ArticleBMC genomics2016
Comprehensive prediction of lncRNA-RNA interactions in human transcriptome.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 71 citations in OpenAlex.
- Transcriptional regulatory network analysis identifies conserved cis-antisense ncRNAs in the vancomycin and ceftriaxone stress response ofFrontiers in molecular biosciences · 2026Article
- MicroRNA-Mediated Regulation of Vascular Endothelium: From Pro-Inflammation to Atherosclerosis.International journal of molecular sciences · 2025Review
- Evolutionarily conserved 12-oxophytodienoate reductaseHorticulture research · 2024Article
- How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Web Services for RNA-RNA Interaction Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Unique role for lncRNA HOTAIR in defining depot-specific gene expression patterns in human adipose-derived stem cells.Genes & development · 2022Article
- Overexpression of DDIT4 and TPTEP1 are associated with metastasis and advanced stages in colorectal cancer patients: a study utilizing bioinformatics prediction and experimental validation.Cancer cell international · 2021Article
- Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity.Science advances · 2021Article
- Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer.Non-coding RNA · 2021Review
- Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer.Frontiers in genetics · 2021Review
- Comprehensive Analysis of LincRNAs in Classical and Basal-Like Subtypes of Pancreatic Cancer.Cancers · 2020Article
- The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases.Non-coding RNA · 2020Review
- LncRNAs in molluscan and mammalian stages of parasitic schistosomes are developmentally-regulated and coordinately expressed with protein-coding genes.RNA biology · 2020Article
- Identification of Aberrantly-Expressed Long Non-Coding RNAs in Osteoblastic Cells from Osteoporotic Patients.Biomedicines · 2020Article
- Expression levels and associations of five long non-coding RNAs in gastric cancer and their clinical significance.Oncology letters · 2020Article
- Regulatory Nucleotide Sequence Signals for Expression of the Genes Encoding Ribosomal Proteins.Frontiers in genetics · 2020Article
- The Human-Specific and Smooth Muscle Cell-Enriched LncRNA SMILR Promotes Proliferation by Regulating Mitotic CENPF mRNA and Drives Cell-Cycle Progression Which Can Be Targeted to Limit Vascular Remodeling.Circulation research · 2019Article
- LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data.Frontiers in genetics · 2019Article
- Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors.Frontiers in oncology · 2019Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRecent studies have revealed that large numbers of non-coding RNAs are transcribed in humans, but only a few of them have been identified with their functions. Identification of the interaction target RNAs of the non-coding RNAs is an important step in predicting their functions. The current experimental methods to identify RNA-RNA interactions, however, are not fast enough to apply to a whole human transcriptome. Therefore, computational predictions of RNA-RNA interactions are desirable, but this is a challenging task due to the huge computational costs involved.
resultsHere, we report comprehensive predictions of the interaction targets of lncRNAs in a whole human transcriptome for the first time. To achieve this, we developed an integrated pipeline for predicting RNA-RNA interactions on the K computer, which is one of the fastest super-computers in the world. Comparisons with experimentally-validated lncRNA-RNA interactions support the quality of the predictions. Additionally, we have developed a database that catalogs the predicted lncRNA-RNA interactions to provide fundamental information about the targets of lncRNAs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.