AIMC Topic: Arabidopsis

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Consistent prediction of GO protein localization.

Scientific reports May 17, 2018
The GO-Cellular Component (GO-CC) ontology provides a controlled vocabulary for the consistent description of the subcellular compartments or macromolecular complexes where proteins may act. Current machine learning-based methods used for the automat...
Computational Biology Proteomics Proteins Software Animals Drosophila melanogaster Molecular Sequence Annotation Gene Ontology Arabidopsis Databases, Protein Solanum lycopersicum Saccharomyces cerevisiae
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Optimizing the Use of a Liquid Handling Robot to Conduct a High Throughput Forward Chemical Genetics Screen of Arabidopsis thaliana.

Journal of visualized experiments : JoVE Apr 30, 2018
Chemical genetics is increasingly being employed to decode traits in plants that may be recalcitrant to traditional genetics due to gene redundancy or lethality. However, the probability of a synthetic small molecule being bioactive is low; therefore...
Arabidopsis Chemical Engineering Robotics
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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...
Machine Learning Software Terminal Repeat Sequences Genome, Plant Conserved Sequence DNA, Plant Genome, Insect Retroelements Evolution, Molecular Animals Drosophila Proteins Arabidopsis Proteins Computational Biology Drosophila melanogaster Arabidopsis Decision Trees
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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 Machine Learning Algorithms Deoxyribonuclease I Response Elements
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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...
Arabidopsis Mice Computational Biology Chickens Saccharomyces cerevisiae Molecular Sequence Annotation Gene Ontology Humans Animals Cattle
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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...
Regulatory Sequences, Nucleic Acid Deoxyribonuclease I Dinucleotide Repeats Algorithms Support Vector Machine Genome, Plant Arabidopsis Oryza Binding Sites
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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...
Knowledge Bases Chloroplasts Metabolic Networks and Pathways Arabidopsis Subcellular Fractions 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...
Algorithms Computational Biology Humans Arabidopsis Datasets as Topic Saccharomyces cerevisiae Adenosine RNA, Messenger Support Vector Machine Nucleotides
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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...
Peptide Chain Initiation, Translational Support Vector Machine Drosophila melanogaster Animals Arabidopsis Mice Computational Biology Humans Rats Software
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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...
Escherichia coli Gene Ontology Arabidopsis Saccharomyces cerevisiae Proteins Mice Drosophila melanogaster Protein Interaction Mapping Models, Molecular Data Mining Molecular Sequence Annotation Computational Biology Protein Interaction Domains and Motifs Humans High-Throughput Nucleotide Sequencing Computer Simulation Support Vector Machine Datasets as Topic Animals
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