AIMC Topic: Eukaryota

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Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder.

Nature communications May 4, 2025
Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protei...
Eukaryota Peptides Autoencoder Mitochondria Humans Protein Transport Animals
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Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.

Genome research Feb 14, 2025
Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations...
Computational Biology Gastrointestinal Microbiome Databases, Protein Animals Deep Learning Eukaryota Metagenome Ruminants Metagenomics Rumen Fungi
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CNN-BLSTM based deep learning framework for eukaryotic kinome classification: An explainability based approach.

Computational biology and chemistry Aug 8, 2024
Classification of protein families from their sequences is an enduring task in Proteomics and related studies. Numerous deep-learning models have been moulded to tackle this challenge, but due to the black-box character, they still fall short in reli...
Algorithms Protein Kinases Deep Learning Eukaryota
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DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes.

Scientific reports Apr 21, 2024
Deep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. ...
Neural Networks, Computer Deep Learning Computational Biology Eukaryotic Cells Genome Eukaryota Transcription Factors Prokaryotic Cells Binding Sites
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An atlas of protein homo-oligomerization across domains of life.

Cell Feb 6, 2024
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a s...
Bacteria Proteome Proteins Humans Artificial Intelligence Archaea Eukaryota
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Machine learning-aided scoring of synthesis difficulties for designer chromosomes.

Science China. Life sciences Mar 3, 2023
Designer chromosomes are artificially synthesized chromosomes. Nowadays, these chromosomes have numerous applications ranging from medical research to the development of biofuels. However, some chromosome fragments can interfere with the chemical syn...
Eukaryota Chromosomes Machine Learning
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DeepmRNALoc: A Novel Predictor of Eukaryotic mRNA Subcellular Localization Based on Deep Learning.

Molecules (Basel, Switzerland) Mar 1, 2023
The subcellular localization of messenger RNA (mRNA) precisely controls where protein products are synthesized and where they function. However, obtaining an mRNA's subcellular localization through wet-lab experiments is time-consuming and expensive,...
Eukaryota Endoplasmic Reticulum Computational Biology RNA, Messenger Proteins Deep Learning
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AI reveals structures of protein complexes.

Science (New York, N.Y.) Nov 11, 2021
Eukaryota Deep Learning Proteins Software Protein Conformation Protein Interaction Mapping Artificial Intelligence Fungal Proteins
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Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen.

Nature communications Jun 10, 2021
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere...
Retroelements Crossing Over, Genetic Sequence Inversion Genes, Duplicate Polymorphism, Single Nucleotide INDEL Mutation Ascomycota Genome-Wide Association Study Computer Simulation Models, Genetic Chromosomes Pedigree Evolution, Molecular Genomics Arabidopsis Phylogeny Meiosis Eukaryota Genetic Variation Machine Learning Genome Polymorphism, Genetic
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Identifying genomic islands with deep neural networks.

BMC genomics Jun 2, 2021
BACKGROUND: Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic info...
Neural Networks, Computer Eukaryota Genomics Gene Transfer, Horizontal Genomic Islands
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