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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-642-29627-7_30openalex-snapshot

Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer

inferredcites →https://doi.org/10.1007/s12035-018-1246-yopenalex-snapshot

R-Loops in Motor Neuron Diseases

inferredcites →https://doi.org/10.1016/j.cell.2017.05.010openalex-snapshot

A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome Instability

inferredcites →https://doi.org/10.1016/j.cell.2017.07.043openalex-snapshot

Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses

inferredcites →https://doi.org/10.1016/j.cell.2019.06.001openalex-snapshot

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription

inferredcites →https://doi.org/10.1016/j.cell.2019.08.055openalex-snapshot

R Loops: From Physiological to Pathological Roles

inferredcites →https://doi.org/10.1016/j.celrep.2018.04.025openalex-snapshot

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage

inferredcites →https://doi.org/10.1016/j.celrep.2019.09.052openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.celrep.2020.107870openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.celrep.2020.108166openalex-snapshot

BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation

inferredcites →https://doi.org/10.1016/j.jmb.2016.08.031openalex-snapshot

R Loops and Links to Human Disease

inferredcites →https://doi.org/10.1016/j.jmb.2017.12.016openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2011.04.026openalex-snapshot

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

inferredcites →https://doi.org/10.1016/j.molcel.2012.01.017openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2012.04.009openalex-snapshot

R Loops: From Transcription Byproducts to Threats to Genome Stability

inferredcites →https://doi.org/10.1016/j.molcel.2015.04.001openalex-snapshot

SMADs and YAP Compete to Control Elongation of β-Catenin:LEF-1-Recruited RNAPII during hESC Differentiation

inferredcites →https://doi.org/10.1016/j.molcel.2016.05.032openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2016.11.030openalex-snapshot

RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells

inferredcites →https://doi.org/10.1016/j.molcel.2017.10.008openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2017.12.029openalex-snapshot

The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations

inferredcites →https://doi.org/10.1016/j.molcel.2018.10.011openalex-snapshot

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

inferredcites →https://doi.org/10.1016/j.molcel.2019.01.024openalex-snapshot

R-Loops as Cellular Regulators and Genomic Threats

inferredcites →https://doi.org/10.1016/j.molcel.2019.10.002openalex-snapshot

R-Loops Promote Antisense Transcription across the Mammalian Genome

inferredcites →https://doi.org/10.1016/j.molcel.2020.06.017openalex-snapshot

METTL3 and N6-Methyladenosine Promote Homologous Recombination-Mediated Repair of DSBs by Modulating DNA-RNA Hybrid Accumulation

inferredcites →https://doi.org/10.1016/j.tibs.2014.01.003openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.xinn.2021.100141openalex-snapshot

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

inferredcites →https://doi.org/10.1038/nature10730openalex-snapshot

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

inferredcites →https://doi.org/10.1038/nature13374openalex-snapshot

BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2

inferredcites →https://doi.org/10.1038/nature13986openalex-snapshot

Topologically associating domains are stable units of replication-timing regulation

inferredcites →https://doi.org/10.1038/nbt.3295openalex-snapshot

High-throughput sequencing of DNA G-quadruplex structures in the human genome

inferredcites →https://doi.org/10.1038/ncomms15908openalex-snapshot

Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis

inferredcites →https://doi.org/10.1038/ncomms2792openalex-snapshot

G-quadruplex structures are stable and detectable in human genomic DNA

inferredcites →https://doi.org/10.1038/ng.2653openalex-snapshot

The Genotype-Tissue Expression (GTEx) project

inferredcites →https://doi.org/10.1038/ng.2764openalex-snapshot

The Cancer Genome Atlas Pan-Cancer analysis project

inferredcites →https://doi.org/10.1038/ng.3142openalex-snapshot

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nsmb.3122openalex-snapshot

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

inferredcites →https://doi.org/10.1038/s41422-019-0235-7openalex-snapshot

m6A promotes R-loop formation to facilitate transcription termination

inferredcites →https://doi.org/10.1038/s41467-018-02893-xopenalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41467-018-02894-wopenalex-snapshot

Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

inferredcites →https://doi.org/10.1038/s41467-018-06677-1openalex-snapshot

DHX9 helicase promotes R-loop formation in cells with impaired RNA splicing

inferredcites →https://doi.org/10.1038/s41467-020-17176-7openalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41467-020-17858-2openalex-snapshot

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

inferredcites →https://doi.org/10.1038/s41477-017-0004-xopenalex-snapshot

The R-loop is a common chromatin feature of the Arabidopsis genome

inferredcites →https://doi.org/10.1038/s41556-020-0514-zopenalex-snapshot

Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance

inferredcites →https://doi.org/10.1038/s41556-021-00663-4openalex-snapshot

R-loops as Janus-faced modulators of DNA repair

inferredcites →https://doi.org/10.1038/s41580-019-0206-3openalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41586-019-1186-3openalex-snapshot

Next-generation characterization of the Cancer Cell Line Encyclopedia

inferredcites →https://doi.org/10.1038/s41586-020-2493-4openalex-snapshot

Expanded encyclopaedias of DNA elements in the human and mouse genomes

inferredcites →https://doi.org/10.1038/s41586-020-2497-0openalex-snapshot

Nucleolar RNA polymerase II drives ribosome biogenesis

inferredcites →https://doi.org/10.1038/s41586-021-03538-8openalex-snapshot

RNA transcripts stimulate homologous recombination by forming DR-loops

inferredcites →https://doi.org/10.1038/s41594-018-0131-8openalex-snapshot

DNA G-quadruplex structures mold the DNA methylome

inferredcites →https://doi.org/10.1038/s41594-020-0408-6openalex-snapshot

RTEL1 suppresses G-quadruplex-associated R-loops at difficult-to-replicate loci in the human genome

inferredcites →https://doi.org/10.1038/s41596-019-0154-6openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1613181114openalex-snapshot

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

inferredcites →https://doi.org/10.1073/pnas.1810409116openalex-snapshot

DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells

inferredcites →https://doi.org/10.1080/15548627.2020.1796292openalex-snapshot

SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btt730openalex-snapshot

CrossMap: a versatile tool for coordinate conversion between genome assemblies

inferredcites →https://doi.org/10.1093/nar/gkaa1070openalex-snapshot

The UCSC Genome Browser database: 2021 update

inferredcites →https://doi.org/10.1093/nar/gkaa1074openalex-snapshot

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

inferredcites →https://doi.org/10.1093/nar/gkaa1113openalex-snapshot

The Gene Ontology resource: enriching a GOld mine

inferredcites →https://doi.org/10.1093/nar/gkaa500openalex-snapshot

qDRIP: a method to quantitatively assess RNA–DNA hybrid formation genome-wide

inferredcites →https://doi.org/10.1093/nar/gkaa841openalex-snapshot

Detection of genomic G-quadruplexes in living cells using a small artificial protein

inferredcites →https://doi.org/10.1093/nar/gks1193openalex-snapshot

NCBI GEO: archive for functional genomics data sets—update

inferredcites →https://doi.org/10.1093/nar/gkw1054openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkw425openalex-snapshot

QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

inferredcites →https://doi.org/10.1093/nar/gkx724openalex-snapshot

Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome

inferredcites →https://doi.org/10.1093/nar/gky1032openalex-snapshot

Human Disease Ontology 2018 update: classification, content and workflow expansion

inferredcites →https://doi.org/10.1101/gad.1200804openalex-snapshot

Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA

inferredcites →https://doi.org/10.1101/gad.280834.116openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gad.313973.118openalex-snapshot

NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes

inferredcites →https://doi.org/10.1101/gad.336024.119openalex-snapshot

UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide

inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

inferredcites →https://doi.org/10.1101/gr.136184.111openalex-snapshot

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

inferredcites →https://doi.org/10.1101/gr.158436.113openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.219394.116openalex-snapshot

RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases

inferredcites →https://doi.org/10.1101/gr.229102openalex-snapshot

The Human Genome Browser at UCSC

inferredcites →https://doi.org/10.1101/gr.237362.118openalex-snapshot

Human proteins that interact with RNA/DNA hybrids

inferredcites →https://doi.org/10.1126/sciadv.abe3516openalex-snapshot

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

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-018-1478-1openalex-snapshot

DNA Topoisomerase I differentially modulates R-loops across the human genome

inferredcites →https://doi.org/10.1186/s13072-015-0040-6openalex-snapshot

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

inferredcites →https://doi.org/10.12688/f1000research.9090.1openalex-snapshot

AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations

inferredcites →https://doi.org/10.1371/journal.pgen.1007781openalex-snapshot

RNase H1 directs origin-specific initiation of DNA replication in human mitochondria

inferredcites →https://doi.org/10.15252/embj.2020106394openalex-snapshot

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

inferredcites →https://doi.org/10.26508/lsa.202000762openalex-snapshot

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

inferredcites →https://doi.org/10.3390/ncrna4020009openalex-snapshot

Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops

inferredcites →https://doi.org/10.7554/elife.08007openalex-snapshot

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome

inferredcites →https://doi.org/10.7554/elife.17548openalex-snapshot

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage

inferredcites →https://doi.org/10.7554/elife.28306openalex-snapshot

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4804941openalex-extracted

inferred← citeshttps://doi.org/10.1002/cpz1.1037openalex-snapshot

Approaches for Mapping and Analysis of R‐loops

inferred← citeshttps://doi.org/10.1002/imt2.70150openalex-snapshot

Hyperoside alleviates endometrial stromal cell senescence in unexplained recurrent spontaneous abortion via DHX9‐mediated R‐loop resolution

inferred← citeshttps://doi.org/10.1002/wrna.1840openalex-snapshot

Emerging roles of RNA‐binding proteins in fatty liver disease

inferred← citeshttps://doi.org/10.1007/s10495-024-02039-zopenalex-snapshot

Dysregulation of R-loop homeostasis shapes the immunosuppressive microenvironment and induces malignant progression in melanoma

inferred← citeshttps://doi.org/10.1007/s10753-024-02232-xopenalex-snapshot

Identification and Construction of a R-loop Mediated Diagnostic Model and Associated Immune Microenvironment of COPD through Machine Learning and Single-Cell Transcriptomics

inferred← citeshttps://doi.org/10.1016/bs.acr.2024.06.010openalex-snapshot

Unraveling the complexity: Advanced methods in analyzing DNA, RNA, and protein interactions

inferred← citeshttps://doi.org/10.1016/j.ab.2024.115532openalex-snapshot

The bisulfite reaction with cytosine and genomic DNA structure

inferred← citeshttps://doi.org/10.1016/j.canlet.2026.218388openalex-snapshot

BPHL promotes TNBC stemness by resolving R-loops via POLR2A lactylation inhibition and BARD1-mediated ubiquitination

inferred← citeshttps://doi.org/10.1016/j.cell.2024.04.025openalex-snapshot

ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity

inferred← citeshttps://doi.org/10.1016/j.cellin.2023.100112openalex-snapshot

The CHCHD2/Sirt1 corepressors involve in G9a-mediated regulation of RNase H1 expression to control R-loop

inferred← citeshttps://doi.org/10.1016/j.celrep.2026.117408openalex-snapshot

NAT10-dependent N4-acetylcytidine reprograms R-loops and promotes cancer stem cell growth

inferred← citeshttps://doi.org/10.1016/j.celrep.2026.117696openalex-snapshot

A genome-wide functional analysis of conserved intronic regions reveals essential roles for speckle-associated retained introns

inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2026.108947openalex-snapshot

R-loop-driven molecular subtypes reveal prognostic and immunogenomic features in uterine corpus endometrial carcinoma

inferred← citeshttps://doi.org/10.1016/j.dnarep.2025.103859openalex-snapshot

Harnessing R-loop dynamics: Challenging cancer therapy resistance

inferred← citeshttps://doi.org/10.1016/j.gendis.2024.101401openalex-snapshot

Update on R-loops in genomic integrity: Formation, functions, and implications for human diseases

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2026.152307openalex-snapshot

The biogenesis of extrachromosomal circular DNA is associated with enhancer-promoter dynamics and chromatin architecture

inferred← citeshttps://doi.org/10.1016/j.intimp.2026.116421openalex-snapshot

A multi-omics R-loop–linked risk program highlights CKS2-positive proliferative tumor cells as drivers of glioma growth

inferred← citeshttps://doi.org/10.1016/j.isci.2024.110584openalex-snapshot

Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases

inferred← citeshttps://doi.org/10.1016/j.isci.2025.113348openalex-snapshot

Senataxin regulates cisplatin resistance through an R-loop-mediated mechanism in HPV-associated head and neck cancer

inferred← citeshttps://doi.org/10.1016/j.jare.2022.10.016openalex-snapshot

Genome-wide map of R-loops reveals its interplay with transcription and genome integrity during germ cell meiosis

inferred← citeshttps://doi.org/10.1016/j.jbc.2025.108200openalex-snapshot

p53-mediated regulation of LINE1 retrotransposon-derived R-loops

inferred← citeshttps://doi.org/10.1016/j.jbc.2025.108514openalex-snapshot

High-frequency transcription leads to rapid R-loop formation

inferred← citeshttps://doi.org/10.1016/j.jbc.2026.111308openalex-snapshot

Thymine DNA glycosylase binds to R-loops and excises 5-formyl and 5-carboxyl cytosine from DNA/RNA hybrids

inferred← citeshttps://doi.org/10.1016/j.molcel.2025.02.019openalex-snapshot

Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops

inferred← citeshttps://doi.org/10.1016/j.molp.2022.12.012openalex-snapshot

R-loopAtlas: An integrated R-loop resource from 254 plant species sustained by a deep-learning-based tool

inferred← citeshttps://doi.org/10.1016/j.prp.2026.156656openalex-snapshot

Consensus subtypes and a generalizable prognostic signature defined by an R-loop score in hepatocellular carcinoma: Multi-omics analyses pinpoint KIF2A-positive proliferative tumor cells

inferred← citeshttps://doi.org/10.1016/j.tplants.2024.06.011openalex-snapshot

Non-B DNA in plant genomes: prediction, mapping, and emerging roles

inferred← citeshttps://doi.org/10.1021/acs.analchem.2c04353openalex-snapshot

Mass Spectrometry for Assessing Protein–Nucleic Acid Interactions

inferred← citeshttps://doi.org/10.1038/s41380-026-03498-3openalex-snapshot

The novel role of GADD45A in the etiology of autism: modulating neuronal excitability via TET1/R-loop dependent regulation of KCNQ5

inferred← citeshttps://doi.org/10.1038/s41416-024-02729-0openalex-snapshot

PARP inhibition leads to synthetic lethality with key splicing-factor mutations in myelodysplastic syndromes

inferred← citeshttps://doi.org/10.1038/s41467-023-44544-wopenalex-snapshot

PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity

inferred← citeshttps://doi.org/10.1038/s41467-025-64174-8openalex-snapshot

Dual roles of DEAD-box RNA helicase Brr2 in genome stability regulation

inferred← citeshttps://doi.org/10.1038/s41598-026-60844-9openalex-snapshot

Vitamin D3 ameliorates R-loop-induced replication stress and chromosomal instability in MED12-mutant uterine fibroids

inferred← citeshttps://doi.org/10.1038/s42003-025-07815-4openalex-snapshot

Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3

inferred← citeshttps://doi.org/10.1038/s44318-024-00134-0openalex-snapshot

MCM8 interacts with DDX5 to promote R-loop resolution

inferred← citeshttps://doi.org/10.1038/s44319-026-00850-0openalex-snapshot

AURORA A interacts with DICER and SETD2 to promote S-phase progression

inferred← citeshttps://doi.org/10.1089/scd.2023.0196openalex-snapshot

R-Loop Defines Neural Stem/Progenitor Cells During Mouse Neurodevelopment

inferred← citeshttps://doi.org/10.1093/bib/bbac441openalex-snapshot

An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops

inferred← citeshttps://doi.org/10.1093/g3journal/jkaf299openalex-snapshot

In silico mapping of non-canonical DNA structures across the human ribosomal DNA locus

inferred← citeshttps://doi.org/10.1093/jxb/erac433openalex-snapshot

R-loops: emerging key regulators in plants

inferred← citeshttps://doi.org/10.1093/nar/gkac537openalex-snapshot

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

inferred← citeshttps://doi.org/10.1093/nar/gkac732openalex-snapshot

Exploration and analysis of R-loop mapping data with RLBase

inferred← citeshttps://doi.org/10.1093/nar/gkae933openalex-snapshot

Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila

inferred← citeshttps://doi.org/10.1093/nar/gkaf518openalex-snapshot

Specific origin selection and excess functional MCM2–7 loading in ORC-deficient cells

inferred← citeshttps://doi.org/10.1093/nar/gkaf792openalex-snapshot

Genome-wide in vivo and ex vivo mapping of R-loops using engineered N-terminal hybrid-binding domain of RNase H3 (enDR3)

inferred← citeshttps://doi.org/10.1093/nar/gkag816openalex-snapshot

When circular RNAs meet the genome: CiR-loops as chromatin regulators and disease drivers

inferred← citeshttps://doi.org/10.1093/nargab/lqaf077openalex-snapshot

Enhancing R-loop prediction with high-throughput sequencing data

inferred← citeshttps://doi.org/10.1097/md.0000000000042833openalex-snapshot

Unraveling R-loops: The hidden drivers of inflammation and immune dysregulation

inferred← citeshttps://doi.org/10.1101/2022.02.18.480986openalex-snapshot

Systematic Evaluation of Different R-loop Mapping Methods: Achieving Consensus, Resolving Discrepancies and Uncovering Distinct Types of RNA:DNA Hybrids

inferred← citeshttps://doi.org/10.1101/2024.02.22.581374openalex-snapshot

Senataxin modulates resistance to cisplatin through an R-loop mediated mechanism in HPV-associated Head and Neck Squamous Cell Carcinoma

inferred← citeshttps://doi.org/10.1101/2024.04.12.589154openalex-snapshot

p53 mediated regulation of LINE1 retrotransposition derived R-loops

inferred← citeshttps://doi.org/10.1101/gr.278236.123openalex-snapshot

Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA

inferred← citeshttps://doi.org/10.1126/sciadv.adt8346openalex-snapshot

ZC3H4 safeguards genome integrity by preventing transcription-replication conflicts at noncoding RNA loci

inferred← citeshttps://doi.org/10.1126/science.adp1562openalex-snapshot

A long noncoding eRNA forms R-loops to shape emotional experience–induced behavioral adaptation

inferred← citeshttps://doi.org/10.1146/annurev-genom-120324-010100openalex-snapshot

Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes

inferred← citeshttps://doi.org/10.1172/jci163325openalex-snapshot

SF3B1 mutation and ATM deletion codrive leukemogenesis via centromeric R-loop dysregulation

inferred← citeshttps://doi.org/10.1186/s12935-025-03775-1openalex-snapshot

Identifying PSIP1 as a critical R-loop regulator in osteosarcoma via machine-learning and multi-omics analysis

inferred← citeshttps://doi.org/10.1186/s12943-023-01924-6openalex-snapshot

Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.1186/s13046-022-02319-zopenalex-snapshot

LncRNA-mediated DNA methylation: an emerging mechanism in cancer and beyond

inferred← citeshttps://doi.org/10.1186/s13046-025-03461-0openalex-snapshot

The LncRNA STEAP3-AS1 promotes liver metastasis in colorectal cancer by regulating histone lactylation through chromatin remodelling

inferred← citeshttps://doi.org/10.1371/journal.ppat.1012341openalex-snapshot

Epstein-Barr virus reactivation induces divergent abortive, reprogrammed, and host shutoff states by lytic progression

inferred← citeshttps://doi.org/10.18632/aging.206132openalex-snapshot

Werner syndrome RECQ helicase participates in and directs maintenance of the protein complexes of constitutive heterochromatin in proliferating human cells

inferred← citeshttps://doi.org/10.21203/rs.3.rs-1822741/v1openalex-snapshot

The G9a/CHCHD2/Sirt1 Regulatory Module Acts on RNase H1 to Control R-Loop Formation at rDNA Sites

inferred← citeshttps://doi.org/10.3389/fcimb.2026.1852766openalex-snapshot

Alternative nucleic acid structures in microbial biology: regulatory functions and antimicrobial opportunities

inferred← citeshttps://doi.org/10.3389/fcvm.2026.1782258openalex-snapshot

Reduced R-loop abundance at proinflammatory loci: a shared epigenetic mechanism in inflammatory and metabolic diseases

inferred← citeshttps://doi.org/10.3389/fimmu.2024.1487372openalex-snapshot

Integrated single-cell and bulk transcriptome analysis of R-loop score-based signature with regard to immune microenvironment, lipid metabolism and prognosis in HCC

inferred← citeshttps://doi.org/10.3389/fimmu.2026.1758954openalex-snapshot

The role of R-loop aberrations in lower-grade gliomas: prognostic, immune, and metabolic implications from multi-omics and machine learning analysis

inferred← citeshttps://doi.org/10.3389/fimmu.2026.1839925openalex-snapshot

Machine learning-derived R-loop-related diagnostic signature for psoriasis: a multi-cohort and single-cell validation study

inferred← citeshttps://doi.org/10.3389/fimmu.2026.1911700openalex-snapshot

SSB deficiency-induced R-loop accumulation triggers podocyte inflammation in DKD

inferred← citeshttps://doi.org/10.3389/frhem.2023.1297657openalex-snapshot

R-loops in normal and malignant hematopoiesis

inferred← citeshttps://doi.org/10.3390/genes13122181openalex-snapshot

Pathophysiological Role and Diagnostic Potential of R-Loops in Cancer and Beyond

inferred← citeshttps://doi.org/10.3390/molecules29204920openalex-snapshot

The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.6084/m9.figshare.24979522openalex-snapshot

Additional file 1 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.24980069openalex-snapshot

Additional file 2 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665948openalex-snapshot

Additional file 3 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665951openalex-snapshot

Additional file 4 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665954openalex-snapshot

Additional file 5 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665957openalex-snapshot

Additional file 6 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665960openalex-snapshot

Additional file 7 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665963openalex-snapshot

Additional file 8 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665966openalex-snapshot

Additional file 9 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665969openalex-snapshot

Additional file 10 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665972openalex-snapshot

Additional file 11 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665975openalex-snapshot

Additional file 12 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.6084/m9.figshare.26665978openalex-snapshot

Additional file 13 of Aberrant R-loop–mediated immune evasion, cellular communication, and metabolic reprogramming affect cancer progression: a single-cell analysis

inferred← citeshttps://doi.org/10.64898/2026.06.01.729367openalex-snapshot

R-loop Prediction Reveals Generalization Limits of DNA Foundation Models Beyond Regulatory Genomics

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