AIMC Topic: RNA, Long Noncoding

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A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs.

Briefings in functional genomics
Long noncoding RNAs (lncRNAs) have been discovered to be extensively involved in eukaryotic epigenetic, transcriptional, and post-transcriptional regulatory processes with the advancements in sequencing technology and genomics research. Therefore, th...

Evolutionary learning-derived lncRNA signature with biomarker discovery for predicting stage of colon adenocarcinoma.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
In recent years, long non-coding RNAs (lncRNAs) have emerged as potential regulators of biological processes and genes, with the potential to serve as valuable biomarkers for cancer diagnosis and prognosis prediction. This work proposes an evolutiona...

HRGCNLDA: Forecasting of lncRNA-disease association based on hierarchical refinement graph convolutional neural network.

Mathematical biosciences and engineering : MBE
Long non-coding RNA (lncRNA) is considered to be a crucial regulator involved in various human biological processes, including the regulation of tumor immune checkpoint proteins. It has great potential as both a cancer biomolecular biomarker and ther...

Deqformer: high-definition and scalable deep learning probe design method.

Briefings in bioinformatics
Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing d...

BioKA: a curated and integrated biomarker knowledgebase for animals.

Nucleic acids research
Biomarkers play an important role in various area such as personalized medicine, drug development, clinical care, and molecule breeding. However, existing animals' biomarker resources predominantly focus on human diseases, leaving a significant gap i...

Prediction of LncRNA-protein Interactions Using Auto-Encoder, SE-ResNet Models and Transfer Learning.

MicroRNA (Shariqah, United Arab Emirates)
BACKGROUND: Long non-coding RNA (lncRNA) plays a crucial role in various biological processes, and mutations or imbalances of lncRNAs can lead to several diseases, including cancer, Prader-Willi syndrome, autism, Alzheimer's disease, cartilage-hair h...

Machine Learning-derived Multi-omics Prognostic Signature of Pyroptosis-related lncRNA with Regard to ZKSCAN2-DT and Tumor Immune Infiltration in Colorectal Cancer.

Combinatorial chemistry & high throughput screening
BACKGROUND: Colorectal cancer (CRC) has become the most prevalent gastrointestinal malignant tumor, ranking third (10.2%) in incidence and second (9.2%) in death among all malignancies globally. The most common histological subtype of CRC is colon ad...

LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism.

Bioinformatics (Oxford, England)
MOTIVATION: There is mounting evidence that the subcellular localization of lncRNAs can provide valuable insights into their biological functions. In the real world of transcriptomes, lncRNAs are usually localized in multiple subcellular localization...

DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome.

Bioinformatics (Oxford, England)
MOTIVATION: Enhancers are vital cis-regulatory elements that regulate gene expression. Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer regions in the genome. The tissue-specific expression of eRNAs is crucial in th...

EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.

Briefings in bioinformatics
Long non-coding RNAs (lncRNAs) played essential roles in nearly every biological process and disease. Many algorithms were developed to distinguish lncRNAs from mRNAs in transcriptomic data and facilitated discoveries of more than 600 000 of lncRNAs....