AIMC Topic: Gene Expression Profiling

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Compound Activity Prediction with Dose-Dependent Transcriptomic Profiles and Deep Learning.

Journal of chemical information and modeling
Predicting compound activity in assays is a long-standing challenge in drug discovery. Computational models based on compound-induced gene expression signatures from a single profiling assay have shown promise toward predicting compound activity in o...

Using deep learning to quantify neuronal activation from single-cell and spatial transcriptomic data.

Nature communications
Neuronal activity-dependent transcription directs molecular processes that regulate synaptic plasticity, brain circuit development, behavioral adaptation, and long-term memory. Single cell RNA-sequencing technologies (scRNAseq) are rapidly developing...

Novel gene signatures predicting and immune infiltration analysis in Parkinson's disease: based on combining random forest with artificial neural network.

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology
BACKGROUND: Parkinson's disease (PD) ranks as the second most prevalent neurodegenerative disorder globally, and its incidence is rapidly rising. The diagnosis of PD relies on clinical characteristics. Although current treatments aim to alleviate sym...

Advances in artificial intelligence for the diagnosis and treatment of ovarian cancer (Review).

Oncology reports
Artificial intelligence (AI) has emerged as a crucial technique for extracting high‑throughput information from various sources, including medical images, pathological images, and genomics, transcriptomics, proteomics and metabolomics data. AI has be...

DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics.

Genome biology
Existing RNA velocity estimation methods strongly rely on predefined dynamics and cell-agnostic constant transcriptional kinetic rates, assumptions often violated in complex and heterogeneous single-cell RNA sequencing (scRNA-seq) data. Using a graph...

Bioinformatics and Machine Learning Methods Identified MGST1 and QPCT as Novel Biomarkers for Severe Acute Pancreatitis.

Molecular biotechnology
Severe acute pancreatitis (SAP) is a life-threatening gastrointestinal emergency. The study aimed to identify biomarkers and investigate molecular mechanisms of SAP. The GSE194331 dataset from GEO database was analyzed using bioinformatics. Different...

Identification of Co-diagnostic Genes for Heart Failure and Hepatocellular Carcinoma Through WGCNA and Machine Learning Algorithms.

Molecular biotechnology
This research delves into the intricate relationship between hepatocellular carcinoma (HCC) and heart failure (HF) by exploring shared genetic characteristics and molecular processes. Employing advanced methodologies such as differential analysis, we...

Time-Course Transcriptome Analysis Reveals Distinct Phases and Identifies Two Key Genes during Severe Fever with Thrombocytopenia Syndrome Virus Infection in PMA-Induced THP-1 Cells.

Viruses
In recent years, there have been significant advancements in the research of Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV). However, several limitations and challenges still exist. For instance, researchers face constraints regarding expe...

Exploring the advances of single-cell RNA sequencing in thyroid cancer: a narrative review.

Medical oncology (Northwood, London, England)
Thyroid cancer, a prevalent form of endocrine malignancy, has witnessed a substantial increase in occurrence in recent decades. To gain a comprehensive understanding of thyroid cancer at the single-cell level, this narrative review evaluates the appl...

scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles.

Genome biology
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) da...