AIMC Topic: Molecular Sequence Annotation
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DEEPre: sequence-based enzyme EC number prediction by deep learning.
Bioinformatics (Oxford, England)
Mar 1, 2018
MOTIVATION: Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive t...
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.
Circulation. Genomic and precision medicine
Feb 1, 2018
BACKGROUND: A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene On...
Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Nucleic acids research
Jan 4, 2018
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,...
The Reactome Pathway Knowledgebase.
Nucleic acids research
Jan 4, 2018
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended version of a clas...
Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2018
Spatial analysis of functional enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network regions that are statistically overrepresented for functional groups or quantitative phenotypes of i...
Annotating gene sets by mining large literature collections with protein networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2018
Analysis of patient genomes and transcriptomes routinely recognizes new gene sets associated with human disease. Here we present an integrative natural language processing system which infers common functions for a gene set through automatic mining o...
DeepLoc: prediction of protein subcellular localization using deep learning.
Bioinformatics (Oxford, England)
Nov 1, 2017
MOTIVATION: The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of...
Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning.
Bioinformatics (Oxford, England)
Oct 15, 2017
MOTIVATION: One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The in...
An efficient graph kernel method for non-coding RNA functional prediction.
Bioinformatics (Oxford, England)
Sep 1, 2017
MOTIVATION: The importance of RNA protein-coding gene regulation is by now well appreciated. Non-coding RNAs (ncRNAs) are known to regulate gene expression at practically every stage, ranging from chromatin packaging to mRNA translation. However the ...
Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery.
Briefings in bioinformatics
Sep 1, 2017
Gene Ontology (GO) semantic similarity tools enable retrieval of semantic similarity scores, which incorporate biological knowledge embedded in the GO structure for comparing or classifying different proteins or list of proteins based on their GO ann...
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