AIMC Topic: Genomics

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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...

Spatial domain identification method based on multi-view graph convolutional network and contrastive learning.

PLoS computational biology
Spatial transcriptomics is a rapidly developing field of single-cell genomics that quantitatively measures gene expression while providing spatial information within tissues. A key challenge in spatial transcriptomics is identifying spatially structu...

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 ...

Integrative transcriptomic and genomic insights into diabetic kidney disease: evidence from multi-omics analysis and experimental validation.

Renal failure
Diabetic kidney disease (DKD) remains a critical challenge in diabetes management, necessitating a deep understanding of its molecular underpinnings for better diagnosis and treatment strategies. This study was conducted to identify and validate nove...

Bio-digital feedback loop systems: a synergistic integration of predictive genomics, genome editing, and AI-driven phenomic synthesis for next-generation edible and medicinal mushroom breeding.

Antonie van Leeuwenhoek
Edible mushrooms face persistent challenges in yield optimization, bioactive compound production, and climate resilience that conventional breeding methods struggle to address. Traditional approaches such as cross-breeding, protoplast fusion, and mut...

Integrative genomics and genetics from evolutionary insights to precision breeding in peanuts (Arachis Hypogaea L.).

Functional & integrative genomics
Peanut (Arachis hypogaea L.), a globally important oilseed crop, increasingly challenged by rising edible oil demands as well as biotic and abiotic stresses. This review synthesizes recent advances in peanut genomics, evolutionary biology, and breedi...

Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis.

BMC bioinformatics
BACKGROUND: Cancer is a complex disease influenced by numerous concurrent genetic factors that result in diverse tumor microenvironments (TMEs) across different cancer types. Large-scale genomic projects, such as The Cancer Genome Atlas, have undersc...

Genomic Identification and Validation of Candidate Genes Associated with Alkalinity Tolerance in Exopalaemon carinicauda.

Marine biotechnology (New York, N.Y.)
China harbors extensive saline-alkaline water resources with considerable potential for aquaculture development. However, their utilization is constrained by high pH, elevated carbonate alkalinity, and complex ionic composition. Exopalaemon carinicau...

An interpretable generative multimodal neuroimaging-genomics framework for decoding Alzheimer's disease.

Journal of neural engineering
Alzheimer's disease (AD) is the most prevalent form of dementia worldwide, encompassing a prodromal stage known as mild cognitive impairment (MCI), where patients may either progress to AD or remain stable. The objective of the work was to capture st...

Machine learning and statistical inference in microbial population genomics.

Genome biology
The availability of large genome datasets has changed the microbiology research landscape. Analyzing such data requires computationally demanding analyses, and new approaches have come from different data analysis philosophies. Machine learning and s...