AIMC Topic: Saccharomyces cerevisiae

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Protein-protein interaction prediction based on ordinal regression and recurrent convolutional neural networks.

BMC bioinformatics Oct 8, 2021
BACKGROUND: Protein protein interactions (PPIs) are essential to most of the biological processes. The prediction of PPIs is beneficial to the understanding of protein functions and thus is helpful to pathological analysis, disease diagnosis and drug...
Neural Networks, Computer Proteins Amino Acid Sequence Saccharomyces cerevisiae Humans
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Protein Abundance Prediction Through Machine Learning Methods.

Journal of molecular biology Sep 23, 2021
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing...
Machine Learning Algorithms Computational Biology Protein Biosynthesis Schizosaccharomyces Enzymes Biological Evolution Escherichia coli Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Kluyveromyces Codon Usage
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Genetic dissection of complex traits using hierarchical biological knowledge.

PLoS computational biology Sep 17, 2021
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical bio...
Gene Ontology Hydroxyurea Chromosome Mapping Multifactorial Inheritance Glycine Knowledge Bases Saccharomyces cerevisiae Benomyl Nucleotidyltransferases Computational Biology Systems Biology Models, Genetic Metabolic Networks and Pathways Copper Mutation Glucose Machine Learning Phenotype Genome-Wide Association Study Polymorphism, Single Nucleotide Neural Networks, Computer
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iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae.

Methods (San Diego, Calif.) Apr 18, 2021
The 5-methyluridine (mU)modification plays important roles in a series of biological processes. Accurate identification of mU sites will be helpful to decode its biological functions. Although experimental techniques have been proposed to detect mU, ...
Support Vector Machine Saccharomyces cerevisiae Uridine Transcriptome Computational Biology
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A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements.

eLife Apr 16, 2021
Ribozyme switches are a class of RNA-encoded genetic switch that support conditional regulation of gene expression across diverse organisms. An improved elucidation of the relationships between sequence, structure, and activity can improve our capaci...
RNA, Catalytic Base Sequence Nucleic Acid Conformation Saccharomyces cerevisiae Sequence Analysis, RNA Models, Genetic Escherichia coli Structure-Activity Relationship Ligands High-Throughput Nucleotide Sequencing Gene Expression Regulation Neural Networks, Computer Machine Learning Computer-Aided Design Aptamers, Nucleotide
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Full-length ribosome density prediction by a multi-input and multi-output model.

PLoS computational biology Mar 26, 2021
Translation elongation is regulated by a series of complicated mechanisms in both prokaryotes and eukaryotes. Although recent advance in ribosome profiling techniques has enabled one to capture the genome-wide ribosome footprints along transcripts at...
Deep Learning Computational Biology RNA, Messenger Models, Genetic Escherichia coli Saccharomyces cerevisiae Codon Ribosomes Peptide Chain Elongation, Translational
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Machine learning applied for metabolic flux-based control of micro-aerated fermentations in bioreactors.

Biotechnology and bioengineering Mar 17, 2021
Various bio-based processes depend on controlled micro-aerobic conditions to achieve a satisfactory product yield. However, the limiting oxygen concentration varies according to the micro-organism employed, while for industrial applications, there is...
Bioreactors Fermentation Saccharomyces cerevisiae Batch Cell Culture Techniques Metabolic Flux Analysis Machine Learning Ethanol Anaerobiosis Oxygen
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Identification of RNA pseudouridine sites using deep learning approaches.

PloS one Feb 23, 2021
Pseudouridine(Ψ) is widely popular among various RNA modifications which have been confirmed to occur in rRNA, mRNA, tRNA, and nuclear/nucleolar RNA. Hence, identifying them has vital significance in academic research, drug development and gene thera...
RNA, Ribosomal Humans Pseudouridine Mice Animals Computational Biology Deep Learning RNA Saccharomyces cerevisiae
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Deep learning the collisional cross sections of the peptide universe from a million experimental values.

Nature communications Feb 19, 2021
The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million dat...
Caenorhabditis elegans Ions HeLa Cells Saccharomyces cerevisiae Drosophila melanogaster Workflow Amino Acid Sequence Tandem Mass Spectrometry Deep Learning Humans Neural Networks, Computer Proteomics Animals Proteome Peptides Escherichia coli
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A deep learning framework combined with word embedding to identify DNA replication origins.

Scientific reports Jan 12, 2021
The DNA replication influences the inheritance of genetic information in the DNA life cycle. As the distribution of replication origins (ORIs) is the major determinant to precisely regulate the replication process, the correct identification of ORIs ...
DNA Replication Neural Networks, Computer Replication Origin Kluyveromyces Algorithms Deep Learning Transcription, Genetic Databases, Genetic Saccharomyces cerevisiae Schizosaccharomyces Saccharomycetales
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