AIMC Topic: Saccharomyces cerevisiae

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Gene function prediction in five model eukaryotes exclusively based on gene relative location through machine learning.

Scientific reports Jul 8, 2022
The function of most genes is unknown. The best results in automated function prediction are obtained with machine learning-based methods that combine multiple data sources, typically sequence derived features, protein structure and interaction data....
Machine Learning Phenotype Animals Drosophila melanogaster Caenorhabditis elegans Genome Mice Saccharomyces cerevisiae
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SDNN-PPI: self-attention with deep neural network effect on protein-protein interaction prediction.

BMC genomics Jun 27, 2022
BACKGROUND: Protein-protein interactions (PPIs) dominate intracellular molecules to perform a series of tasks such as transcriptional regulation, information transduction, and drug signalling. The traditional wet experiment method to obtain PPIs info...
Neural Networks, Computer Animals Saccharomyces cerevisiae Computational Biology Protein Interaction Mapping Amino Acid Sequence Mice Humans
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Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics.

PLoS biology May 27, 2022
The rate of adaptive evolution depends on the rate at which beneficial mutations are introduced into a population and the fitness effects of those mutations. The rate of beneficial mutations and their expected fitness effects is often difficult to em...
Neural Networks, Computer Algorithms Computer Simulation Acclimatization Bayes Theorem Saccharomyces cerevisiae
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Prediction of protein-protein interaction using graph neural networks.

Scientific reports May 19, 2022
Proteins are the essential biological macromolecules required to perform nearly all biological processes, and cellular functions. Proteins rarely carry out their tasks in isolation but interact with other proteins (known as protein-protein interactio...
Humans Neural Networks, Computer Amino Acid Sequence Proteins Saccharomyces cerevisiae Amino Acids
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Microbial chassis engineering drives heterologous production of complex secondary metabolites.

Biotechnology advances Apr 26, 2022
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nat...
Saccharomyces cerevisiae Metabolic Engineering Artificial Intelligence Escherichia coli Multigene Family Synthetic Biology Polyketides
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Identifying Protein Subcellular Locations With Embeddings-Based node2loc.

IEEE/ACM transactions on computational biology and bioinformatics Apr 1, 2022
Identifying protein subcellular locations is an important topic in protein function prediction. Interacting proteins may share similar locations. Thus, it is imperative to infer protein subcellular locations by taking protein-protein interactions (PP...
Saccharomyces cerevisiae Protein Interaction Mapping Neural Networks, Computer Proteins Humans
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Machine learning algorithm for precise prediction of 2'-O-methylation (Nm) sites from experimental RiboMethSeq datasets.

Methods (San Diego, Calif.) Mar 18, 2022
Analysis of epitranscriptomic RNA modifications by deep sequencing-based approaches brings an essential contribution to the general knowledge on their precise locations and relative stoichiometry in cellular RNAs. To reveal RNA modifications, several...
RNA Methylation Humans RNA, Transfer Machine Learning Saccharomyces cerevisiae Algorithms
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Deep Neural Network and Extreme Gradient Boosting Based Hybrid Classifier for Improved Prediction of Protein-Protein Interaction.

IEEE/ACM transactions on computational biology and bioinformatics Feb 3, 2022
Understanding the behavioral process of life and disease-causing mechanism, knowledge regarding protein-protein interactions (PPI) is essential. In this paper, a novel hybrid approach combining deep neural network (DNN) and extreme gradient boosting ...
Humans Software Amino Acids Neural Networks, Computer Saccharomyces cerevisiae Protein Interaction Mapping
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Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.) Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Ligases Acyltransferases Homologous Recombination Chromosome Segregation Ribosomes Models, Molecular Computer Simulation Multiprotein Complexes Protein Conformation Deep Learning Saccharomyces cerevisiae Proteins Saccharomyces cerevisiae Computational Biology DNA Repair Ubiquitin Membrane Proteins Protein Interaction Maps Proteome Protein Biosynthesis Protein Interaction Mapping Evolution, Molecular
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Yeast cell segmentation in microstructured environments with deep learning.

Bio Systems Oct 9, 2021
Cell segmentation is a major bottleneck in extracting quantitative single-cell information from microscopy data. The challenge is exasperated in the setting of microstructured environments. While deep learning approaches have proven useful for genera...
Microscopy Neural Networks, Computer Saccharomyces cerevisiae Deep Learning
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