AIMC Topic: Molecular Sequence Annotation
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The Genome3D Consortium for Structural Annotations of Selected Model Organisms.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2020
Genome3D consortium is a collaborative project involving protein structure prediction and annotation resources developed by six world-leading structural bioinformatics groups, based in the United Kingdom (namely Blundell, Murzin, Gough, Sternberg, Or...
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.
Journal of Alzheimer's disease : JAD
Jan 1, 2020
BACKGROUND: Gene Ontology (GO) is a major bioinformatic resource used for analysis of large biomedical datasets, for example from genome-wide association studies, applied universally across biological fields, including Alzheimer's disease (AD) resear...
UPCLASS: a deep learning-based classifier for UniProtKB entry publications.
Database : the journal of biological databases and curation
Jan 1, 2020
In the UniProt Knowledgebase (UniProtKB), publications providing evidence for a specific protein annotation entry are organized across different categories, such as function, interaction and expression, based on the type of data they contain. To prov...
Convolutional Neural Network Visualization for Identification of Risk Genes in Bipolar Disorder.
Current molecular medicine
Jan 1, 2020
BACKGROUND: Bipolar disorder (BD) is a type of chronic emotional disorder with a complex genetic structure. However, its genetic molecular mechanism is still unclear, which makes it insufficient to be diagnosed and treated.
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.
Nature genetics
Oct 1, 2019
To increase the utility of Gene Ontology annotations for interpretation of genome-wide experimental data, we have developed GO-CAM, a structured framework for linking multiple GO annotations into an integrated model of a biological system. We expect ...
The PSIPRED Protein Analysis Workbench: 20 years on.
Nucleic acids research
Jul 2, 2019
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 year...
Software
Protein Binding
Proteins
Amino Acid Sequence
History, 21st Century
Models, Molecular
Internet
Protein Conformation, beta-Strand
Sequence Alignment
Sequence Homology, Amino Acid
Protein Interaction Domains and Motifs
Molecular Sequence Annotation
Protein Conformation, alpha-Helical
Gene Ontology
Binding Sites
NetGO: improving large-scale protein function prediction with massive network information.
Nucleic acids research
Jul 2, 2019
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Bas...
Prokaryotic Cells
Amino Acid Sequence
Molecular Sequence Annotation
Gene Ontology
Sequence Homology, Amino Acid
Sequence Analysis, Protein
Protein Interaction Mapping
Sequence Alignment
Internet
Humans
Benchmarking
Machine Learning
Plants
Databases, Protein
Computational Biology
Structure-Activity Relationship
Proteins
Models, Molecular
Software
Animals
GOF/LOF knowledge inference with tensor decomposition in support of high order link discovery for gene, mutation and disease.
Mathematical biosciences and engineering : MBE
Feb 20, 2019
For discovery of new usage of drugs, the function type of their target genes plays an important role, and the hypothesis of "Antagonist-GOF" and "Agonist-LOF" has laid a solid foundation for supporting drug repurposing. In this research, an active ge...
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.
Bioinformatics (Oxford, England)
Feb 1, 2019
SUMMARY: TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable...
The Gene Ontology Resource: 20 years and still GOing strong.
Nucleic acids research
Jan 8, 2019
The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under cont...
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