AIMC Topic: Databases, Genetic

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EasyGeSe - a resource for benchmarking genomic prediction methods.

BMC genomics
BACKGROUND: Genomic prediction is a widely used method to predict phenotypes from genotypic data. Advances in both biological and computer science have enabled the generation of vast amounts of data and the development of new algorithms, specifically...

The impact of PANoptosis-related genes on immune profiles and subtype classification in ischemic stroke.

Scientific reports
Ischemic stroke (IS) is an acute neurological disorder causing brain dysfunction, with high mortality and disability. PANoptosis is a synchronized sort of regulated cell demise that combines the characteristics of pyroptosis, apoptosis, and necroptos...

Black pepper knowledge base (BlackPepKB): a centralized web resource for functional genomics of black pepper (Piper nigrum L.).

BMC genomics
BACKGROUND: Black pepper (Piper nigrum L.) is a highly valued spice crop with significant economic, medicinal, and cultural importance. While genomic and transcriptomic data for black pepper have rapidly accumulated in recent years, there is currentl...

NoAC: an automatic builder for knowledge bases and query interfaces on genomes of non-model organisms.

Journal of molecular biology
The cost of sequencing a genome has become affordable for many research groups. However, with the growing number of sequenced genomes from non-model organisms, manually building functional genome annotation knowledge databases for each species is no ...

Decision tree-based machine learning methods for identifying colorectal cancer-associated microRNA signatures and their regulatory networks.

Scientific reports
This study aimed to identify candidate diagnostic miRNAs from the serum of colorectal cancer (CRC) patients using Boruta, a wrapper-based feature selection technique, in combination with decision tree-based machine learning methods. We analyzed three...

Machine learning-based transcriptomic analysis identifies NAMPT and SAT1 as potential biomarkers and therapeutic targets in ferroptosis-associated rheumatoid arthritis.

PloS one
BACKGROUND: Rheumatoid arthritis (RA) is an autoimmune disease with chronic presentation, involving symmetric joints and systemic involvement. Ferroptosis is iron-dependent programmed cell death through lipid peroxide accumulation, implicated in infl...

Curcumenol exerts anti-pulmonary fibrosis effects through modulation of the immune signature target SPP1: based on comprehensive bioinformatics and experiments validation.

International immunopharmacology
BACKGROUND: The efficacy of Curcuma wenyujin (C. wenyujin) volatile oil components in the treatment of lung diseases, including pulmonary fibrosis (PF), is gradually being recognized. However, the anti-PF potential and underlying mechanisms of curcum...

RENOVO-NF1 accurately predicts NF1 missense variant pathogenicity.

Human genomics
Identification of a pathogenic variant in NF1 is diagnostic for neurofibromatosis, but is often impossible at the moment of variant detection due to many factors including allelic heterogeneity, sequence homology, and the lack of functional assays. C...

Screening of hub genes and immunocytes related to tendon injury based on bioinformatics and machine learning models.

Scientific reports
Tendon injury is a common and challenging clinical problem, and its healing process involves complex cellular and biological factors. Therefore, this study aims to reveal the mechanism of tendon healing and provide theoretical basis for clinical trea...

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

PloS one
This study aimed to identify potential interacting genes between abdominal aortic aneurysm (AAA) and periodontitis. To achieve this, we obtained datasets of AAA and periodontitis from the GEO database, conducted differential analysis on the AAA datas...