULAR CELL

Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae

(2011) A. Noma et al.   RNA

A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop

(2011) S. D'Silva et al.   RNA

ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

(2011) Erwin van den Born et al.   Nature Communications

ATM-Dependent Chromatin Changes Silence Transcription In cis to DNA Double-Strand Breaks

(2010) Niraj M. Shanbhag et al.   CELL

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

Viral AlkB proteins repair RNA damage by oxidative demethylation

(2008) Erwin van den Born et al.   NUCLEIC ACIDS RESEARCH