AIMC Topic: RNA, Messenger
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NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model.
BMC bioinformatics
Aug 19, 2025
BACKGROUND: Accurate identification of translation initiation sites is essential for the proper translation of mRNA into functional proteins. In eukaryotes, the choice of the translation initiation site is influenced by multiple factors, including it...
Deep learning-based high-resolution time inference for deciphering dynamic gene regulation from fixed embryos.
Nature communications
Jul 16, 2025
Embryo development is driven by the spatiotemporal dynamics of complex gene regulatory networks. Uncovering these dynamics requires simultaneous tracking of multiple fluctuating molecular species over time, which exceeds the capabilities of tradition...
Multi-transcriptomics predicts clinical outcome in systemically untreated breast cancer patients with extensive follow-up.
Breast cancer research : BCR
Jul 15, 2025
BACKGROUND: Prognostic tools for determining patients with indolent breast cancers (BCs) are far from optimal, leading to extensive overtreatment. Several studies have demonstrated mRNAs, lncRNAs and miRNAs to have prognostic potential in BC. Because...
Integrated Nanopore and short-read RNA sequencing identifies dysregulation of METTL3- m6A modifications in endocrine therapy- sensitive and resistant breast cancer cells.
Functional & integrative genomics
Jul 9, 2025
The role of epitranscriptomic changes in the development of acquired endocrine therapy (ET)- resistance in estrogen receptor α (ER) expressing breast cancer (BC) is unknown. We tested the hypothesis that inhibition of METTL3, the methyltransferase re...
Decoding the diagnostic biomarkers of mitochondrial dysfunction related gene variants in pediatric T cell acute lymphoblastic leukemia.
Scientific reports
Jul 1, 2025
Mitochondrial dysfunction is crucial in the pathogenesis and drug resistance of pediatric T-cell acute lymphoblastic leukemia (T-ALL), a malignant hematological disorder with unrestrained proliferation of immature T-cells. Therefore, the primary obje...
Identification of key genes associated with cellular aging and mitochondria in acute myocardial infarction.
Scientific reports
Jul 1, 2025
Acute myocardial infarction (AMI) poses a significant global mortality burden. Utilizing bio informatics, this study explored cellular aging-related genes (CARGs) and mitochondrial-related genes (MRGs). in AMI Public AMI datasets were analyzed using ...
rbpTransformer: A novel deep learning model for prediction of piRNA and mRNA bindings.
PloS one
Jun 25, 2025
An important issue in biotechnology is predicting whether a piRNA and an mRNA will or will not bind. Research and treatment of diseases, drug discovery, and the silencing and regulation of genes, transposons, and genomic stability may all benefit fro...
Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.
PloS one
Apr 24, 2025
Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and ...
Deciphering disordered regions controlling mRNA decay in high-throughput.
Nature
Apr 23, 2025
Intrinsically disordered regions within proteins drive specific molecular functions despite lacking a defined structure. Although disordered regions are integral to controlling mRNA stability and translation, the mechanisms underlying these regulator...
Computational models for prediction of m6A sites using deep learning.
Methods (San Diego, Calif.)
Apr 21, 2025
RNA modifications play a crucial role in enhancing the structural and functional diversity of RNA molecules and regulating various stages of the RNA life cycle. Among these modifications, N6-Methyladenosine (m6A) is the most common internal modificat...
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