M6ATMR: identifying N6-methyladenosine sites through RNA sequence similarity matrix reconstruction guided by Transformer [PDF]
PeerJ, 2023 Numerous studies have focused on the classification of N6-methyladenosine (m6A) modification sites in RNA sequences, treating it as a multi-feature extraction task. In these studies, the incorporation of physicochemical properties of nucleotides has been
Shuang Xiang, Te Zhang, Minghao Wu
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RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models [PDF]
HeliyonDeciphering information of RNA sequences reveals their diverse roles in living organisms, including gene regulation and protein synthesis. Aberrations in RNA sequence such as dysregulation and mutations can drive a diverse spectrum of diseases including ...
Muhammad Nabeel Asim +3 more
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Predicting RNA sequence-structure likelihood via structure-aware deep learning [PDF]
BMC BioinformaticsBackground The active functionalities of RNA are recognized to be heavily dependent on the structure and sequence. Therefore, a model that can accurately evaluate a design by giving RNA sequence-structure pairs would be a valuable tool for many ...
You Zhou +3 more
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New generative methods for single-cell transcriptome data in bulk RNA sequence deconvolution [PDF]
Scientific ReportsNumerous methods for bulk RNA sequence deconvolution have been developed to identify cellular targets of diseases by understanding the composition of cell types in disease-related tissues.
Toui Nishikawa +2 more
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The comparative gene expression concern to the seed pigmentation in maize ( L.) [PDF]
Genomics & Informatics, 2020 Maize seed pigmentation is one of the important issue to develop maize seed breeding. The differently gene expression was characterized and compared for three inbred lines, such as the pigment accumulated seed (CM22) and non-pigmented seed (CM5 and CM19)
Kyu Jin Sa, Ik-Young Choi, Ju Kyong Lee
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GEE: An Informatics Tool for Gene Expression Data Explore [PDF]
Healthcare Informatics Research, 2016 ObjectivesMajor public high-throughput functional genomic data repositories, including the Gene Expression Omnibus (GEO) and ArrayExpress have rapidly expanded.
Soo Youn Lee +4 more
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Systematic identification and characterization of RNA editing in prostate tumors. [PDF]
PLoS ONE, 2014 RNA editing modifies the sequence of primary transcripts, potentially resulting in profound effects to RNA structure and protein-coding sequence. Recent analyses of RNA sequence data are beginning to provide insights into the distribution of RNA editing ...
Fan Mo +9 more
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Pharmaceutical Biology, 2020 Context Pulmonary fibrosis (PF) is a highly heterogeneous and lethal pathological process having no effective drug. Engeletin exerts multiple biological activities including anti-inflammatory and lung repair.
Jinjin Zhang +7 more
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Accurate RNA 3D structure prediction using a language model-based deep learning approach [PDF]
Nature Methods 2024, 2022 Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The structural flexibility of RNA, which leads to scarcity of experimentally determined data, complicates ...
arxiv +1 more source
Scaling properties of RNA as a randomly branching polymer [PDF]
J. Chem. Phys. 158, 234901 (2023), 2023 Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching -- for instance, for its spatial compactness or interaction with other biological macromolecules -- RNA branching ...
arxiv +1 more source