AIMC Topic: Gene Expression Profiling

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Robust Diagnosis of Acute Bacterial and Viral Infections via Host Gene Expression Rank-Based Ensemble Machine Learning Algorithm: A Multi-Cohort Model Development and Validation Study.

Clinical chemistry Apr 3, 2025
BACKGROUND: The accurate and prompt diagnosis of infections is essential for improving patient outcomes and preventing bacterial drug resistance. Host gene expression profiling as an approach to infection diagnosis holds great potential in assisting ...
Female Male Middle Aged Machine Learning Algorithms Prospective Studies Bacterial Infections Acute Disease Virus Diseases Gene Expression Profiling Cohort Studies ROC Curve Humans
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Machine Learning Unveils Sphingolipid Metabolism's Role in Tumour Microenvironment and Immunotherapy in Lung Cancer.

Journal of cellular and molecular medicine Apr 1, 2025
TME is a core player in the development of a cancerous lesion, the immune evasive potential of the lesion, and its response to therapy. Sphingolipid metabolism, which governs a number of cellular processes, has been recognised as a player involved in...
Humans Transcriptome Gene Expression Regulation, Neoplastic Lung Neoplasms Immunotherapy Tumor Microenvironment Sphingolipids Machine Learning Prognosis Biomarkers, Tumor Gene Expression Profiling
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adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks.

Bioinformatics (Oxford, England) Mar 29, 2025
MOTIVATION: Several machine learning (ML) algorithms dedicated to the detection of healthy and diseased cell types from single-cell RNA sequencing (scRNA-seq) data have been proposed for biomedical purposes. This raises concerns about their vulnerabi...
Single-Cell Analysis Sequence Analysis, RNA Gene Expression Profiling Transcriptome Humans Machine Learning Algorithms
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A multi-view graph convolutional network framework based on adaptive adjacency matrix and multi-strategy fusion mechanism for identifying spatial domains.

Bioinformatics (Oxford, England) Mar 29, 2025
MOTIVATION: Spatial transcriptomics (ST) addresses the loss of spatial context in single-cell RNA-sequencing by simultaneously capturing gene expression and spatial location information. A critical task of ST is the identification of spatial domains....
Transcriptome Neural Networks, Computer Software Single-Cell Analysis Computational Biology Algorithms Gene Expression Profiling
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uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization.

Bioinformatics (Oxford, England) Mar 29, 2025
SUMMARY: In single-cell transcriptomics, inconsistent cell type annotations due to varied naming conventions and hierarchical granularity impede data integration, machine learning applications, and meaningful evaluations. To address this challenge, w...
Single-Cell Analysis Software Computational Biology Humans Gene Expression Profiling Molecular Sequence Annotation Machine Learning Transcriptome
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A deep learning tissue classifier based on differential co-expression genes predicts the pregnancy outcomes of cattle†.

Biology of reproduction Mar 16, 2025
Economic losses in cattle farms are frequently associated with failed pregnancies. Some studies found that the transcriptomic profiles of blood and endometrial tissues in cattle with varying pregnancy outcomes display discrepancies even before artifi...
Gene Expression Profiling Transcriptome Deep Learning Pregnancy Female Animals Endometrium Insemination, Artificial Cattle Embryo Transfer Pregnancy Outcome
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Screening of mitochondrial-related biomarkers connected with immune infiltration for acute respiratory distress syndrome through WGCNA and machine learning.

Medicine Mar 7, 2025
Septic acute respiratory distress syndrome (ARDS) is a complex and noteworthy type, but its molecular mechanism has not been fully elucidated. The aim is to explore specific biomarkers to diagnose sepsis-induced ARDS. Gene expression data of sepsis a...
Sepsis Gene Regulatory Networks Nomograms Neutrophils Respiratory Distress Syndrome Mitochondria Machine Learning Biomarkers Gene Expression Profiling Humans
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Multi-Manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics.

Briefings in bioinformatics Mar 4, 2025
Identifying spatial domains for spatial transcriptomics is crucial for achieving comprehensive insights into the pathogenesis of gene expression. Increasingly, computational methods based on graph neural networks are being developed for spatial trans...
Computational Biology Algorithms Gene Expression Profiling Transcriptome Humans Neural Networks, Computer
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Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.

Briefings in bioinformatics Mar 4, 2025
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. Despite this progress, the analysis of single-cell and s...
Humans Gene Expression Profiling Transcriptome Deep Learning Data Science Single-Cell Analysis Computational Biology
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BAMBI integrates biostatistical and artificial intelligence methods to improve RNA biomarker discovery.

Briefings in bioinformatics Mar 4, 2025
RNA biomarkers enable early and precise disease diagnosis, monitoring, and prognosis, facilitating personalized medicine and targeted therapeutic strategies. However, identification of RNA biomarkers is hindered by the challenge of analyzing relative...
Biostatistics Algorithms Biomarkers Biomarkers, Tumor Gene Expression Profiling Computational Biology RNA Artificial Intelligence Machine Learning Humans Software
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