AIMC Topic: Transcription Factors
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First-line combination therapy of immunotherapy plus anti-angiogenic drug for thoracic SMARCA4-deficient undifferentiated tumors in AIDS: a case report and review of the literature.
Frontiers in immunology
Jan 9, 2025
BACKGROUND: Thoracic SMARCA4-deficient undifferentiated tumors (SMARCA4-UT) exhibit a notably aggressive phenotype, which is associated with poor patient survival outcomes. These tumors are generally resistant to conventional cytotoxic chemotherapy, ...
ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.
Nature communications
Jan 2, 2025
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the...
Deep learning predicts DNA methylation regulatory variants in specific brain cell types and enhances fine mapping for brain disorders.
Science advances
Jan 1, 2025
DNA methylation (DNAm) is essential for brain development and function and potentially mediates the effects of genetic risk variants underlying brain disorders. We present INTERACT, a transformer-based deep learning model to predict regulatory varian...
Transcription Factor Binding Site Prediction Using CnNet Approach.
IEEE/ACM transactions on computational biology and bioinformatics
Dec 10, 2024
Controlling the gene expression is the most important development in a living organism, which makes it easier to find different kinds of diseases and their causes. It's very difficult to know what factors control the gene expression. Transcription Fa...
Identification of diagnostic genes and the miRNA‒mRNA‒TF regulatory network in human oocyte aging via machine learning methods.
Journal of assisted reproduction and genetics
Nov 14, 2024
PURPOSE: Oocyte aging is a significant factor in the negative reproductive outcomes of older women. However, the pathogenesis of oocyte aging remains unclear. This study aimed to identify the hub genes involved in oocyte aging via bioinformatics meth...
The shared biomarkers and immune landscape in psoriatic arthritis and rheumatoid arthritis: Findings based on bioinformatics, machine learning and single-cell analysis.
PloS one
Nov 7, 2024
OBJECTIVE: Psoriatic arthritis (PsA) and rheumatoid arthritis (RA) are the most common types of inflammatory musculoskeletal disorders that share overlapping clinical features and complications. The aim of this study was to identify shared marker gen...
Exploration of common pathogenesis and candidate hub genes between HIV and monkeypox co-infection using bioinformatics and machine learning.
Scientific reports
Nov 4, 2024
This study explored the pathogenesis of human immunodeficiency virus (HIV) and monkeypox co-infection, identifying candidate hub genes and potential drugs using bioinformatics and machine learning. Datasets for HIV (GSE 37250) and monkeypox (GSE 2412...
Transcriptional regulation of hypoxic cancer cell metabolism and artificial intelligence.
Trends in cancer
Oct 30, 2024
Gene expression regulation in hypoxic tumor microenvironments is mediated by O responsive transcription factors (OR-TFs), fine-tuning cancer cell metabolic demand for O according to its availability. Here, we discuss key OR-TFs and emerging artificia...
Enhancing the Predictive Power of Machine Learning Models through a Chemical Space Complementary DEL Screening Strategy.
Journal of medicinal chemistry
Oct 23, 2024
DNA-encoded library (DEL) technology is an effective method for small molecule drug discovery, enabling high-throughput screening against target proteins. While DEL screening produces extensive data, it can reveal complex patterns not easily recogniz...
Identification of mitophagy-related genes and analysis of immune infiltration in the astrocytes based on machine learning in the pathogenesis of major depressive disorder.
Journal of affective disorders
Sep 14, 2024
BACKGROUNDS: Major depressive disorder (MDD) is a pervasive mental and mood disorder with complicated and heterogeneous etiology. Mitophagy, a selective autophagy of cells, specifically eliminates dysfunctional mitochondria. The mitochondria dysfunct...
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