AIMC Topic: Molecular Sequence Annotation

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UniProt: a worldwide hub of protein knowledge.

Nucleic acids research Jan 8, 2019
The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of the...
Proteome Molecular Sequence Annotation Data Curation Sequence Analysis, Protein Databases, Protein Knowledge Bases
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Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms.

Database : the journal of biological databases and curation Jan 1, 2019
Next-generation sequencing technologies and the availability of an increasing number of mammalian and other genomes allow gene expression studies, particularly RNA sequencing, in many non-model organisms. However, incomplete genome annotation and ass...
Molecular Sequence Annotation Gene Ontology Animals Sequence Analysis, RNA Databases, Genetic Humans
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Exploring microRNA Regulation of Cancer with Context-Aware Deep Cancer Classifier.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2019
BACKGROUND: MicroRNAs (miRNAs) are small, non-coding RNA that regulate gene expression through post-transcriptional silencing. Differential expression observed in miRNAs, combined with advancements in deep learning (DL), have the potential to improve...
Gene Expression Profiling Diagnosis, Computer-Assisted Deep Learning Male Neoplasms Gene Expression Regulation, Neoplastic MicroRNAs High-Throughput Nucleotide Sequencing Computational Biology Sequence Analysis, RNA Neural Networks, Computer Female Humans Databases, Nucleic Acid Molecular Sequence Annotation Gene Ontology
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Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2019
Noncoding single nucleotide polymorphisms (SNPs) and their target genes are important components of the heritability of diseases and other polygenic traits. Identifying these SNPs and target genes could potentially reveal new molecular mechanisms and...
Molecular Sequence Annotation Databases, Nucleic Acid Models, Genetic Sequence Analysis, DNA Algorithms Deep Learning Polymorphism, Single Nucleotide Humans Genome-Wide Association Study Computational Biology Neural Networks, Computer
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LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning.

Bioinformatics (Oxford, England) Nov 15, 2018
MOTIVATION: To characterize long non-coding RNAs (lncRNAs), both identifying and functionally annotating them are essential to be addressed. Moreover, a comprehensive construction for lncRNA annotation is desired to facilitate the research in the fie...
Molecular Sequence Annotation Deep Learning RNA, Long Noncoding Neural Networks, Computer
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WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update.

Nucleic acids research Jul 2, 2018
WEGO (Web Gene Ontology Annotation Plot), created in 2006, is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. Owing largely to the rapid development of high-throughput sequencing and the increas...
Internet High-Throughput Nucleotide Sequencing Gene Ontology Molecular Sequence Annotation Software User-Computer Interface Databases, Genetic
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PANNZER2: a rapid functional annotation web server.

Nucleic acids research Jul 2, 2018
The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by pr...
Software Molecular Sequence Annotation Gene Ontology Databases, Protein Internet Algorithms High-Throughput Nucleotide Sequencing Computational Biology
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Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.

Bioinformatics (Oxford, England) Jun 1, 2018
MOTIVATION: Protein-protein interactions (PPI) play a crucial role in our understanding of protein function and biological processes. The standardization and recording of experimental findings is increasingly stored in ontologies, with the Gene Ontol...
Gene Ontology Entropy Computational Biology Support Vector Machine Molecular Sequence Annotation
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Protein classification using modified n-grams and skip-grams.

Bioinformatics (Oxford, England) May 1, 2018
MOTIVATION: Classification by supervised machine learning greatly facilitates the annotation of protein characteristics from their primary sequence. However, the feature generation step in this process requires detailed knowledge of attributes used t...
Models, Molecular Supervised Machine Learning Protein Conformation Proteins Natural Language Processing Molecular Sequence Annotation Sequence Analysis, Protein
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Machine learning annotation of human branchpoints.

Bioinformatics (Oxford, England) Mar 15, 2018
MOTIVATION: The branchpoint element is required for the first lariat-forming reaction in splicing. However current catalogues of human branchpoints remain incomplete due to the difficulty in experimentally identifying these splicing elements. To addr...
Genetic Variation Software Introns Genome, Human Humans Sensitivity and Specificity RNA Splicing Molecular Sequence Annotation Machine Learning Sequence Analysis, DNA
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