AIMC Topic: Plants

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Machine and Deep Learning: Artificial Intelligence Application in Biotic and Abiotic Stress Management in Plants.

Frontiers in bioscience (Landmark edition) Jan 17, 2024
Biotic and abiotic stresses significantly affect plant fitness, resulting in a serious loss in food production. Biotic and abiotic stresses predominantly affect metabolite biosynthesis, gene and protein expression, and genome variations. However, lig...
Plants Stress, Physiological Machine Learning Deep Learning Artificial Intelligence
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Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis.

Nucleic acids research Jan 5, 2024
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional speci...
Multiomics Internet Plants Signal Transduction Knowledge Bases Databases, Protein Metabolic Networks and Pathways
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Perspectives on Computation in Plants.

Artificial life Aug 1, 2023
Plants thrive in virtually all natural and human-adapted environments and are becoming popular models for developing robotics systems because of their strategies of morphological and behavioral adaptation. Such adaptation and high plasticity offer ne...
Humans Neural Networks, Computer Robotics Plants Adaptation, Physiological
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COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants.

Briefings in functional genomics May 18, 2023
Antiviral defenses are one of the significant roles of RNA interference (RNAi) in plants. It has been reported that the host RNAi mechanism machinery can target viral RNAs for destruction because virus-derived small interfering RNAs (vsiRNAs) are fou...
Deep Learning Antiviral Agents Plants Plant Viruses RNA Interference Copper RNA, Small Interfering
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Integration of machine learning with computational structural biology of plants.

The Biochemical journal Apr 29, 2022
Computational structural biology of proteins has developed rapidly in recent decades with the development of new computational tools and the advancement of computing hardware. However, while these techniques have widely been used to make advancements...
Humans Plants Machine Learning Computational Biology Proteins
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Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Plant Reactome (https://plantreactome.gramene.org) and PubChem ( https://pubchem.ncbi.nlm.nih.gov ) are two reference data portals and resources for curated plant pathways, small molecules, metabolites, gene products, and macromolecular interactions....
Plants Knowledge Bases Proteins Metabolic Networks and Pathways Databases, Factual
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Machine learning for phytopathology: from the molecular scale towards the network scale.

Briefings in bioinformatics Sep 2, 2021
With the increasing volume of high-throughput sequencing data from a variety of omics techniques in the field of plant-pathogen interactions, sorting, retrieving, processing and visualizing biological information have become a great challenge. Within...
NLR Proteins Plants Receptors, Pattern Recognition Support Vector Machine Plant Diseases Viral Proteins Pathogen-Associated Molecular Pattern Molecules Bayes Theorem Protein Serine-Threonine Kinases Protein Interaction Mapping Gene Expression Regulation Plant Pathology Bacterial Proteins Disease Resistance Fungal Proteins Host-Pathogen Interactions
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Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.

Briefings in bioinformatics Sep 2, 2021
This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusabl...
Software Phenotype Data Management Proteomics Proteome Self-Assessment Workflow Humans Plants Neural Networks, Computer Metadata High-Throughput Nucleotide Sequencing Genome, Human International Cooperation
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Accurate prediction of multi-label protein subcellular localization through multi-view feature learning with RBRL classifier.

Briefings in bioinformatics Sep 2, 2021
Multi-label proteins can participate in carrier transportation, enzyme catalysis, hormone regulation and other life activities. Meanwhile, they play a key role in the fields of biopharmaceuticals, gene and cell therapy. This article proposes a predic...
Gene Ontology Viruses Intracellular Space Position-Specific Scoring Matrices Amino Acid Sequence Data Accuracy Gram-Negative Bacteria Amino Acids Plants Computational Biology Support Vector Machine Proteins Databases, Protein Discriminant Analysis
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DeepLearnMOR: a deep-learning framework for fluorescence image-based classification of organelle morphology.

Plant physiology Aug 3, 2021
The proper biogenesis, morphogenesis, and dynamics of subcellular organelles are essential to their metabolic functions. Conventional techniques for identifying, classifying, and quantifying abnormalities in organelle morphology are largely manual an...
Plants Neural Networks, Computer Computer-Aided Design Organelles Plant Cells Fluorescence Reproducibility of Results Deep Learning
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