UCL Institute of Cardiovascular Science


September 2019

Editor – Barbara Kramarz

Congratulations to Ruth on her first anniversary as Professorial Research Fellow!

This time last year Dr Ruth Lovering was promoted to Professorial Research Fellow. The promotion was a recognition of over a decade of Ruth’s achievements in Functional Gene Annotation. Since then Ruth has continued to excel in curationof published knowledge about human proteins and miRNAs, and has continued to share her skills and knowledge with UCL’s students and researchers while teaching an MSc module and running Bioinformatics Resources workshops. Congratulations, Ruth!

New ARUK-UCL Gene Ontology annotation milestone reached

We are very pleased to announce that last summer the total number of GO annotations, contributed through the ARUK-UCL initiatives and associated with neurological pathways impaired in Alzheimer’s disease, reached 8181 annotations for 1281 gene products (QuickGO, EBI statistics: 31stAugust 2019). These numbers are a result of our ongoing and previous annotation initiatives, specifically the blood-brain barrier annotation project, annotation of proteins interacting with amyloid-beta and tau, annotation of proteins involved in microglial processes in dementia, as well as annotation of microRNAs that regulate the expression of these Alzheimer’s disease-related proteins. We thank Alzheimer’s Research UK for their continuous support! http://tinyurl.com/GO-ARUK-UCL

Blood-brain barrier annotation progress

Mila and Barbara have begun GO annotation of, respectively, endothelial connective junctions in the brain and proteins involved in transport across the blood-brain barrier (BBB), reviewed by Sweeney et al., 2019. The lists of UniProtKB identifiers, which Mila and Barbara have identified for the reviewed proteins, can be viewed in the most recent accordion sections on our ARUK-funded GO annotation webpage. To date, Mila has captured biological information about ten endothelial junction proteins listed, resulting in 145 GO annotations; whereas, Barbara has so far contributed 91 GO annotations for eleven proteins from the BBB transport list. 

Congratulations and farewell to Shirin!

Last January we welcomed to our group Shirin Saverimuttu who has been working on her MSc GO annotation project with us. Shirin has now completed the annotation of microRNAs targeting the amyloid-beta receptors, reviewed by Jarosz-Griffiths et al., 2016, which we annotated previously (Kramarz et al., 2018). 

We wish Shirin every success in her future career!

Promoting our contribution to the Gene Ontology resource

Ruth’s abstract has been selected for both oral and poster presentations at the RNA Informatics Conference at Wellcome Genome Campus, Hinxton, UK, this month. We thank the organisers for this opportunity to introduce the GO resource and our microRNA biocuration work

Barbara has been invited to give presentations about GO, aiming to introduce the resource and explain how biological data curation, and our work specifically, can help to improve the analyses and interpretation of large datasets. Barbara presented at Anti-Doping Lab Qatar (ADLQ) on 29thAugust 2019, and will be presenting at Qatar University (QU) on 5thSeptember 2019 at 1-2pm.

Meetings attended

In June Ruth presented a poster describing our annotation of dementia-related microRNAs, at the UCL Neuroscience Symposium and then gave an invited presentation entitled ‘What is the biological knowledge represented in the Gene Ontology and how does it contribute to the Knowledge Commons’ at ‘The Road to a Well-constructed Knowledge Commons for the Life Sciences’ meeting in Trondheim, Norway.

Recent Publications

Koopmans F, van Nierop P, … Kramarz B, … Lovering RC, … Foulger RE, … Thomas PD, Smit AB, Verhage M. SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron (Cell Press). 2019 Jun 3. doi: 10.1016/j.neuron.2019.05.002. PMID:31171447.