User: Denise - Open Targets

Reputation:
4,500
Status:
Trusted
Location:
UK, Hinxton, EMBL-EBI
Website:
http://www.ebi.ac.uk/a...
Twitter:
@deniseOme
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
3 years, 9 months ago
Email:
r*******@yahoo.com

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. 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

<prev • 471 results • page 1 of 48 • next >
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Comment: C: Open Targets and programmatic access
... Following some discussion here with the team and looking at the phenotypes for the *Scn1a* in mouse mutants, we can see there is substantially premature death or poor growth in these mice. These are difficult to map to a specific human disease. This might be one reason why they don't pass the thresh ...
written 2 days ago by Denise - Open Targets4.5k
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Comment: C: How I can find flanking regions
... Flanking region is any sequence that is next to any site in the genome, either side, up or downstream. You can choose how much flanking sequence you want depending on what you want to do with this information (e.g. design primers for PCR, carry out sequence alignments for closely related species ver ...
written 2 days ago by Denise - Open Targets4.5k
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Answer: C: Why there are some discrepancies between VEP output and "variation" section of E
... When I see variant allele I read the allele at the given variant locus. Variant allele can be reference, ancestral, derived, alternate, transcript allele, wild type, etc. The alternate allele is the allele not observed on the reference assembly (GRCh38 for example). The later is also known as refere ...
written 2 days ago by Denise - Open Targets4.5k
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Comment: C: Open Targets and programmatic access
... @Eric, we have the mouse models associated with *SCN1A* in the target profile page of *[SCN1A][1]*. They are listed in the Mouse phenotypes tab. However in order to associate *SCN1A* with a disease we rely on data from Phenodigm, which unfortunately has been archived by the Sanger. I'm guessing the ...
written 3 days ago by Denise - Open Targets4.5k
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Comment: C: Should bioinformaticians learn the scientific names of plants and animals?
... On the subject of taxonomy, a post on [A Brief History of the Science of Naming Things][1]. [1]: https://medium.com/s/story/a-brief-history-of-the-science-of-naming-things-b42a9b05c366 ...
written 4 days ago by Denise - Open Targets4.5k
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Answer: A: Should bioinformaticians learn the scientific names of plants and animals?
... Whether you want to memorise the names or not, it's a matter of choice, time, effort you are willing to dedicate. However we should comply with the the standards and recommendations on taxonomy, which in my view does share qualities with any ontology (i.e. hierarchy, standards). [How to write scie ...
written 5 days ago by Denise - Open Targets4.5k
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Comment: C: How can I add the specie associated name to ensembls ID in a fasta file (cds) ?
... You can tell a lot of an [Ensembl Gene ID][1] as @Erin Lim pointed you to the Ensembl help page. The ID will have a three letter code e.g. MUS for mouse (latin name is *Mus musculus*) for the BRAF orthologue in mouse: ENSMUSG00000002413. So if you know the 3 letter code, you know the species name ...
written 16 days ago by Denise - Open Targets4.5k
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Answer: A: download mm9 mouse genome fasta file
... Download mm9 (aka NCBIm37) from the [Ensembl FTP][1]. You will have both the repeat masked and not masked sequences. Check their [README][2] for all the details. [1]: ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/dna/ [2]: ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/dna/ ...
written 5 weeks ago by Denise - Open Targets4.5k
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Answer: A: Is there a way to retrieve peptide motifs based on MAF/VEP output?
... All I know is that there is an existing program that can give you the flanking sequence of the SNPs as As,Cs, Gs, Ts rather than amino acids. In [BioMart][1], choose "Human Somatic Short Variants (SNPs and indels excluding flagged variants)", then under Attributes select Flanking sequences and enter ...
written 6 weeks ago by Denise - Open Targets4.5k
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Comment: C: Open Targets and programmatic access
... Check the [Take a REST of manual searches with the Open Targets API][1] webinar for more details. Plus additional webinars on the REST theme, as part of the EMBL-EBI programmatically series of webinars [1]: https://youtu.be/KQbfhwpeEvc ...
written 6 weeks ago by Denise - Open Targets4.5k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Open Targets and programmatic access
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Commentator 9 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 13 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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