AIMC Topic: Genes, Plant

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SemanticGO: a tool for gene functional similarity analysis in Arabidopsis thaliana and rice.

Plant science : an international journal of experimental plant biology
Gene or pathway functional similarities are important information for researchers. However, these similarities are often described sparsely and qualitatively. The latent semantic analysis of Arabidopsis thaliana (Arabidopsis) Gene Ontology (GO) data ...

JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants.

BMC genomics
BACKGROUND: Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energ...

StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis.

BMC genomics
BACKGROUND: Recently, a number of studies have been conducted to investigate how plants respond to stress at the cellular molecular level by measuring gene expression profiles over time. As a result, a set of time-series gene expression data for the ...

QTG-Finder: A Machine-Learning Based Algorithm To Prioritize Causal Genes of Quantitative Trait Loci in Arabidopsis and Rice.

G3 (Bethesda, Md.)
Linkage mapping is one of the most commonly used methods to identify genetic loci that determine a trait. However, the loci identified by linkage mapping may contain hundreds of candidate genes and require a time-consuming and labor-intensive fine ma...

MCRiceRepGP: a framework for the identification of genes associated with sexual reproduction in rice.

The Plant journal : for cell and molecular biology
Rice is an important cereal crop, being a staple food for over half of the world's population, and sexual reproduction resulting in grain formation underpins global food security. However, despite considerable research efforts, many of the genes, esp...

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species.

Scientific reports
Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such ec...

Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations.

PloS one
Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biolog...

Machine learning-driven GWAS uncovers novel candidate genes for resistance to frosty pod rot and witches' broom disease in cacao.

The plant genome
Cacao (Theobroma cacao), the source of chocolate, is threatened by devastating diseases like frosty pod rot (FPR) and witches' broom disease (WBD), impacting global production and farmer livelihoods. Here, we employ a machine learning-driven genome-w...

Machine learning based prediction by PlantCdMiner and experimental validation of cadmium-responsive genes in plants.

Journal of hazardous materials
Plants have evolved diverse adaptive mechanisms to sense and respond to environmental stimuli such as cadmium stress. The regulation of gene expression plays a critical role in plant responses to abiotic stress. However, homologous genes from differe...

Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping.

Plant physiology
Stomata are adjustable pores on leaf surfaces that regulate the tradeoff of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping ep...