AIMC Topic: Transcriptome

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Integrated transcriptomic meta-analysis and comparative artificial intelligence models in maize under biotic stress.

Scientific reports Sep 23, 2023
Biotic stress imposed by pathogens, including fungal, bacterial, and viral, can cause heavy damage leading to yield reduction in maize. Therefore, the identification of resistant genes paves the way to the development of disease-resistant cultivars a...
Bayes Theorem Zea mays Algorithms Artificial Intelligence Transcriptome
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STGNNks: Identifying cell types in spatial transcriptomics data based on graph neural network, denoising auto-encoder, and k-sums clustering.

Computers in biology and medicine Sep 9, 2023
BACKGROUND: Spatial transcriptomics technologies fully utilize spatial location information, tissue morphological features, and transcriptional profiles. Integrating these data can greatly advance our understanding about cell biology in the morpholog...
Transcriptome Cluster Analysis Breast Neoplasms Gene Expression Profiling Neural Networks, Computer Algorithms Humans
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Recent methodological advances towards single-cell proteomics.

Proceedings of the Japan Academy. Series B, Physical and biological sciences Sep 6, 2023
Studying the central dogma at the single-cell level has gained increasing attention to reveal hidden cell lineages and functions that cannot be studied using traditional bulk analyses. Nonetheless, most single-cell studies exploiting genomic and tran...
Genomics Proteomics Metabolomics Artificial Intelligence Transcriptome
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Breast cancer histopathology image-based gene expression prediction using spatial transcriptomics data and deep learning.

Scientific reports Aug 21, 2023
Tumour heterogeneity in breast cancer poses challenges in predicting outcome and response to therapy. Spatial transcriptomics technologies may address these challenges, as they provide a wealth of information about gene expression at the cell level, ...
Mammary Neoplasms, Animal Deep Learning Electric Power Supplies Gene Expression Profiling Transcriptome Animals
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De novo drug design based on patient gene expression profiles via deep learning.

Molecular informatics Aug 21, 2023
Computational de novo drug design is a challenging issue in medicine, and it is desirable to consider all of the relevant information of the biological systems in a disease state. Here, we propose a novel computational method to generate drug candida...
Transcriptome Deep Learning Molecular Structure Humans Drug Design Alzheimer Disease
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Enhancing the prediction of IDC breast cancer staging from gene expression profiles using hybrid feature selection methods and deep learning architecture.

Medical & biological engineering & computing Aug 2, 2023
Prediction of the stage of cancer plays an important role in planning the course of treatment and has been largely reliant on imaging tools which do not capture molecular events that cause cancer progression. Gene-expression data-based analyses are a...
Deep Learning Neoplasm Staging Gene Expression Profiling Transcriptome Humans Female Breast Neoplasms
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Machine-learning and combined analysis of single-cell and bulk-RNA sequencing identified a DC gene signature to predict prognosis and immunotherapy response for patients with lung adenocarcinoma.

Journal of cancer research and clinical oncology Jul 28, 2023
BACKGROUND: Innate immune effectors, dendritic cells (DCs), influence cancer prognosis and immunotherapy significantly. As such, dendritic cells are important in killing tumors and influencing tumor microenvironment, whereas their roles in lung adeno...
Single-Cell Analysis Adenocarcinoma of Lung Prognosis Tumor Microenvironment Lung Neoplasms Transcriptome Immunotherapy Biomarkers, Tumor Female Dendritic Cells Sequence Analysis, RNA Humans Male Machine Learning Middle Aged
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Deep learning exploration of single-cell and spatially resolved cancer transcriptomics to unravel tumour heterogeneity.

Computers in biology and medicine Jul 18, 2023
Tumour heterogeneity is one of the critical confounding aspects in decoding tumour growth. Malignant cells display variations in their gene transcription profiles and mutation spectra even when originating from a single progenitor cell. Single-cell a...
Humans Transcriptome Precision Medicine Deep Learning Neoplasms Gene Expression Profiling
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Deep learning of 2D-Restructured gene expression representations for improved low-sample therapeutic response prediction.

Computers in biology and medicine Jul 18, 2023
Clinical outcome prediction is important for stratified therapeutics. Machine learning (ML) and deep learning (DL) methods facilitate therapeutic response prediction from transcriptomic profiles of cells and clinical samples. Clinical transcriptomic ...
Humans Algorithms Gene Expression Profiling Transcriptome Deep Learning Benchmarking
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Interpretable deep learning for improving cancer patient survival based on personal transcriptomes.

Scientific reports Jul 13, 2023
Precision medicine chooses the optimal drug for a patient by considering individual differences. With the tremendous amount of data accumulated for cancers, we develop an interpretable neural network to predict cancer patient survival based on drug p...
Humans Research Deep Learning Neural Networks, Computer Neoplasms Transcriptome
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