Research graph
References from 3plex enables deep computational investigation of triplex forming lncRNAs. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/s41580-020-00315-9
10.1038/s41580-020-00315-9 · External reference
10.1016/j.tcb.2021.02.002
10.1016/j.tcb.2021.02.002 · External reference
10.1016/s0959-440x(96)80051-0
10.1016/s0959-440x(96)80051-0 · External reference
10.1093/nar/gkn493
10.1093/nar/gkn493 · External reference
Comprehensive multi-omics analysis uncovers a group of TGF-β-regulated genes among lncRNA EPR direct transcriptional targets
10.1093/nar/gkaa628 · 2020 · External reference
10.1093/nar/gkac083
10.1093/nar/gkac083 · External reference
Unraveling the structure and biological functions of RNA triple helices
10.1002/wrna.1598 · 2020 · External reference
10.1016/j.chembiol.2016.09.011
10.1016/j.chembiol.2016.09.011 · External reference
Chromatin Isolation by RNA Purification (ChIRP)
2012 · External reference
MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures
2015 · External reference
10.1002/0471142727.mb2125s101
10.1002/0471142727.mb2125s101 · External reference
10.1126/science.1237973
10.1126/science.1237973 · External reference
10.1016/j.cub.2017.01.011
10.1016/j.cub.2017.01.011 · External reference
GRID-seq reveals the global RNA-chromatin interactome
10.1038/nbt.3968 · 2017 · External reference
RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions
10.1038/s41467-020-14337-6 · 2020 · External reference
Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics
10.1093/nar/gkaa457 · 2020 · External reference
RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins
10.1073/pnas.2116222119 · 2022 · External reference
Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
10.7554/elife.27024 · 2018 · External reference
10.1016/j.molcel.2012.01.017
10.1016/j.molcel.2012.01.017 · External reference
Isolation and genome-wide characterization of cellular DNA:RNA triplex structures
10.1093/nar/gky1305 · 2019 · External reference
10.1101/gr.130237.111
10.1101/gr.130237.111 · External reference
Detection of RNA-DNA binding sites in long noncoding RNAs
10.1093/nar/gkz037 · 2019 · External reference
10.1093/bioinformatics/btu643
10.1093/bioinformatics/btu643 · External reference
10.1016/j.csbj.2022.06.017 · Admitted local publication
Deep learning based DNA:RNA triplex forming potential prediction
10.1186/s12859-020-03864-0 · 2020 · External reference
A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactions
10.1093/bib/bbac445 · 2022 · External reference
Computational methods to study DNA:DNA:RNA triplex formation by lncRNAs
10.3390/ncrna9010010 · 2023 · External reference
10.1038/nature06496
10.1038/nature06496 · External reference
Total Binding Affinity profiles of regulatory regions predict transcription factor binding and gene expression in human cells
2015 · External reference
Practical guidance in genome-wide RNA:DNA triple helix prediction
10.3390/ijms21030830 · 2020 · External reference
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches
10.1093/bib/bbac205 · 2022 · External reference
10.1021/acs.accounts.0c00734
10.1021/acs.accounts.0c00734 · External reference
10.1093/nar/gky722
10.1093/nar/gky722 · External reference
10.1093/nar/30.1.207
10.1093/nar/30.1.207 · External reference
The european nucleotide archive in 2022
2022 · External reference
10.1093/nar/gky955
10.1093/nar/gky955 · External reference
MIR205HG/LEADR long noncoding RNA binds to primed proximal regulatory regions in prostate basal cells through a triplex- and alu-mediated mechanism
10.3389/fcell.2022.909097 · 2022 · External reference
10.1038/s41467-021-21217-0
10.1038/s41467-021-21217-0 · External reference
10.1038/nature11247
10.1038/nature11247 · External reference
10.1038/nbt.1508
10.1038/nbt.1508 · External reference
10.1214/11-aoas466
10.1214/11-aoas466 · External reference
10.1093/bioinformatics/btq033
10.1093/bioinformatics/btq033 · External reference
ViennaRNA Package 2.0
10.1186/1748-7188-6-26 · 2011 · External reference
pROC: an open-source package for R and S+ to analyze and compare ROC curves
10.1186/1471-2105-12-77 · 2011 · External reference
Snakemake--a scalable bioinformatics workflow engine
10.1093/bioinformatics/bts480 · 2012 · External reference
10.1093/nar/gkp335
10.1093/nar/gkp335 · External reference
Evaluating tools for transcription factor binding site prediction
10.1186/s12859-016-1298-9 · 2016 · External reference
10.1093/nar/gkab1113
10.1093/nar/gkab1113 · External reference
FIMO: scanning for occurrences of a given motif
10.1093/bioinformatics/btr064 · 2011 · External reference
10.1093/hmg/ddv343
10.1093/hmg/ddv343 · External reference
10.1172/jci87927
10.1172/jci87927 · External reference
10.1146/annurev-cellbio-100617-062719
10.1146/annurev-cellbio-100617-062719 · External reference
Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation
10.1186/s13100-019-0173-4 · 2019 · External reference
10.1093/nar/gkz573
10.1093/nar/gkz573 · External reference
10.1093/nar/gkaa880
10.1093/nar/gkaa880 · External reference
Genome-wide computational analysis of potential long noncoding RNA mediated DNA: DNA: RNA triplexes in the human genome
10.1186/s12967-017-1282-9 · 2017 · External reference
Super-lncRNAs: identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation
10.1261/rna.061317.117 · 2017 · External reference
