AIMC Topic: Gene Expression

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Application of transfer learning to predict drug-induced human in vivo gene expression changes using rat in vitro and in vivo data.

PloS one Nov 30, 2023
The liver is the primary site for the metabolism and detoxification of many compounds, including pharmaceuticals. Consequently, it is also the primary location for many adverse reactions. As the liver is not readily accessible for sampling in humans;...
Humans Neural Networks, Computer Liver Gene Expression Animals Rats Machine Learning Learning
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Transformer with convolution and graph-node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image.

Medical image analysis Nov 20, 2023
Inferring gene expressions from histopathological images has long been a fascinating yet challenging task, primarily due to the substantial disparities between the two modality. Existing strategies using local or global features of histological image...
Humans Neural Networks, Computer Phenotype Image Processing, Computer-Assisted Gene Expression
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N-of-one differential gene expression without control samples using a deep generative model.

Genome biology Nov 16, 2023
Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls, trained solely on healthy tissues. The unsupervised model learns a low-dimensional representation and can...
RNA-Seq Gene Expression Machine Learning Learning
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FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi.

PLoS computational biology Nov 16, 2023
mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly importan...
Saccharomyces cerevisiae Transcription Factors Gene Expression Deep Learning Computational Biology
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Deep-learning-assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision.

Science advances Nov 8, 2023
Owing to the nondeterministic and nonlinear nature of gene expression, the steady-state intracellular protein abundance of a clonal population forms a distribution. The characteristics of this distribution, including expression strength and noise, ar...
Gene Expression Profiling Gene Expression High-Throughput Nucleotide Sequencing Escherichia coli Proteins Deep Learning Escherichia coli
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Curcumin Modulates NOX Gene Expression and ROS Production via P-Smad3C in TGF-β-Activated Hepatic Stellate Cells.

Iranian biomedical journal Oct 28, 2023
BACKGROUND: Liver fibrosis, associated with hepatic stellate cells (HSCs), occurs when a healthy liver sustains damage, thereby impairing its function. NADPH oxidases (NOXs), specifically isoforms 1, 2, and 4, play a role in reactive oxygen species (...
Curcumin NADPH Oxidases Transforming Growth Factor beta Hepatic Stellate Cells Liver Cirrhosis Reactive Oxygen Species Signal Transduction Gene Expression Humans RNA, Messenger
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Associations of maternal stress, gene expression, and newborn birthweight in the Democratic Republic of Congo.

American journal of biological anthropology Oct 27, 2023
OBJECTIVES: Maternal stress has long been associated with lower birthweight, which is associated with adverse health outcomes including many adult diseases. The underlying mechanisms remain elusive although changes in gene expression may play a role....
Placenta Gene Expression Young Adult Democratic Republic of the Congo Female Humans Adult Infant, Newborn Birth Weight Pregnancy Transcriptome Stress, Psychological
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Joint triplet loss with semi-hard constraint for data augmentation and disease prediction using gene expression data.

Scientific reports Oct 24, 2023
The accurate prediction of patients with complex diseases, such as Alzheimer's disease (AD), as well as disease stages, including early- and late-stage cancer, is challenging owing to substantial variability among patients and limited availability of...
Alzheimer Disease Learning Neoplasms Deep Learning Gene Expression Humans
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GeneSegNet: a deep learning framework for cell segmentation by integrating gene expression and imaging.

Genome biology Oct 19, 2023
When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphological features of cells. We developed a dee...
Deep Learning Image Processing, Computer-Assisted Tomography, X-Ray Computed Gene Expression RNA
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Explainable artificial intelligence to predict and identify prostate cancer tissue by gene expression.

Computer methods and programs in biomedicine Jul 10, 2023
BACKGROUND AND OBJECTIVE: Prostate cancer is one of the most prevalent forms of cancer in men worldwide. Traditional screening strategies such as serum PSA levels, which are not necessarily cancer-specific, or digital rectal exams, which are often in...
Prostatic Neoplasms Male Gene Expression Artificial Intelligence Sensitivity and Specificity Humans
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