AIMC Topic: Arabidopsis Proteins
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Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock.
Nature communications
Aug 5, 2025
The circadian clock of plants contributes to their survival and fitness. However, understanding clock function at the transcriptome level and its response to the environment requires assaying across high resolution time-course experiments. Generating...
Consensus structure prediction of A. thaliana's MCTP4 structure using prediction tools and coarse grained simulations of transmembrane domain dynamics.
PloS one
Jul 15, 2025
Multiple C2 Domains and Transmembrane region Proteins (MCTPs) in plants have been identified as important functional and structural components of plasmodesmata cytoplasmic bridges, which are vital for cell-cell communication. MCTPs are endoplasmic re...
A generalized platform for artificial intelligence-powered autonomous enzyme engineering.
Nature communications
Jul 1, 2025
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we r...
Enhancing Arabidopsis thaliana ubiquitination site prediction through knowledge distillation and natural language processing.
Methods (San Diego, Calif.)
Oct 22, 2024
Protein ubiquitination is a critical post-translational modification (PTM) involved in diverse biological processes and plays a pivotal role in regulating physiological mechanisms and disease states. Despite various efforts to develop ubiquitination ...
An automatic method to quantify trichomes in Arabidopsis thaliana.
Plant science : an international journal of experimental plant biology
Jul 19, 2022
Trichomes are unicellular or multicellular hair-like appendages developed on the aerial plant epidermis of most plant species that act as a protective barrier against natural hazards. For this reason, evaluating the density of trichomes is a valuable...
A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.
BMC plant biology
Dec 14, 2021
BACKGROUND: Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to ...
Robotic Assay for Drought (RoAD): an automated phenotyping system for brassinosteroid and drought responses.
The Plant journal : for cell and molecular biology
Aug 10, 2021
Brassinosteroids (BRs) are a group of plant steroid hormones involved in regulating growth, development, and stress responses. Many components of the BR pathway have previously been identified and characterized. However, BR phenotyping experiments ar...
DeepTetrad: high-throughput image analysis of meiotic tetrads by deep learning in Arabidopsis thaliana.
The Plant journal : for cell and molecular biology
Oct 22, 2019
Meiotic crossovers facilitate chromosome segregation and create new combinations of alleles in gametes. Crossover frequency varies along chromosomes and crossover interference limits the coincidence of closely spaced crossovers. Crossovers can be mea...
Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence.
Proteins
Jul 8, 2019
Sequence based DNA-binding protein (DBP) prediction is a widely studied biological problem. Sliding windows on position specific substitution matrices (PSSMs) rows predict DNA-binding residues well on known DBPs but the same models cannot be applied ...
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...
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