AIMC Topic: Genome, Plant
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MCRiceRepGP: a framework for the identification of genes associated with sexual reproduction in rice.
The Plant journal : for cell and molecular biology
Aug 16, 2018
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...
A machine learning based framework to identify and classify long terminal repeat retrotransposons.
PLoS computational biology
Apr 23, 2018
Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. A...
Prediction of DNase I hypersensitive sites in plant genome using multiple modes of pseudo components.
Analytical biochemistry
Mar 28, 2018
DNase I hypersensitive sites (DHSs) are accessible chromatin zones hypersensitive to DNase I endonucleases in plant genome. DHSs have been used as markers for the presence of transcriptional regulatory elements. It is an important complement to devel...
pDHS-SVM: A prediction method for plant DNase I hypersensitive sites based on support vector machine.
Journal of theoretical biology
May 26, 2017
DNase I hypersensitive sites (DHSs) are accessible chromatin regions hypersensitive to cleavages by DNase I endonucleases. DHSs are indicative of cis-regulatory DNA elements (CREs), all of which play important roles in global gene expression regulati...
DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool.
Nucleic acids research
Aug 24, 2015
There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provi...
A knowledge base for Vitis vinifera functional analysis.
BMC systems biology
Jun 1, 2015
BACKGROUND: Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals in wine production concern ...
Environment ensemble models for genomic prediction in common bean (Phaseolus vulgaris L.).
The plant genome
Jun 1, 2025
For important food crops such as the common bean (Phaseolus vulgaris, L.), global demand continues to outpace the rate of genetic gain for quantitative traits. In this study, we leveraged the multi-environment trial (MET) dataset from the cooperative...
Genomic selection: Essence, applications, and prospects.
The plant genome
Jun 1, 2025
Genomic selection (GS) emerged as a key part of the solution to ensure the food supply for the growing human population thanks to advances in genotyping and other enabling technologies and improved understanding of the genotype-phenotype relationship...
Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.
Genome biology and evolution
May 30, 2025
Plant DNA methylation changes occur hundreds to thousands of times faster than DNA mutations and can be transmitted transgenerationally, making them useful for studying population-scale patterns in clonal or selfing species. However, a state-of-the-a...
Precise genome editing process and its applications in plants driven by AI.
Functional & integrative genomics
May 24, 2025
Genome editing technologies have emerged as the keystone of biotechnological research, enabling precise gene modification. The field has evolved rapidly through revolutionary advancements, transitioning from early explorations to the breakthrough of ...
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