Search Results - Long non-coding RNA secondary structures

3S: Shotgun secondary structure determination of long non-coding RNAs by Novikova, Irina V., Dharap, Ashutosh, Hennelly, Scott P., Sanbonmatsu, Karissa Y.

“…Long non-coding RNAs (lncRNAs) have emerged as an important class of RNAs playing key roles in development, disease and epigenetics…”
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A Graph-Based Algorithm for Detecting Long Non-Coding RNAs Through RNA Secondary Structure Analysis by Cabrera-Ibarra, Hugo, Hernández-Granados, David, Riego-Ruiz, Lina

“… Among them, long non-coding RNAs (lncRNAs) have been shown to regulate diverse cellular processes, such as cell development, stress response, and transcriptional regulation…”
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Towards structural classification of long non-coding RNAs by Sanbonmatsu, Karissa Y.

“… Previous structural studies are reviewed, and a pipeline is presented to determine secondary structures of long non-coding RNAs…”
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Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex by Jenkins, Adam M, Waterhouse, Robert M, Muskavitch, Marc AT

“…Background Long non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential…”
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An exon-biased biophysical approach and NMR spectroscopy define the secondary structure of a conserved helical element within the HOTAIR long non-coding RNA by Abzhanova, Ainur, Hirschi, Alexander, Reiter, Nicholas J.

“…•-Combined NMR with chemical probing methods provide accuracy in the secondary structure determination of large RNA molecules…”
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A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures by Bohdan, Davyd R, Voronina, Valeria V, Bujnicki, Janusz M, Baulin, Eugene F

“… We surveyed long-range tertiary interactions and motifs in a non-redundant set of non-coding RNA 3D structures…”
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Sizing up long non-coding RNAs: Do lncRNAs have secondary and tertiary structure? by Novikova, Irina V., Hennelly, Scott P., Sanbonmatsu, Karissa Y.

“…Long noncoding RNAs (lncRNAs) play a key role in many important areas of epigenetics, stem cell biology, cancer, signaling and brain function…”
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Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation by Sharma, Harshita, Valentine, Matthew N. Z., Toki, Naoko, Sueki, Hiromi Nishiyori, Gustincich, Stefano, Takahashi, Hazuki, Carninci, Piero

“… Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene…”
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Identification of long non-coding transcripts with feature selection: a comparative study by Ventola, Giovanna M. M., Noviello, Teresa M. R., D’Aniello, Salvatore, Spagnuolo, Antonietta, Ceccarelli, Michele, Cerulo, Luigi

“… Among them, open reading frame, conservation scores, nucleotide arrangements, and RNA secondary structure have been used with success in literature to recognize intergenic long non-coding RNAs…”
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Prediction of Secondary Structure for Long Non-Coding RNAs using a Recursive Cutting Method based on Deep Learning by Omnes, Loic, Angel, Eric, Bartet, Pierre, Radvanyi, Francois, Tahi, Fariza

“…Accurately predicting the secondary structure of RNA, particularly for long non-coding RNA, has direct implications in healthcare, where it can be used for diagnostic, therapeutic, and drug discovery purposes…”
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LncRNA ARGI Contributes to Virus‐Induced Pancreatic β Cell Inflammation Through Transcriptional Activation of IFN‐Stimulated Genes by González‐Moro, Itziar, Garcia‐Etxebarria, Koldo, Mendoza, Luis Manuel, Fernández‐Jiménez, Nora, Mentxaka, Jon, Olazagoitia‐Garmendia, Ane, Arroyo, María Nicol, Sawatani, Toshiaki, Moreno‐Castro, Cristina, Vinci, Chiara, Op de Beek, Anne, Cnop, Miriam, Igoillo‐Esteve, Mariana, Santin, Izortze

“… Interestingly, SNPs in long non‐coding RNAs (lncRNAs) may result in the disruption of their secondary structure, affecting their function, and in turn, the expression of potentially pathogenic pathways…”
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Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease by Fernandes, Juliane C. R., Acuña, Stephanie M., Aoki, Juliana I., Floeter-Winter, Lucile M., Muxel, Sandra M.

“…), and long non-coding RNAs (lncRNAs). The lncRNAs in association with other molecules can coordinate several physiological processes and their dysfunction may impact in several pathologies, including cancer and infectious diseases…”
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Structural architecture of the human long non-coding RNA, steroid receptor RNA activator by Novikova, Irina V., Hennelly, Scott P., Sanbonmatsu, Karissa Y.

“…While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood…”
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LncDC: a machine learning-based tool for long non-coding RNA detection from RNA-Seq data by Li, Minghua, Liang, Chun

“… Here, we present our tool LncDC (Long non-coding RNA detection) that is able to accurately predict lncRNAs with an XGBoost model using features extracted from RNA sequences, secondary structures, and translated proteins…”
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A novel lnc-LAMC2-1:1 SNP promotes colon adenocarcinoma progression by targeting miR-216a-3p/HMGB3 by Ji, Fulong, Yao, Zhiwei, Liu, Chunxiang, Fu, Siqi, Ren, Bingbing, Liu, Yong, Ma, Lushun, Wei, Jianming, Sun, Daqing

“…Single nucleotide polymorphisms (SNPs) was associated with altering the secondary structure of long non-coding RNA (lncRNA…”
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Sizing up long non-coding RNAs: Do lncRNAs have secondary and tertiary structure? by Irina V. Novikova, Karissa Y. Sanbonmatsu, Scott P. Hennelly

“…Long noncoding RNAs (lncRNAs) play a key role in many important areas of epigenetics, stem cell biology, cancer, signaling and brain function…”
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Ghost authors revealed: The structure and function of human N6‐methyladenosine RNA methyltransferases by Breger, Kurtis, Kunkler, Charlotte N, O'Leary, Nathan J, Hulewicz, Jacob P, Brown, Jessica A

“…‐coding RNAs, including long non‐coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6A marks can alter RNA secondary structure and initiate unique RNA…”
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RNA secondary structure profiling in zebrafish reveals unique regulatory features by Kaushik, Kriti, Sivadas, Ambily, Vellarikkal, Shamsudheen Karuthedath, Verma, Ankit, Jayarajan, Rijith, Pandey, Satyaprakash, Sethi, Tavprithesh, Maiti, Souvik, Scaria, Vinod, Sivasubbu, Sridhar

“…). This study provides the secondary structure map of zebrafish coding and non-coding RNAs. The single nucleotide pairing probabilities of 54,083 distinct transcripts in the zebrafish genome were documented…”
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Application of Random Forest in Limited Size Human Long Non-coding RNAs Identification with Secondary Structure Features by Anuntakarun, Songtham, Wattanapornprom, Warin, Lertampaiporn, Supatcha

“… Various significant features in describing RNA sequence including sequenced based features, secondary structure features, base-pair features and structural robustness features were used in this study…”
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RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure by Rivas, Elena

“…Many biologically important RNAs fold into specific 3D structures conserved through evolution…”
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