AIMC Topic: Transcriptome

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A tuberculosis ontology for host systems biology.

Tuberculosis (Edinburgh, Scotland)
A major hurdle facing tuberculosis (TB) investigators who want to utilize a rapidly growing body of data from both systems biology approaches and omics technologies is the lack of a standard vocabulary for data annotation and reporting. Lacking a mea...

Computer vision for image-based transcriptomics.

Methods (San Diego, Calif.)
Single-cell transcriptomics has recently emerged as one of the most promising tools for understanding the diversity of the transcriptome among single cells. Image-based transcriptomics is unique compared to other methods as it does not require conver...

De novo transcriptome assembly of pummelo and molecular marker development.

PloS one
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...

Genetic Bee Colony (GBC) algorithm: A new gene selection method for microarray cancer classification.

Computational biology and chemistry
Naturally inspired evolutionary algorithms prove effectiveness when used for solving feature selection and classification problems. Artificial Bee Colony (ABC) is a relatively new swarm intelligence method. In this paper, we propose a new hybrid gene...

Unraveling risk factors and transcriptomic signatures in liver cancer progression and mortality through machine learning and bioinformatics.

Briefings in functional genomics
Liver cancer (LC) is the second leading cause of cancer-related deaths globally, yet the molecular mechanisms linking its progression with associated risk factors (RFs) remain poorly understood. To address this, we developed an integrative multi-stag...

Integrative Analysis of Endothelial Cell Senescence-Related Genes in Idiopathic Pulmonary Fibrosis.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease in which endothelial cell senescence (ECS) plays a key role. By integrating two GEO transcriptome datasets (145 IPF patients and 84 controls) and applying LASSO, SVM-RFE, ...

Identification and Validation of Phagocytosis-Regulating Factors as Potential Prognostic and Diagnostic Biomarkers for Intracerebral Hemorrhage Through Single-Cell and Bulk Transcriptomic.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Intracerebral hemorrhage (ICH) is a major cause of death and disability worldwide. Despite treatment advances, reliable prognostic biomarkers are still lacking. While phagocytosis regulation is implicated in ICH pathogenesis, its potential for diagno...

Path2Omics Enhances Transcriptomic and Methylation Prediction Accuracy from Tumor Histopathology.

Cancer research
UNLABELLED: Precision oncology is becoming increasingly integral to clinical practice, demonstrating notable improvements in treatment outcomes. Whereas molecular data provide comprehensive insights, obtaining such data remains costly and time-consum...

Identification and validation of susceptibility modules and hub genes in polyarticular juvenile idiopathic arthritis using WGCNA and machine learning.

Autoimmunity
BACKGROUND: Juvenile idiopathic arthritis (JIA), superseding juvenile rheumatoid arthritis (JRA), is a chronic autoimmune disease affecting children and characterized by various types of childhood arthritis. JIA manifests clinically with joint inflam...

The Maternal Blood Transcriptome Reflects Changes in Fetal Growth and Is an Accurate Predictor of Birth Weight in Cattle.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Harnessing information from maternal blood to predict fetal growth is an emerging area of research in livestock production, offering a noninvasive tool to monitor development. This study aimed to investigate temporal changes in blood gene expression ...