AIMC Topic: Gene Regulatory Networks

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Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights.

BioEssays : news and reviews in molecular, cellular and developmental biology May 8, 2024
Understanding the influence of cis-regulatory elements on gene regulation poses numerous challenges given complexities stemming from variations in transcription factor (TF) binding, chromatin accessibility, structural constraints, and cell-type diffe...
Animals Gene Regulatory Networks Computational Biology Transcription Factors Humans Machine Learning CRISPR-Cas Systems Gene Expression Regulation Regulatory Elements, Transcriptional
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Identification of LPCAT1 as a key biomarker for Crohn's disease based on bioinformatics and machine learnings and experimental verification.

Gene May 3, 2024
Epithelial-mesenchymal transition (EMT) plays a crucial role in regulating inflammatory responses and fibrosis formation. This study aims to explore the molecular mechanisms of EMT-related genes in Crohn's disease (CD) through bioinformatics methods ...
Humans Machine Learning Biomarkers Gene Expression Profiling HT29 Cells 1-Acylglycerophosphocholine O-Acyltransferase Gene Regulatory Networks MicroRNAs Computational Biology RNA, Long Noncoding Signal Transduction Epithelial-Mesenchymal Transition Crohn Disease
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Identifying lncRNAs and mRNAs related to survival of NSCLC based on bioinformatic analysis and machine learning.

Aging May 1, 2024
Non-small cell lung cancer (NSCLC) is the most common histopathological type, and it is purposeful for screening potential prognostic biomarkers for NSCLC. This study aims to identify the lncRNAs and mRNAs related to survival of non-small cell lung c...
RNA, Messenger Gene Expression Regulation, Neoplastic Nomograms Carcinoma, Non-Small-Cell Lung Humans Gene Regulatory Networks Lung Neoplasms Machine Learning Computational Biology Prognosis Biomarkers, Tumor RNA, Long Noncoding Gene Expression Profiling
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Weighted Gene Co-expression Network Analysis and Machine Learning Validation for Identifying Major Genes Related to Sjogren's Syndrome.

Biochemical genetics Apr 28, 2024
Sjogren's syndrome (SS) is an autoimmune disorder characterized by dry mouth and dry eyes. Its pathogenic mechanism is currently unclear. This study aims to integrate weighted gene co-expression network analysis (WGCNA) and machine learning to identi...
Gene Expression Profiling Gene Regulatory Networks Databases, Genetic Sjogren's Syndrome Humans Machine Learning
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Integrating machine learning algorithms and single-cell analysis to identify gut microbiota-related macrophage biomarkers in atherosclerotic plaques.

Frontiers in cellular and infection microbiology Apr 23, 2024
OBJECTIVE: The relationship between macrophages and the gut microbiota in patients with atherosclerosis remains poorly defined, and effective biological markers are lacking. This study aims to elucidate the interplay between gut microbial communities...
Gene Regulatory Networks Gastrointestinal Microbiome Antigens, CD Macrophages Atherosclerosis Humans Biomarkers Plaque, Atherosclerotic Interferon Regulatory Factors Machine Learning Gene Expression Profiling Agammaglobulinaemia Tyrosine Kinase Receptors, CCR1 Algorithms Antigens, Differentiation, Myelomonocytic Single-Cell Analysis CD68 Molecule
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Machine learning and weighted gene co-expression network analysis identify a three-gene signature to diagnose rheumatoid arthritis.

Frontiers in immunology Apr 22, 2024
BACKGROUND: Rheumatoid arthritis (RA) is a systemic immune-related disease characterized by synovial inflammation and destruction of joint cartilage. The pathogenesis of RA remains unclear, and diagnostic markers with high sensitivity and specificity...
Kinesins Humans Ribonucleoside Diphosphate Reductase Machine Learning Biomarkers Gene Expression Profiling Computational Biology Transcriptome Synovial Membrane Gene Regulatory Networks Support Vector Machine Arthritis, Rheumatoid Databases, Genetic
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Tissue specific tumor-gene link prediction through sampling based GNN using a heterogeneous network.

Medical & biological engineering & computing Apr 18, 2024
A tissue sample is a valuable resource for understanding a patient's symptoms and health status in relation to tumor growth. Recent research seeks to establish a connection between tissue-specific tumor samples and genetic markers (genes). This break...
ROC Curve Gene Regulatory Networks Gene Expression Regulation, Neoplastic Organ Specificity Algorithms Biomarkers, Tumor Neoplasms Humans Neural Networks, Computer
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CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression.

PLoS computational biology Apr 17, 2024
Network inference is used to model transcriptional, signaling, and metabolic interactions among genes, proteins, and metabolites that identify biological pathways influencing disease pathogenesis. Advances in machine learning (ML)-based inference mod...
Saccharomyces cerevisiae Machine Learning Algorithms Computer Simulation Gene Expression Profiling Gene Regulatory Networks Computational Biology Gene Expression Regulation
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Identification and validation of potential diagnostic signature and immune cell infiltration for HIRI based on cuproptosis-related genes through bioinformatics analysis and machine learning.

Frontiers in immunology Apr 16, 2024
BACKGROUND AND AIMS: Cuproptosis has emerged as a significant contributor in the progression of various diseases. This study aimed to assess the potential impact of cuproptosis-related genes (CRGs) on the development of hepatic ischemia and reperfusi...
Gene Expression Profiling Transcriptome Protein Interaction Maps Gene Regulatory Networks Mice Computational Biology Databases, Genetic Liver Machine Learning Reperfusion Injury Biomarkers Animals Humans Male
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Identification and validation of aging-related genes in heart failure based on multiple machine learning algorithms.

Frontiers in immunology Apr 15, 2024
BACKGROUND: In the face of continued growth in the elderly population, the need to understand and combat age-related cardiac decline becomes even more urgent, requiring us to uncover new pathological and cardioprotective pathways.
Transcriptome Machine Learning Algorithms Humans Databases, Genetic Gene Regulatory Networks Aging Computational Biology Heart Failure Gene Expression Profiling
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