AIMC Topic: Molecular Sequence Annotation

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Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.

FEMS microbiology reviews Jan 16, 2023
Annotating protein sequences according to their biological functions is one of the key steps in understanding microbial diversity, metabolic potentials, and evolutionary histories. However, even in the best-studied prokaryotic genomes, not all protei...
Algorithms Artificial Intelligence Molecular Sequence Annotation Machine Learning Prokaryotic Cells
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CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.

Nucleic acids research Jan 6, 2023
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation a...
Software Anti-Bacterial Agents Databases, Factual Machine Learning Likelihood Functions Molecular Sequence Annotation Data Curation Drug Resistance, Microbial Genes, Bacterial
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Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support effort...
Binding Sites Databases, Protein Amino Acid Sequence Ligands Knowledge Bases Molecular Sequence Annotation
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E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants.

Bioinformatics (Oxford, England) Nov 30, 2022
MOTIVATION: The advent of massive DNA sequencing technologies is producing a huge number of human single-nucleotide polymorphisms occurring in protein-coding regions and possibly changing their sequences. Discriminating harmful protein variations fro...
Humans Artificial Intelligence Polymorphism, Single Nucleotide Amino Acids Amino Acid Sequence Molecular Sequence Annotation Computational Biology Proteins
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Hierarchical deep learning for predicting GO annotations by integrating protein knowledge.

Bioinformatics (Oxford, England) Sep 30, 2022
MOTIVATION: Experimental testing and manual curation are the most precise ways for assigning Gene Ontology (GO) terms describing protein functions. However, they are expensive, time-consuming and cannot cope with the exponential growth of data genera...
Molecular Sequence Annotation Gene Ontology Computational Biology Proteins Deep Learning
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TransformerGO: predicting protein-protein interactions by modelling the attention between sets of gene ontology terms.

Bioinformatics (Oxford, England) Apr 12, 2022
MOTIVATION: Protein-protein interactions (PPIs) play a key role in diverse biological processes but only a small subset of the interactions has been experimentally identified. Additionally, high-throughput experimental techniques that detect PPIs are...
Molecular Sequence Annotation Gene Ontology Algorithms Computational Biology Saccharomyces cerevisiae Humans Machine Learning
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SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants.

Briefings in bioinformatics Mar 10, 2022
Although there are a large number of structural variations in the chromosomes of each individual, there is a lack of more accurate methods for identifying clinical pathogenic variants. Here, we proposed SVPath, a machine learning-based method to pred...
Machine Learning Polymorphism, Single Nucleotide Molecular Sequence Annotation Humans Virulence Exons
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ECO: the Evidence and Conclusion Ontology, an update for 2022.

Nucleic acids research Jan 7, 2022
The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows...
Molecular Sequence Annotation Computational Biology Humans Gene Ontology Databases, Genetic Software
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scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species.

Nucleic acids research Jan 7, 2022
Previous studies on enhancers and their target genes were largely based on bulk samples that represent 'average' regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populati...
Consensus Sequence Eukaryotic Cells Mice Software Cell Lineage Databases, Genetic Humans Animals Enhancer Elements, Genetic Unsupervised Machine Learning Internet Chromatin Single-Cell Analysis Drosophila melanogaster Genetic Heterogeneity Gene Expression Regulation Gene Regulatory Networks Molecular Sequence Annotation Promoter Regions, Genetic Organ Specificity
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LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system.

Nucleic acids research Jan 7, 2022
LncRNAWiki, a knowledgebase of human long non-coding RNAs (lncRNAs), has been rapidly expanded by incorporating more experimentally validated lncRNAs. Since it was built based on MediaWiki as its database system, it fails to manage data in a structur...
Software Databases, Genetic Humans Knowledge Bases RNA, Long Noncoding Molecular Sequence Annotation Internet
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