User: Denise - Open Targets

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4,080
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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:
1 day, 17 hours ago
Joined:
3 years, 1 month ago
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r*******@yahoo.com

I design and deliver the Outreach activities for Open Targets at EMBL-EBI with my love of genomes, user support, training, and communication in genomics and bioinformatics. Exploring aspects of early drug discovery and disease biology. Previously worked in Ensembl and Ensembl Genomes, GENCODE, EUCOMM and Pig Genome projects, with post-doctorate in human population genetics (at the Wellcome Trust Sanger Institute) and sex chromosome evolution (at the Australian National University).

Posts by Denise - Open Targets

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News: Open Targets API upgrades to a new version, v3
... If you have read our tutorial [Open Targets and programmatic access][1], you will be pleased to know that we upgraded our [API to version 3 for faster drug target discovery][2]. These are the highlights of our latest Open Targets API: * new URL * new methods * new infrastructure (Google App Engine ...
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Answer: C: Convert Gene IDs into ENTREZ or ENSEMBLE format (honey bee / apis mellifera)
... It seems IDs such as [GB40001][1] are THE Gene IDs used in Ensembl Metazoa. [1]: http://metazoa.ensembl.org/Apis_mellifera/Gene/Summary?g=GB40001;r=1:20378265-20378549;t=GB40001-RA;db=core ...
written 9 days ago by Denise - Open Targets4.1k
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Answer: A: literature review by a web server
... Building up on one of @genomax' suggestion, i.e. [Open Targets][1]. The 17.06 release of the Open Targets Platform shows [2122 targets associated with asthma][2] based on the literature evidence only. We mine the scientific literature (no reviews, just research articles) and look for the co-occurr ...
written 5 weeks ago by Denise - Open Targets4.1k
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Comment: C: Tools for evaluating overall distribution of different diseases
... What do you mean by overall distribution of diseases? ...
written 8 weeks ago by Denise - Open Targets4.1k
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Comment: C: Do multiple SNPs exist in same chromosome to be called allele?
... I've got a population genetics bias, so when I read a SNP has two alleles, I think of the alleles in the population as a whole, rather than the two alleles in a (diploid) genome. However if an individual has a trisomy, they will have three alleles. ...
written 9 weeks ago by Denise - Open Targets4.1k
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Comment: C: Do multiple SNPs exist in same chromosome to be called allele?
... An allele is a state, form, or a type that varies at one locus within a given sample/population. They are not one single base only. Insertions (or deletion) of several bases at one locus (in one individual within a population) mean that at that locus the alleles with be the string of bases (the i ...
written 9 weeks ago by Denise - Open Targets4.1k
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Comment: C: Do multiple SNPs exist in same chromosome to be called allele?
... Although the sheer majority of single nucleotide polymorphism contains two alleles only, there can be loci with 3 alleles as well e.g. [rs2032582][1] and [rs3091244][2]. [1]: http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=7:87530802-87531802;v=rs2032582;vdb=variation;vf=1453429 [2]: h ...
written 9 weeks ago by Denise - Open Targets4.1k
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Answer: A: pathway analysis tools
... These are some I've come across with: [OminPath][1] with a Python module, [Reactome][2] and [GSEA][3]. [1]: http://omnipathdb.org/ [2]: http://reactome.org/ [3]: http://software.broadinstitute.org/gsea/index.jsp ...
written 9 weeks ago by Denise - Open Targets4.1k
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Comment: C: How do you use Biomart to get info about genes that didn't originate from Ensemb
... No, don't go looking for an alternative to BioMart! It's such a great, easy to use tool. In addition to @Jean-Karim Heriche's answer, note that XMs are RefSeq mRNA predicted IDs. So that's the external reference ID you need to select. Also, leave the versioning out: so use XM_415059 but *not* XM_41 ...
written 9 weeks ago by Denise - Open Targets4.1k
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Comment: C: Why genomic information shown in UCSC/Ensembl browser for a specific gene is dif
... Can you give us some examples of genes whose coordinates from the bed file don't match what you see on the UCSC and Ensembl browsers? Things to double check: same assembly, same version of the GENCODE gene set, whether you are dealing with the 'canonical' (whatever that means) or longest transcript, ...
written 9 weeks ago by Denise - Open Targets4.1k

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?
Scholar 5 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: why drop out the protein coding genes ?
Scholar 5 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Popular Question 6 months ago, created a question with more than 1,000 views. For Open Targets, validating targets for drug development in the treatment of diseases.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Scholar 9 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Scholar 9 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Scholar 10 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Teacher 10 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?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: why drop out the protein coding genes ?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Scholar 13 months ago, created an answer that has been accepted. For A: What is FPG in Genetics?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What is FPG in Genetics?
Popular Question 13 months ago, created a question with more than 1,000 views. For Welcome Ensembl REST with more endpoints!

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