AIMC Topic: Arabidopsis

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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...
Evolution, Molecular Drosophila Proteins Drosophila melanogaster Genome, Plant Animals Computational Biology Decision Trees Arabidopsis Genome, Insect Retroelements Terminal Repeat Sequences Conserved Sequence DNA, Plant Arabidopsis Proteins Machine Learning Software
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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...
Sequence Analysis, DNA Genome, Plant Arabidopsis Deoxyribonuclease I Response Elements Machine Learning Algorithms
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NoGOA: predicting noisy GO annotations using evidences and sparse representation.

BMC bioinformatics Jul 21, 2017
BACKGROUND: Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of anno...
Cattle Mice Computational Biology Chickens Humans Animals Arabidopsis Saccharomyces cerevisiae Molecular Sequence Annotation Gene Ontology
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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...
Genome, Plant Arabidopsis Regulatory Sequences, Nucleic Acid Deoxyribonuclease I Support Vector Machine Oryza Binding Sites Dinucleotide Repeats Algorithms
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ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network.

Plant physiology Apr 25, 2017
Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (sto...
Arabidopsis Subcellular Fractions Knowledge Bases Chloroplasts Metabolic Networks and Pathways Internet
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Identifying N-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine.

Scientific reports Apr 25, 2017
N6-methyladenosine (mA) refers to methylation of the adenosine nucleotide acid at the nitrogen-6 position. It plays an important role in a series of biological processes, such as splicing events, mRNA exporting, nascent mRNA synthesis, nuclear transl...
Support Vector Machine Nucleotides Datasets as Topic Arabidopsis Saccharomyces cerevisiae Adenosine Algorithms Computational Biology RNA, Messenger Humans
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Transductive learning as an alternative to translation initiation site identification.

BMC bioinformatics Feb 2, 2017
BACKGROUND: The correct protein coding region identification is an important and latent problem in the molecular biology field. This problem becomes a challenge due to the lack of deep knowledge about the biological systems and unfamiliarity of conse...
Drosophila melanogaster Arabidopsis Peptide Chain Initiation, Translational Mice Computational Biology Rats Humans Support Vector Machine Software Animals
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Prediction of Protein-Protein Interactions by Evidence Combining Methods.

International journal of molecular sciences Nov 22, 2016
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of c...
Saccharomyces cerevisiae Drosophila melanogaster Molecular Sequence Annotation Animals Protein Interaction Domains and Motifs Mice Arabidopsis Computational Biology Gene Ontology Support Vector Machine Protein Interaction Mapping Humans Data Mining Computer Simulation High-Throughput Nucleotide Sequencing Datasets as Topic Escherichia coli Proteins Models, Molecular
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Inferring Unknown Biological Function by Integration of GO Annotations and Gene Expression Data.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2016
Characterizing genes with semantic information is an important process regarding the description of gene products. In spite that complete genomes of many organisms have been already sequenced, the biological functions of all of their genes are still ...
Saccharomyces cerevisiae Molecular Sequence Annotation Gene Ontology Genes Models, Genetic Databases, Genetic Cluster Analysis Arabidopsis Transcriptome Computational Biology Machine Learning Gene Expression Profiling
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phenoSeeder - A Robot System for Automated Handling and Phenotyping of Individual Seeds.

Plant physiology Sep 23, 2016
The enormous diversity of seed traits is an intriguing feature and critical for the overwhelming success of higher plants. In particular, seed mass is generally regarded to be key for seedling development but is mostly approximated by using scanning ...
Quantitative Trait Loci Robotics Phenotype Arabidopsis Automation Ecotype Imaging, Three-Dimensional Hordeum Seeds
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