AIMC Topic: Gene Expression Regulation, Plant

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Identification of the expressome by machine learning on omics data.

Proceedings of the National Academy of Sciences of the United States of America Aug 16, 2019
Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome...
Gene Expression Profiling Zea mays Genome, Plant Gene Expression Regulation, Plant Databases, Nucleic Acid Machine Learning
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Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne).

PloS one Jul 30, 2019
Perennial ryegrass (Lolium perenne) is a forage and amenity grass species widely cultivated in temperate regions worldwide. As such, perennial ryegrass populations are exposed to a range of environmental conditions and stresses on a seasonal basis an...
Lolium Transcriptome Gene Expression Regulation, Plant Dehydration Gene Expression Profiling Plant Leaves Genotype Droughts Plant Proteins Plant Roots Gene Ontology
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De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms.

Scientific reports Jan 23, 2019
Agave, monocotyledonous succulent plants, is endemic to arid regions of North America, exhibiting exceptional tolerance to their xeric environments. They employ various strategies to overcome environmental constraints, such as crassulacean acid metab...
Gene Expression Regulation, Plant Transcriptome Agave Dehydration Stress, Physiological Gene Ontology
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Comparative Analysis of the Cytology and Transcriptomes of the Cytoplasmic Male Sterility Line H276A and Its Maintainer Line H276B of Cotton (Gossypium barbadense L.).

International journal of molecular sciences Oct 25, 2017
In this study, the tetrad stage of microspore development in a new cotton ( L.) cytoplasmic male sterility (CMS) line, H276A, was identified using paraffin sections at the abortion stage. To explore the molecular mechanism underlying CMS in cotton, a...
Gene Expression Regulation, Plant Computational Biology Plant Infertility Gene Ontology Gene Expression Profiling Gossypium Transcriptome
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Machine-learning meta-analysis reveals ethylene as a central component of the molecular core in abiotic stress responses in Arabidopsis.

Nature communications May 22, 2025
Understanding how plants adapt their physiology to overcome severe and often multifactorial stress conditions in nature is vital in light of the climate crisis. This remains a challenge given the complex nature of the underlying molecular mechanisms....
Transcriptome Arabidopsis Plant Shoots Arabidopsis Proteins Machine Learning Plant Roots Stress, Physiological Gene Expression Profiling Gene Expression Regulation, Plant Ethylenes
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Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.

The Plant cell May 9, 2025
Systems biology aims to uncover gene regulatory networks (GRNs) for agricultural traits, but validating them in crops is challenging. We addressed this challenge by learning and validating model-to-crop transcription factor (TF) regulons governing ni...
Transcription Factors Zea mays Nitrogen Machine Learning Gene Regulatory Networks Gene Expression Regulation, Plant Crops, Agricultural Plant Proteins Arabidopsis Regulon
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Predicting Fitness-Related Traits Using Gene Expression and Machine Learning.

Genome biology and evolution Feb 3, 2025
Evolution by natural selection occurs at its most basic through the change in frequencies of alleles; connecting those genomic targets to phenotypic selection is an important goal for evolutionary biology in the genomics era. The relative abundance o...
Machine Learning Phenotype Transcriptome Photosynthesis Genetic Fitness Ipomoea Selection, Genetic Gene Expression Regulation, Plant
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Deep learning with a small dataset predicts chromatin remodelling contribution to winter dormancy of apple axillary buds.

Tree physiology Jul 2, 2024
Epigenetic changes serve as a cellular memory for cumulative cold recognition in both herbaceous and tree species, including bud dormancy. However, most studies have discussed predicted chromatin structure with respect to histone marks. In the presen...
Chromatin Assembly and Disassembly Plant Dormancy Seasons Flowers Malus Gene Expression Regulation, Plant Cold Temperature Deep Learning Epigenesis, Genetic Bayes Theorem
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Decoding the cis-regulation of tomato fruit development with deep learning.

The Plant cell May 24, 2022
Fruit Deep Learning Plant Proteins Solanum lycopersicum Gene Expression Regulation, Plant
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Genome-wide cis-decoding for expression design in tomato using cistrome data and explainable deep learning.

The Plant cell May 24, 2022
In the evolutionary history of plants, variation in cis-regulatory elements (CREs) resulting in diversification of gene expression has played a central role in driving the evolution of lineage-specific traits. However, it is difficult to predict expr...
Gene Expression Regulation, Plant Regulatory Sequences, Nucleic Acid Deep Learning Transcription Factors Fruit Plant Proteins Solanum lycopersicum
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