AIMC Topic: RNA, Messenger

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ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors.

BMC bioinformatics
BACKGROUND: microRNAs (miRNAs) play a vital role in development, oncogenesis, and apoptosis by binding to mRNAs to regulate the posttranscriptional level of coding genes in mammals, plants, and insects. Recent studies have demonstrated that the expre...

An improved poly(A) motifs recognition method based on decision level fusion.

Computational biology and chemistry
Polyadenylation is the process of addition of poly(A) tail to mRNA 3' ends. Identification of motifs controlling polyadenylation plays an essential role in improving genome annotation accuracy and better understanding of the mechanisms governing gene...

Molecular classification of amyotrophic lateral sclerosis by unsupervised clustering of gene expression in motor cortex.

Neurobiology of disease
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and ultimately fatal neurodegenerative disease, caused by the loss of motor neurons in the brain and spinal cord. Although 10% of ALS cases are familial (FALS), the majority are sporadic (S...

Machine learning-assisted design of immunomodulatory lipid nanoparticles for delivery of mRNA to repolarize hyperactivated microglia.

Drug delivery
Regulating inflammatory microglia presents a promising strategy for treating neurodegenerative and autoimmune disorders, yet effective therapeutic agents delivery to these cells remains a challenge. This study investigates modified lipid nanoparticle...

FASTK post-transcriptional regulators - a 'FAST-tracK' in mitochondrial gene expression.

Biochemical Society transactions
Fas-activated serine/threonine kinase (FASTK) proteins comprise one of the largest families of mitochondrial post-transcriptional regulators. Members are classified based on their conserved C-terminus, which shows homology with the PD-(D/E)XK superfa...

TransCNN: A novel architecture combining transformer and TextCNN for detecting N4-acetylcytidine sites in human mRNA.

Analytical biochemistry
N4-acetylcytidine (ac4C), a pivotal post-transcriptional RNA modification, is central to understanding transcriptional regulation and diverse biological processes. As a key determinant of RNA structural stability and functional regulation, ac4C has b...

Assessing Substrate Scope of the Cyclodehydratase LynD by mRNA Display-Enabled Machine Learning Models.

Biochemistry
Many members of the broad family of enzymes, known as YcaOs have been shown to install azoline heterocycles post-translationally into peptide substrates. These moieties can help rigidify structures and contribute to the potent bioactivities of the ev...

ENsiRNA: A Multimodality Method for siRNA-mRNA and Modified siRNA Efficacy Prediction Based on Geometric Graph Neural Network.

Journal of molecular biology
With the rise of small interfering RNA (siRNA) as a therapeutic tool, effective siRNA design is crucial. Current methods often emphasize sequence-related features, overlooking structural information. To address this, we introduce ENsiRNA, a multimoda...

Characterization of ROMK cellular heterogeneity along the mouse kidney thick ascending limb.

Pflugers Archiv : European journal of physiology
The renal thick ascending limb (TAL) plays a key role in water and ion homeostasis. Apical potassium secretion via the renal outer medullary potassium channel (ROMK) is essential for transepithelial sodium reabsorption via the furosemide-sensitive Na...

Identification of key genes regulating colorectal cancer stem cell characteristics by bioinformatics analysis.

Medicine
Cancer stem cells (CSCs), distinguished by their abilities to differentiate and self-renew, play a pivotal role in the progression of colorectal cancer (CRC). However, the mechanisms that sustain CSCs in CRC remain unclear. This study aimed to identi...