AIMC Topic: Genome, Plant
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Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.
Nature communications
Jun 4, 2019
DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifica...
New Deep Learning Genomic-Based Prediction Model for Multiple Traits with Binary, Ordinal, and Continuous Phenotypes.
G3 (Bethesda, Md.)
May 7, 2019
Multiple-trait experiments with mixed phenotypes (binary, ordinal and continuous) are not rare in animal and plant breeding programs. However, there is a lack of statistical models that can exploit the correlation between traits with mixed phenotypes...
Multi-trait, Multi-environment Deep Learning Modeling for Genomic-Enabled Prediction of Plant Traits.
G3 (Bethesda, Md.)
Dec 10, 2018
Multi-trait and multi-environment data are common in animal and plant breeding programs. However, what is lacking are more powerful statistical models that can exploit the correlation between traits to improve prediction accuracy in the context of ge...
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.
PloS one
Nov 30, 2018
Recent advances in high-throughput technologies have resulted in a tremendous increase in the amount of omics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge...
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 ...
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