User: Denise - Open Targets

Reputation:
4,710
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Trusted
Location:
UK, Hinxton, EMBL-EBI
Website:
http://www.ebi.ac.uk/a...
Twitter:
@deniseOme
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Google Scholar Page
Last seen:
57 minutes ago
Joined:
4 years, 3 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 at the EMBL-EBI. 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 • 492 results • page 1 of 50 • next >
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Comment: C: Finding SNPs RSID from older papers
... NM_001105580:c.1394T>C is a HGVS notation, so I'd expect you could annotate variants like that and find their genomic coordinates plus functional consequences on human transcripts using the VEP. VEP does take [HGVS identifiers ][1] [1]: http://www.ensembl.org/info/docs/tools/vep/vep_formats.h ...
written 4 days ago by Denise - Open Targets4.7k
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Answer: A: Finding SNPs RSID from older papers
... I can't access the full text as the paper has been published by Elsevier. But let's have a look at what is available without paying for access. Note the publishing date: Jan 2009. [GRCh37][1] was released in Feb 2009. So the data would have been in [NCBI36][2] at the best; perhaps [NCBI35][3]? L ...
written 5 days ago by Denise - Open Targets4.7k
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Comment: C: ENSEMBL Gene IDs for Human Inflammation
... In BioMart, choose Ensembl genes 95 (database), then Human genes (dataset). Select the Filters option in the left hand side. `Phenotype` will be one of the options (written in capital letters). You will expand it and select which phenotype you are interested in from the drop down menu. Phenotype i ...
written 5 days ago by Denise - Open Targets4.7k
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Tool: Open Targets Genetics: variant-centric resource for drug target identification and prioritisation
... Looking for a resource to help you identify causal associations between genetic variants, genes, and diseases in humans? Would you like this information to be open source, open access, and available in an easy-to-use web interface? [Open Targets][1] has launched [Open Targets Genetics][2], a varian ...
gwas tool snp phenotype gene drug written 7 weeks ago by Denise - Open Targets4.7k
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Comment: C: Best Bioinformatics Tools & Databases Targeting Genetics Disorders
... Yes, we do have plans to include disease prevalence in the Disease profile page such as the profile page for [Duchenne muscular dystrophy][1]. This would come from WHO and Orphanet. However we cannot give you a timeline for this... As per HI genes we may be able to add this annotation to our Target ...
written 4 months ago by Denise - Open Targets4.7k
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Answer: A: Best Bioinformatics Tools & Databases Targeting Genetics Disorders
... To elaborate on @EricLim suggestion, the Open Targets Platform uses genetics, omics and chemical information to associate genes (our proxies to drug targets) with diseases (both Mendelian, rare diseases and more common, complex ones). [Open Targets is also available in programmatic access][2] with o ...
written 4 months ago by Denise - Open Targets4.7k
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Comment: C: We are looking for a software engineer and a senior scientific programmer to wor
... Done. More precisely Hinxton, outside Cambridge UK. ...
written 5 months ago by Denise - Open Targets4.7k
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Comment: C: GWAS summary file including risk allele, protective allele and disease
... No, the authors not always provide this information to the journal or make it available through supplementary materials. I'd have thought that some of the info you are after is available Ensembl, known as "associated allele" in the "[Phenotype data][1]" table for a given rsID. [1]: http://www.ens ...
written 5 months ago by Denise - Open Targets4.7k
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Comment: C: Where Can I Find GERMLINE Mutation Databases Specialized In CERVICAL Cancer?
... Try the [Open Targets Platform][1]. It's not a germline mutation database, but it does integrate and score germline variants (including mutations) as well as other types of data to associate diseases e.g. cervical carcinoma with targets (aka genes/proteins). The current version shows germline varia ...
written 5 months ago by Denise - Open Targets4.7k
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Comment: C: How can I figure out the NCBI annotation version of a GFF file?
... This could give you some clues: * chicken ([release 102][1] from 2016?) * cattle ([release 104][2] from 2017? if it's *B. taurus*) * pig ([release 105][3] from 2017?). [1]: ftp://ftp.ncbi.nih.gov/genomes/Gallus_gallus/ARCHIVE/ANNOTATION_RELEASE.102/ [2]: ftp://ftp.ncbi.nih.gov/genomes/Bos_ta ...
written 5 months ago by Denise - Open Targets4.7k

Latest awards to Denise - Open Targets

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Popular Question 7 months ago, created a question with more than 1,000 views. For Open Targets and programmatic access
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Popular Question 11 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 13 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Commentator 16 months 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
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Popular Question 19 months ago, created a question with more than 1,000 views. For Open Targets, validating targets for drug development in the treatment of diseases.
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