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References from Exploring the landscape of tools and resources for the analysis of long non-coding RNAs. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/538275a
10.1038/538275a · External reference
10.1093/nar/gkv1189
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10.1093/nar/gkac1071 · External reference
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10.1038/nature11247
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Long non-coding RNAs: definitions, functions, challenges and recommendations
2023 · External reference
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10.1146/annurev-biochem-062917-012708
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Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets
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R.N.A.s in disease
10.1002/1873-3468.13182 · 2018 · External reference
Roles of long non-coding RNAs in the development of aging-related neurodegenerative diseases
2022 · External reference
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10.1016/j.cell.2015.01.009
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Muscle physiology: a peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle
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10.1016/j.molcel.2013.07.022
10.1016/j.molcel.2013.07.022 · External reference
10.1016/j.cell.2007.05.022
10.1016/j.cell.2007.05.022 · External reference
10.4161/rna.29624
10.4161/rna.29624 · External reference
Deficiency in the nuclear long noncoding RNA Charme causes myogenic defects and heart remodeling in mice
10.15252/embj.201899697 · 2018 · External reference
10.1038/nsmb.2764
10.1038/nsmb.2764 · External reference
10.1093/nar/gkaa921
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10.1093/nar/gkaa1076 · 2021 · External reference
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts
2020 · External reference
LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations
10.1093/nar/gkac999 · 2023 · External reference
Lncipedia 5: towards a reference set of human long non-coding rnas
10.1093/nar/gky1031 · 2019 · External reference
10.1093/nar/gku988
10.1093/nar/gku988 · External reference
RAIN: RNA-protein association and interaction networks
10.1093/database/baw167 · 2017 · External reference
10.1093/nar/gkac1000
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10.1093/nar/gkab435
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10.1093/nar/gkac1002
10.1093/nar/gkac1002 · External reference
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility
10.1093/nar/gkab997 · 2022 · External reference
RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome
2023 · External reference
Artificial intelligence methods enhance the discovery of RNA interactions
10.3389/fmolb.2022.1000205 · 2022 · External reference
10.1093/nar/gkab1112
10.1093/nar/gkab1112 · External reference
RISE: a database of RNA interactome from sequencing experiments
10.1093/nar/gkx864 · 2018 · External reference
RAID v2.0: an updated resource of RNA-associated interactions across organisms
10.1093/nar/gkw1052 · 2017 · External reference
Lncrrisearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data
10.3389/fgene.2019.00462 · 2019 · External reference
TANRIC: an interactive open platform to explore the function of IncRNAs in cancer
10.1158/0008-5472.can-15-0273 · 2015 · External reference
LncSLdb: a resource for long non-coding RNA subcellular localization
2018 · External reference
Lnclocation: efficient subcellular location prediction of long non-coding rna-based multi-source heterogeneous feature fusion
10.3390/ijms21197271 · 2020 · External reference
GM-lncLoc: LncRNAs subcellular localization prediction based on graph neural network with meta-learning
2023 · External reference
GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation
2023 · External reference
10.1038/nbt.1883
10.1038/nbt.1883 · External reference
10.1093/bioinformatics/bts094
10.1093/bioinformatics/bts094 · External reference
10.1089/cmb.2012.0021
10.1089/cmb.2012.0021 · External reference
10.1128/mcb.01394-14
10.1128/mcb.01394-14 · External reference
CPAT: coding-potential assessment tool using an alignment-free logistic regression model
10.1093/nar/gkt006 · 2013 · External reference
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome
2017 · External reference
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
2014 · External reference
10.1093/nar/gkw798
10.1093/nar/gkw798 · External reference
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning
10.1093/bib/bbac583 · 2023 · External reference
IncRScan-SVM: a tool for predicting long non-coding RNAs using support vector machine
2015 · External reference
10.1093/bioinformatics/btr209
10.1093/bioinformatics/btr209 · External reference
10.1261/rna.2536111
10.1261/rna.2536111 · External reference
10.1093/nar/gkz410
10.1093/nar/gkz410 · External reference
10.1093/nar/gkaa806
10.1093/nar/gkaa806 · External reference
lncEvo: automated identification and conservation study of long noncoding RNAs
10.1186/s12859-021-03991-2 · 2021 · External reference
A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs
10.1261/rna.074724.120 · 2021 · External reference
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
10.1093/database/bav082 · 2015 · External reference
Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks
2013 · External reference
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts
2017 · External reference
10.1042/bst20191059
10.1042/bst20191059 · External reference
Predicting RNA-protein interactions using only sequence information
10.1186/1471-2105-12-489 · 2011 · External reference
Rpiter: a hierarchical deep learning framework for ncRNA-protein interaction prediction
10.3390/ijms20051070 · 2019 · External reference
DM-RPIs: predicting ncRNA-protein interactions using stacked ensembling strategy
10.1016/j.compbiolchem.2019.107088 · 2019 · External reference
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA–protein interaction prediction
2021 · External reference
IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction
2016 · External reference
Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks
2017 · External reference
HLPI-Ensemble: prediction of human lncRNA-protein interactions based on ensemble strategy
2018 · External reference
RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information
2020 · External reference
LPGNMF: predicting long non-coding RNA and protein interaction using graph regularized nonnegative matrix factorization
10.1109/tcbb.2018.2861009 · 2020 · External reference
BGFE: a deep learning model for ncRNA-protein interaction predictions based on improved sequence information
2019 · External reference
CatRAPID signature: identification of ribonucleoproteins and RNA-binding regions
10.1093/bioinformatics/btv629 · 2016 · External reference
CatRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions
10.1093/nar/gkab393 · 2021 · External reference
RBPsuite: RNA-protein binding sites prediction suite based on deep learning
10.1186/s12864-020-07291-6 · 2020 · External reference
10.1093/bioinformatics/btx361
10.1093/bioinformatics/btx361 · External reference
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data
2018 · External reference
10.1038/s41422-021-00476-y
10.1038/s41422-021-00476-y · External reference
LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning
10.1093/bioinformatics/bty428 · 2018 · External reference
MicroRNA targets in Drosophila
10.1186/gb-2003-5-1-r1 · 2003 · External reference
The biochemical basis of microRNA targeting efficacy
10.1126/science.aav1741 · 2019 · External reference
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
10.1186/s12859-019-3105-x · 2019 · External reference
10.1038/nmeth.1611
10.1038/nmeth.1611 · External reference
10.1016/j.cell.2011.07.014
10.1016/j.cell.2011.07.014 · External reference
10.1016/j.cell.2011.09.028
10.1016/j.cell.2011.09.028 · External reference
10.1038/nature12986
10.1038/nature12986 · External reference
A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs
10.15252/embj.2021108918 · 2022 · External reference
The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart
10.7554/elife.81360 · 2023 · External reference
Epigenetic regulation of wnt7b expression by the cis-acting long noncoding rna lnc-rewind in muscle stem cells
10.7554/elife.54782 · 2021 · External reference
Function by structure: spotlights on xist long non-coding RNA
10.3389/fmolb.2017.00090 · 2017 · External reference
10.1016/j.molcel.2015.03.006
10.1016/j.molcel.2015.03.006 · External reference
Identifying structural domains and conserved regions in the long non-coding RNA lncTCF7
10.3390/ijms20194770 · 2019 · External reference
10.1186/1748-7188-6-26
10.1186/1748-7188-6-26 · External reference
RNAstructure: software for RNA secondary structure prediction and analysis
10.1186/1471-2105-11-129 · 2010 · External reference
PknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
10.1093/nar/gkm258 · 2007 · External reference
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
10.1186/1471-2105-15-147 · 2014 · External reference
Rtools: a web server for various secondary structural analyses on single RNA sequences
10.1093/nar/gkw337 · 2016 · External reference
Rtools: a web server for various secondary structural analyses on single RNA sequences
2023 · External reference
Knotify+: toward the prediction of RNA H-type pseudoknots, including bulges and internal loops
10.3390/biom13020308 · 2023 · External reference
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming
10.1093/nar/gks412 · 2012 · External reference
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
10.1093/bioinformatics/btr215 · 2011 · External reference
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
2011 · External reference
Web-Beagle: a web server for the alignment of RNA secondary structures
10.1093/nar/gkv489 · 2015 · External reference
MultiSETTER: web server for multiple RNA structure comparison
10.1186/s12859-015-0696-8 · 2015 · External reference
BRIO: s web server for RNA sequence and structure motif scan
10.1093/nar/gkab400 · 2021 · External reference
Prediction of RNA secondary structure including pseudoknots for long sequences
10.1093/bib/bbab395 · 2022 · External reference
Discovering sequence and structure landscapes in RNA interaction motifs
10.1093/nar/gkz250 · 2019 · External reference
10.1002/iub.2694
10.1002/iub.2694 · External reference
10.1101/2023.04.14.536965
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10.1038/s43018-020-00114-3 · External reference
10.1038/s41568-021-00353-1
10.1038/s41568-021-00353-1 · External reference
Long noncoding RNAs: fine-tuners hidden in the cancer signaling network
10.1038/s41420-021-00678-8 · 2021 · External reference
The non-coding side of medulloblastoma
10.3389/fcell.2020.00275 · 2020 · External reference
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
10.1038/s42003-019-0741-7 · 2020 · External reference
10.1093/nar/gkab1035
10.1093/nar/gkab1035 · External reference
Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits
2016 · External reference
10.1038/nature20612
10.1038/nature20612 · External reference
The long non-coding RNA nuclear-enriched abundant transcript 1-2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis
10.1186/1756-6606-6-31 · 2013 · External reference
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases
10.1093/nar/gky905 · 2019 · External reference
lncRNASNP v3: an updated database for functional variants in long non-coding RNAs
10.1093/nar/gkac981 · 2023 · External reference
10.1186/s13059-014-0550-8
10.1186/s13059-014-0550-8 · External reference
10.1093/bioinformatics/btp616
10.1093/bioinformatics/btp616 · External reference
10.1093/nar/gkv007
10.1093/nar/gkv007 · External reference
10.1038/s41592-022-01629-6
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Advances in endogenous RNA pull-down: a straightforward dextran sulfate-based method enhancing RNA recovery
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