User: Denise - Open Targets

Reputation:
5,090
Status:
Trusted
Location:
UK, Hinxton, EMBL-EBI
Website:
http://www.ebi.ac.uk/a...
Twitter:
@deniseOme
Scholar ID:
Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
5 years, 5 months 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 • 505 results • page 1 of 51 • next >
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Comment: C: a gene become a drug target
... Maybe this is more a philosophical question. The target itself is usually a product of a gene, either a protein or its mRNA. It also need to be tractable and [tractability][1] (or druggability) can be defined in different ways. The Open Targets Platform has the [batch search tool][2] that can tell y ...
written 3 months ago by Denise - Open Targets5.1k
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Answer: A: Standard pipeline for drug target discovery and identification
... Not sure what you mean by "standard pipeline for drug target identification"??!?! I'd recommend this [review][1] for more details. Lately, there is a lot of focus on looking at genetics as genetic variants (both common and rare) seems to be a good predictor for approved drug indications (see the ori ...
written 3 months ago by Denise - Open Targets5.1k
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Answer: A: How to find mutations uniqueness in different resources/databases?
... Not sure if I understand it correctly. If the variant (mutation) you have identified is in dbSNP (there is an rs ID for it, which you've seen in Ensembl), it's **not** novel. You could also a look at [gnomAD][1], [Open Targets Genetics][2], [Open Targets Platform][3], [UniProt][4]... [1]: https: ...
written 4 months ago by Denise - Open Targets5.1k
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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 7 months ago by Denise - Open Targets5.1k
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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 9 months ago by Denise - Open Targets5.1k
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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 11 months ago by Denise - Open Targets5.1k
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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 11 months ago by Denise - Open Targets5.1k
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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 12 months ago by Denise - Open Targets5.1k
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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 12 months ago by Denise - Open Targets5.1k
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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 12 months ago by Denise - Open Targets5.1k

Latest awards to Denise - Open Targets

Scholar 5 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Scholar 7 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Popular Question 10 months ago, created a question with more than 1,000 views. For Open Targets, identifying targets for drug development in the treatment of diseases.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Scholar 12 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Scholar 12 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Popular Question 22 months ago, created a question with more than 1,000 views. For Open Targets and programmatic access
Scholar 23 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Open Targets and programmatic access
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Open Targets, identifying targets for drug development in the treatment of diseases.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Open Targets and programmatic access
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: Find an gene as an example of how the human is related to other primates with bl
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Scholar 2.8 years ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: why drop out the protein coding genes ?

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