AIMC Topic: Gene Expression Regulation
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Construction of the miRNA/Pyroptosis-Related Molecular Regulatory Axis in Abdominal Aortic Aneurysm: Evidence From Transcriptome Data Combined With Multiple Machine Learning Approaches Followed by Experiment Validation.
Journal of immunology research
Oct 30, 2024
Abdominal aortic aneurysm (AAA) represents a permanent and localized widening of the abdominal aorta, posing a potentially lethal risk of aortic rupture. Several recent studies have highlighted the role of pyroptosis, a pro-inflammatory programed ce...
Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology.
RNA biology
Oct 7, 2024
Regulatory non-coding RNAs (ncRNAs) are increasingly recognized as integral to the control of biological processes. This is often through the targeted regulation of mRNA expression, but this is by no means the only mechanism through which regulatory ...
Interpreting cis-regulatory interactions from large-scale deep neural networks.
Nature genetics
Sep 16, 2024
The rise of large-scale, sequence-based deep neural networks (DNNs) for predicting gene expression has introduced challenges in their evaluation and interpretation. Current evaluations align DNN predictions with orthogonal experimental data, providin...
Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Aug 19, 2024
The 3' untranslated regions (3'UTRs) of messenger RNAs contain many important cis-regulatory elements that are under functional and evolutionary constraints. It is hypothesized that these constraints are similar to grammars and syntaxes in human lang...
Deep Learning Sequence Models for Transcriptional Regulation.
Annual review of genomics and human genetics
Aug 6, 2024
Deciphering the regulatory code of gene expression and interpreting the transcriptional effects of genome variation are critical challenges in human genetics. Modern experimental technologies have resulted in an abundance of data, enabling the develo...
Identification of Key Efferocytosis-Related Genes and Mechanisms in Diabetic Retinopathy.
Molecular biotechnology
Jul 31, 2024
This study aimed to explore the key efferocytosis-related genes in diabetic retinopathy (DR) and their regulatory mechanisms. Public DR-related gene expression datasets, GSE160306 (training) and GSE60436 (validation), were downloaded. Differentially ...
Identification of core genes in intervertebral disc degeneration using bioinformatics and machine learning algorithms.
Frontiers in immunology
Jul 10, 2024
BACKGROUND: Intervertebral Disc Degeneration (IDD) is a major cause of lower back pain and a significant global health issue. However, the specific mechanisms of IDD remain unclear. This study aims to identify key genes and pathways associated with I...
Four Genes with Seven Targeted Drugs might be Treatment for Diabetic Nephropathy and Acute Coronary Syndrome.
The Tohoku journal of experimental medicine
Jun 27, 2024
Diabetes nephropathy (DN) is a main risk factor for acute coronary syndrome (ACS), but the molecular mechanism is unknown. This research used bioinformatics approaches to uncover potential molecular mechanisms and drugs for DN and ACS. GSE142153 and ...
Machine Learning Strategies in MicroRNA Research: Bridging Genome to Phenome.
Omics : a journal of integrative biology
May 15, 2024
MicroRNAs (miRNAs) have emerged as a prominent layer of regulation of gene expression. This article offers the salient and current aspects of machine learning (ML) tools and approaches from genome to phenome in miRNA research. First, we underline tha...
Fundamentals for predicting transcriptional regulations from DNA sequence patterns.
Journal of human genetics
May 10, 2024
Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information of the regulatory el...
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