Biochimica et biophysica acta. Gene regulatory mechanisms
34461313
Transcription plays a central role in defining the identity and functionalities of cells, as well as in their responses to changes in the cellular environment. The Gene Ontology (GO) provides a rigorously defined set of concepts that describe the fun...
Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understan...
Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying ...
BACKGROUND: Paralogs formed through gene duplication and isoforms formed through alternative splicing have been important processes for increasing protein diversity and maintaining cellular homeostasis. Despite their recognized importance and the adv...
Biochimica et biophysica acta. Gene regulatory mechanisms
34673265
To control gene transcription, DNA-binding transcription factors recognise specific sequence motifs in gene regulatory regions. A complete and reliable GO annotation of all DNA-binding transcription factors is key to investigating the delicate balanc...
BACKGROUND: Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can predict the locations of enhan...
To accelerate cancer research that correlates biomarkers with clinical endpoints, methods are needed to ascertain outcomes from electronic health records at scale. Here, we train deep natural language processing (NLP) models to extract outcomes for p...
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...
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...
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...