Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions

HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia

(2022) Huacheng Luo et al.   MOLECULAR CELL

Best practices for the visualization, mapping, and manipulation of R‐loops

(2021) Frédéric Chédin et al.   EMBO JOURNAL

A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide

(2021) Phillip Wulfridge et al.   eLife

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor

(2021) Kang Wang et al.   Science Advances

Correlation AnalyzeR: functional predictions from gene co-expression correlations

(2021) Henry E. Miller et al.   BMC BIOINFORMATICS

ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates

(2021) Rhys Newell et al.   GENOMICS

UPF1 promotes the formation of R loops to stimulate DNA double-strand break repair

(2021) Greg H. P. Ngo et al.   Nature Communications

The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions

(2021) Charanya Kumar et al.   eLife

Defining R-loop classes and their contributions to genome instability

(2021) Daisy Castillo-Guzman et al.   DNA REPAIR

R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation

(2021) Ruoyao Lin et al.   NUCLEIC ACIDS RESEARCH

Ultra-Deep Coverage Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

(2020) Maika Malig et al.   JOURNAL OF MOLECULAR BIOLOGY

Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA

(2020) Hai Pan et al.   NUCLEIC ACIDS RESEARCH

RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2

(2020) Célia Alecki et al.   Nature Communications

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility

(2020) Henry E. Miller et al.   Cancers

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

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

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

R-loop induced G-quadruplex in non-template promotes transcription by successive R-loop formation

(2020) Chun-Ying Lee et al.   Nature Communications

Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming

(2020) Pengze Yan et al.   Cell Reports

R-loops coordinate with SOX2 in regulating reprogramming to pluripotency

(2020) Yaoyi Li et al.   Science Advances

Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution

(2020) Oscar D Villarreal et al.   Life Science Alliance

MYC Oncogene Contributions to Release of Cell Cycle Brakes

(2019) Lucía García-Gutiérrez et al.   Genes

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes

(2019) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

R-ChIP for genome-wide mapping of R-loops by using catalytically inactive RNASEH1

(2019) Jia-Yu Chen et al.   Nature Protocols

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation

(2019) Isabel Ferreirós-Vidal et al.   PLOS BIOLOGY

Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach

(2019) Qingqing Yan et al.   Cell Reports

The molecular landscape of ETMR at diagnosis and relapse

(2019) Sander Lambo et al.   NATURE

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast

(2018) Stella R. Hartono et al.   JOURNAL OF MOLECULAR BIOLOGY

Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers

(2018) Vladimir A Kuznetsov et al.   NUCLEIC ACIDS RESEARCH

Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair

(2018) Wei-Ting Lu et al.   Nature Communications

Massive mining of publicly available RNA-seq data from human and mouse

(2018) Alexander Lachmann et al.   Nature Communications

EWS–FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma

(2018) Aparna Gorthi et al.   NATURE

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

GADD45A binds R-loops and recruits TET1 to CpG island promoters

(2018) Khelifa Arab et al.   NATURE GENETICS

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

(2017) Liang Chen et al.   MOLECULAR CELL

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin

(2017) Aleix Bayona-Feliu et al.   Nature Communications

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Machine learning model for sequence-driven DNA G-quadruplex formation

(2017) Aleksandr B. Sahakyan et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

(2016) Lamia Wahba et al.   GENES & DEVELOPMENT

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

(2016) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends

(2016) Julia H. Chariker et al.   PLoS One

EpiMINE, a computational program for mining epigenomic data

(2016) SriGanesh Jammula et al.   Epigenetics & Chromatin

Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots

(2016) Merja Heinäniemi et al.   eLife

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences

(2015) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Feature Selection with theBorutaPackage

(2015) Miron B. Kursa et al.   Journal of Statistical Software

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

(2014) Heeyoun Bunch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination

(2013) P. A. Ginno et al.   GENOME RESEARCH

R Loops Are Linked to Histone H3 S10 Phosphorylation and Chromatin Condensation

(2013) Maikel Castellano-Pozo et al.   MOLECULAR CELL

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

R-loop-mediated genomic instability is caused by impairment of replication fork progression

(2011) W. Gan et al.   GENES & DEVELOPMENT

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer

(2009) Charles J. David et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY