Search Results - Long non-coding RNA secondary structures

A Graph-Based Algorithm for Detecting Long Non-Coding RNAs Through RNA Secondary Structure Analysis

Authors: Hugo Cabrera-Ibarra David Hernández-Granados Lina Riego-Ruiz

Source: Algorithms, Vol 18, Iss 10, p 652 (2025)

Subject Terms: RNA, lncRNAs, secondary structure, rooted tree graphs, algorithm, Saccharomyces cerevisiae, Industrial engineering. Management engineering, T55.4-60.8, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4893/18/10/652; https://doaj.org/toc/1999-4893

Access URL: https://doaj.org/article/66ad222c2bf24e93a2115dd8a0461e54

A Graph-Based Algorithm for Detecting Long Non-Coding RNAs Through RNA Secondary Structure Analysis.

Authors: Cabrera-Ibarra, Hugo Hernández-Granados, David Riego-Ruiz, Lina

Source: Algorithms; Oct2025, Vol. 18 Issue 10, p652, 18p

Subject Terms: GRAPH algorithms, STRUCTURAL analysis (Science), LINCRNA, RNA, BIOMARKERS, NUCLEOTIDE sequence

The molecular structure of long non-coding RNAs: emerging patterns and functional implications.

Authors: Chillón, Isabel Marcia, Marco

Source: Critical reviews in biochemistry and molecular biology. 55(6):662-690

Subject Terms: RNA chemical probing, RNA evolution, RNA protein interactions, RNA secondary and tertiary structure, RNA triple helix, kissing loops, pseudoknots, right-turns, structural biology

File Description: print

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-541558

sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure.

Authors: Bugnon, Leandro A Persia, Leandro Di Gerard, Matias et al.

Source: Briefings in Bioinformatics. Jul2024, Vol. 25 Issue 4, p1-11. 11p.

Subject Terms: *DYNAMIC programming, NUCLEOTIDE sequence, NON-coding RNA, DEEP learning, RNA

An exon-biased biophysical approach and NMR spectroscopy define the secondary structure of a conserved helical element within the HOTAIR long non-coding RNA

Authors: Ainur Abzhanova Alexander Hirschi Nicholas J. Reiter

Source: Journal of Structural Biology. 213:107728

Subject Terms: 0301 basic medicine, RNA Folding, 0303 health sciences, 03 medical and health sciences, Magnetic Resonance Spectroscopy, Humans, Nucleic Acid Conformation, RNA, Long Noncoding, Exons, Ultracentrifugation

Access URL: https://pubmed.ncbi.nlm.nih.gov/33753203
https://europepmc.org/article/MED/33753203
https://pubmed.ncbi.nlm.nih.gov/33753203/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8217201
https://www.sciencedirect.com/science/article/pii/S1047847721000332

G·U base pairing motifs in long non-coding RNAs.

Authors: Sabalette, Karina Belen Makarova, Liubov Marcia, Marco

Source: Biochimie. 214(Pt A):123-140

Subject Terms: G·U wobble, Pseudoknots, RNA conservation, Triple helix, lncRNA functional domains, lncRNA protein interactions, lncRNA structure, non canonical watson crick interaction

File Description: print

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-541552

SSS-test: a novel test for detecting positive selection on RNA secondary structure

Authors: Maria Beatriz Walter Costa Christian Höner zu Siederdissen Marko Dunjić et al.

Source: BMC Bioinformatics, Vol 20, Iss 1, Pp 1-19 (2019)

Subject Terms: Long non-coding RNA, Positive selection, RNA secondary structure, Psychiatric disorders, Primate genomes, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-019-2711-y; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/d093d1a135674950815824fbb782c6ab

Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.

Authors: Li P Liu ZP

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2883, pp. 363-376.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Deep Learning* , RNA, Long Noncoding*/genetics , RNA, Long Noncoding*/metabolism , Computational Biology*/methods, Humans ; Neural Networks, Computer ; Protein Binding ; Proteins/metabolism ; Proteins/chemistry ; Proteins/genetics ; RNA-Binding Proteins/metabolism ; RNA-Binding Proteins/chemistry ; RNA-Binding Proteins/genetics ; Software

Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus.

Authors: Triebel, Sandra Lamkiewicz, Kevin Ontiveros, Nancy et al.

Source: Scientific Reports; 7/2/2024, Vol. 14 Issue 1, p1-12, 12p

Subject Terms: HEPATITIS C virus, NON-coding RNA, RNA, VIRAL genomes, SEQUENCE spaces

A Perspective on the Algorithms Predicting and Evaluating the RNA Secondary Structure

Authors: Fiscon G Iannello G Paci P

Source: Journal of Genetics and Genome Research 3 (2016).
info:cnr-pdr/source/autori:Giulia Fiscon, Giulio Iannello and Paola Paci/titolo:A perspective on the algorithms predicting and evaluating the RNA secondary structure/doi:/rivista:Journal of Genetics and Genome Research/anno:2016/pagina_da:/pagina_a:/intervallo_pagine:/volume:3

Subject Terms: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, COMPUTATIONAL AND SYSTEMS BIOLOGY, RNA secondary structures, Long non-coding RNA secondary structures, RNA structure prediction tools, Dynamic programming algorithms

File Description: application/pdf

Access URL: http://www.cnr.it/prodotto/i/358694
https://publications.cnr.it/doc/358694
https://clinmedjournals.org/articles/jggr/journal-of-genetics-and-genome-research-jggr-3-023.php?jid=jggr
https://hdl.handle.net/20.500.14243/322642

In vivo RNA structure influences the translation and stability of plant long noncoding RNAs.

Authors: Dong, Qianli Yang, Bibo Sun, Wenqing et al.

Source: Plant Commun ; ISSN:2590-3462

Subject Terms: Long non-coding RNAs (lncRNAs), RNA stability, RNA structural motifs, RNA structure, Translation

Relation: https://doi.org/10.1016/j.xplc.2025.101575; https://pubmed.ncbi.nlm.nih.gov/41146492

Availability: https://doi.org/10.1016/j.xplc.2025.101575
https://pubmed.ncbi.nlm.nih.gov/41146492

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

Authors: Kevin V. Morris Leonard Lipovich Per Johnsson et al.

Source: Biochimica et Biophysica Acta (BBA) - General Subjects. 1840:1063-1071

Subject Terms: Evolution, Molecular, 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, Animals, Humans, RNA, Antisense, RNA, Long Noncoding, 16. Peace & justice, Conserved Sequence

Access URL: https://europepmc.org/articles/pmc3909678?pdf=render
https://pubmed.ncbi.nlm.nih.gov/24184936
https://pubmed.ncbi.nlm.nih.gov/24184936/
https://www.ncbi.nlm.nih.gov/pubmed/24184936
http://europepmc.org/articles/PMC3909678
https://www.sciencedirect.com/science/article/pii/S0304416513004753

Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes

Authors: He, F Wei, R Zhou, Z et al.

Index Terms: Journal Article

URL: http://hdl.handle.net/11343/249770

Evolutionarily conserved RNA secondary structures in coding and non-coding sequences at the 3′ end of the hepatitis G virus/GB-virus C genome

Authors: Peter Simmonds N. M. Cuceanu Andrew Tuplin

Source: Journal of General Virology. 82:713-722

Subject Terms: 0301 basic medicine, Protein Folding, 0303 health sciences, Base Sequence, Flaviviridae, Molecular Sequence Data, Viral Nonstructural Proteins, Biological Evolution, Protein Structure, Secondary, 3. Good health, 03 medical and health sciences, RNA, Viral, Thermodynamics, 3' Untranslated Regions, Conserved Sequence

Access URL: https://pubmed.ncbi.nlm.nih.gov/11257175
https://www.ncbi.nlm.nih.gov/pubmed/11257175
https://europepmc.org/article/MED/11257175
https://www.immunology.ox.ac.uk/publications/626542
https://www.expmedndm.ox.ac.uk/publications/626542
https://www.research.ed.ac.uk/portal/en/publications/evolutionarily-conserved-rna-secondary-structures-in-coding-and-noncoding-sequences-at-the-3-end-of-the-hepatitis-g-virusgbvirus-c-genome(886f2127-c6d4-4a0e-aff8-88e1037ce60e).html

Genome-wide long non-coding RNA expression profile and its regulatory role in the ileocecal valve from Mycobacterium avium subsp. paratuberculosis -infected cattle.

Authors: Badia-Bringué, Gerard Asselstine, Victoria Cánovas, Ángela et al.

Source: Frontiers in Veterinary Science. 2025, p1-9. 9p.

The Secondary Structure of Potato Spindle Tuber Viroid Determines Its Infectivity in Nicotiana benthamiana.

Authors: Nie, Yuxin Zhang, Yuhong Wu, Jian

Source: Viruses (1999-4915); Dec2023, Vol. 15 Issue 12, p2307, 11p

Subject Terms: CIRCULAR RNA, TUBERS, VIROIDS, NON-coding RNA, POTATOES, GEL electrophoresis, NICOTIANA benthamiana

Computational Approaches for Long Non-coding RNA Research / 長鎖ノンコーディングRNAのためのバイオインフォマティクス

Authors: Junichi IWAKIRI Michiaki HAMADA 岩切 淳一 et al.

Source: 生物物理 / Seibutsu Butsuri. 2016, 56(4):217

Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning.

Authors: Singh, Jaswinder Paliwal, Kuldip Zhang, Tongchuan et al.

Source: Bioinformatics; Sep2021, Vol. 37 Issue 17, p2589-2600, 12p

Subject Terms: TERTIARY structure, LINCRNA, DEEP learning, RNA, NON-coding RNA, BUILDING information modeling

Decoding the interactions and functions of non-coding RNA with artificial intelligence.

Authors: Jung V Vincent-Cuaz C Tumescheit C et al.

Source: Nature reviews. Molecular cell biology [Nat Rev Mol Cell Biol] 2025 Oct; Vol. 26 (10), pp. 797-818. Date of Electronic Publication: 2025 Jun 19.

Publication Type: Journal Article; Review

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 100962782 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1471-0080 (Electronic) Linking ISSN: 14710072 NLM ISO Abbreviation: Nat Rev Mol Cell Biol Subsets: MEDLINE

MeSH Terms: RNA, Untranslated*/genetics , RNA, Untranslated*/metabolism , Artificial Intelligence* , Sequence Analysis, RNA*/methods , RNA, Messenger*/genetics , RNA, Messenger*/metabolism, Large Language Models ; Humans ; Animals

Association of SNPs in Long Intergenic Noncoding RNA 00511 (LINC00511) With Breast Cancer Among the Egyptian Population

Authors: British University In Egypt Nadia Hamdy, Professor

Contributors: British University In Egypt Nadia Hamdy, Professor

Source: Studying the Association of Genetic Variations in Long Intergenic Noncoding RNA 00511 (LINC00511) With Breast Cancer Among the Egyptian Population
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