AIMC Topic: Databases, Genetic

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MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Plasmids play an essential role in horizontal gene transfer, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. There exist some plasmids that can transfer, replicate, or persist in multiple or...

Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data.

Database : the journal of biological databases and curation
Curated resources at centralized repositories provide high-value service to users by enhancing data veracity. Curation, however, comes with a cost, as it requires dedicated time and effort from personnel with deep domain knowledge. In this paper, we ...

EnrichDO: a global weighted model for Disease Ontology enrichment analysis.

GigaScience
BACKGROUND: Disease Ontology (DO) has been widely studied in biomedical research and clinical practice to describe the roles of genes. DO enrichment analysis is an effective means to discover associations between genes and diseases. Compared to hundr...

PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining.

Nucleic acids research
The exponential growth of microbial genome data presents unprecedented opportunities for unlocking the potential of microorganisms. The burgeoning field of pangenomics offers a framework for extracting insights from this big biological data. Recent a...

scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies.

Nucleic acids research
Single-cell transcriptome-wide association studies (scTWAS) is a new method for conducting TWAS analysis at the cellular level to identify gene-trait associations with higher precision. This approach helps overcome the challenge of interpreting cell-...

CircaKB: a comprehensive knowledgebase of circadian genes across multiple species.

Nucleic acids research
Circadian rhythms, which are the natural cycles that dictate various physiological processes over a 24-h period, have been increasingly recognized as important in the management and treatment of various human diseases. However, the lack of sufficient...

Machine learning-driven identification of exosome- related biomarkers in head and neck squamous cell carcinoma.

Frontiers in immunology
BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is a common cancer associated with elevated mortality rates. Exosomes, diminutive extracellular vesicles, significantly contribute to tumour development, immunological evasion, and treatment r...

Construction of a prognostic model for endometrial cancer related to programmed cell death using WGCNA and machine learning algorithms.

Frontiers in immunology
BACKGROUND: Programmed cell death (PCD) refers to a regulated and active process of cellular demise, initiated by specific biological signals. PCD plays a crucial role in the development, progression, and drug resistance of uterine corpus endometrial...

Bioinformatics meets machine learning: identifying circulating biomarkers for vitiligo across blood and tissues.

Frontiers in immunology
BACKGROUND: Vitiligo is a skin disorder characterized by the progressive loss of pigmentation in the skin and mucous membranes. The exact aetiology and pathogenesis of vitiligo remain incompletely understood.

Identification of regulatory cell death-related genes during MASH progression using bioinformatics analysis and machine learning strategies.

Frontiers in immunology
BACKGROUND: Metabolic dysfunction-associated steatohepatitis (MASH) is becoming increasingly prevalent. Regulated cell death (RCD) has emerged as a significant disease phenotype and may act as a marker for liver fibrosis. The present study aimed to i...