User: Denise - Open Targets

Reputation:
5,040
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Trusted
Location:
UK, Hinxton, EMBL-EBI
Website:
http://www.ebi.ac.uk/a...
Twitter:
@deniseOme
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 1 day ago
Joined:
5 years ago
Email:
r*******@yahoo.com

Initially trained as a bench scientist with PhD in Biochemistry and Immunology, post-doctorate in Genetics (Australian National University) and in Human Genetics (Wellcome Sanger Institute). In 2007, I transitioned from bench research to computational biology, and four years later started a new career in science outreach in Ensembl. I'm currently leading the Outreach activities for Open Targets at EMBL-EBI with my love of genetic variants, genomes, science communication, and user support. Learning about early drug discovery and disease biology. 

Posts by Denise - Open Targets

<prev • 502 results • page 1 of 51 • next >
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Answer: A: Database listing genes involved in Breast and/or Prostate cancer
... You can look at some of the resources from [Open Targets][1], such as Open Targets Genetics and Open Targets Platform. With the latter, you can find genes associated with [prostate carcinoma][2] and [breast carcinoma][3] based on [somatic mutations][4], germline variants (giving rise to what we call ...
written 9 weeks ago by Denise - Open Targets5.0k
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Answer: A: Diseased tissue gene expression source
... In [Open Targets][1], we use differential expression data from disease vs health tissue comparisons, sourced from Expression Atlas to compute associations between drug targets and diseases. The expression data (in addition to others) is integrated, analysed, scored and displayed as "decreased" or "i ...
written 4 months ago by Denise - Open Targets5.0k
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Answer: A: Pathogenic predictors for Drosophila variants?
... Ensembl Metazoa does provide the Variant Effect Predictor (VEP) for fruit fly. You can use the [online version][1] (if your 10K variants are less than 50MB) or their [Perl script][2]. There used to be [REST API endpoint for the VEP][3] in Ensembl Genomes, so it should work for Drosophila. Be aware t ...
written 6 months ago by Denise - Open Targets5.0k
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Comment: C: ISMB bioinfo-core workshop call for lightning talks
... I'm attending ISMB and some colleagues as well. I will forward this google form to the entire Wellcome Genome campus where many are working on scRNAseq. ...
written 6 months ago by Denise - Open Targets5.0k
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Answer: A: Is there a HGNC symbol or any ENSEMBLE/RefSeq ID for this UniProt : Rheumatoid
... Got your query from Twitter :) This is a TrEMBL [entry][1], meaning an unreviewed sequence with low quality and scored poorly according to UniProt [association score][2] rules. It gives no results in Ensembl (at least for [human][3]), Entrez [Gene][4] or [Open Targets Platform][5], which leads me t ...
written 7 months ago by Denise - Open Targets5.0k
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Comment: C: Ensembl Biomart : One Ensembl transcript ID for several UniprotKB ID
... Please please do get in touch with HGNC (Human gene nomenclature committee) and Ensembl helpdesk regarding this. HGNC has [MICALCL][1] and [MICAL2][2] as two different loci. Maybe this is historical, but all those resources should agree on the official gene symbol and correct the mapping to externa ...
written 7 months ago by Denise - Open Targets5.0k
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Comment: C: How to cluster drugs by up/down gene lists?
... It may be worth exploring the literature for some practical examples, if you have not done so already. Some random examples are below: - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2123-4 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426949/ - https://books.google.com. ...
written 7 months ago by Denise - Open Targets5.0k
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Answer: A: Ensembl Biomart : One Ensembl transcript ID for several UniprotKB ID
... The table you point to in the Ensembl Browser has the protein column called UniProt, which is protein IDs from UniProtKB that match one of the translations of the Ensembl gene/transcript. This means that that column can show either SwissProt IDs (e.g. O94851 and Q6ZW33) or TrEMBL IDs (e.g. E9PNC3 a ...
written 7 months ago by Denise - Open Targets5.0k
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Comment: C: Converting HUGO ID to Entrez gene or Ensembl ID
... How many gene IDs have you got? If it's up to 200, you can use the [Open Targets Platform batch search][1] tool to get an enrichment of pathways from Reactome for your list of HGNC gene IDs. Check a previous post on the theme here in Biostars aka [Open Targets batch search][2]. [1]: https://www ...
written 9 months ago by Denise - Open Targets5.0k
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Answer: A: Medical terms Synonyms
... You can try the Open Targets [LINK][1], which is a literature knowledge graph of biomedical terms extracted from PubMed using NLP. Check this [blog post][2] for details on the API, web interface and pipeline that runs the NLP analysis. [1]: https://www.biostars.org/p/295381/ [2]: http://blog. ...
written 10 months ago by Denise - Open Targets5.0k

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