User: Giulietta - Ensembl Helpdesk

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1,180
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Trusted
Location:
Cambridge, UK
Website:
http://www.ensembl.org
Last seen:
4 years, 6 months ago
Joined:
8 years, 5 months ago
Email:
g*******@gmail.com

I am the project leader of the Ensembl outreach team. Ensembl is a genomics resource that provides high quality and up-to-date annotation for chordate genomes. A joint EMBL-EBI and Wellcome Trust Sanger Institute project, we work closely with other groups on campus such as the 1000 genomes project.

My PhD and post-doc were in wet-lab research (protein folding and biochemical study of protein-protein and protein-lipid interactions). I made the leap into genomics and bioinformatics when I began with the Ensembl project in 2006. I currently teach wet-lab biologists worldwide how to use our resources, and am responsible for user support like videos, helpdesk, etc.

Posts by Giulietta - Ensembl Helpdesk

<prev • 43 results • page 1 of 5 • next >
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Ensembl treatment of pseudoautosomal regions (PAR)- give us your input
... Ensembl is reviewing how we provide access to pseudoautosomal regions (PAR) in human, and we'd like your input. Please let us know how our current PAR strategy works for you. What do you like and what is difficult? If our current strategy (explained below) is not working for you, please let us know ...
ensembl par pseudoautosomal written 4.5 years ago by Giulietta - Ensembl Helpdesk1.2k • updated 4.4 years ago by Biostar ♦♦ 20
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Answer: A: Is There An Easy Way Of Getting Gene Symbols From Genomic Coordinates?
... BioMart does support hg18 (NCBI36). This functionality can be found by going to the e54 archive site, which Ensembl plans to maintain for at least another year and a half. Find it here: http://may2009.archive.ensembl.org/biomart/martview If you know Perl, you can also access the archive through ...
written 5.4 years ago by Giulietta - Ensembl Helpdesk1.2k
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Comment: C: Fast And Accurate Method To Identify Genes In Whole Genome
... Indeed, the Ensembl pipeline is quite involved, but it has to be to yield high quality gene and transcript models for vertebrates. There is a two-day gene annotation course at end of September in Cambridge, UK, so if you do think you might be interested and you are in the country, send our helpdesk ...
written 5.5 years ago by Giulietta - Ensembl Helpdesk1.2k
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Answer: A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
... You can do this with Ensembl with MySQL: Consider the display_xref_id rather than going for external synonym. The external synonym is not always available. The following query should work: select distinct stable_id, display_label from gene g, xref x where x.xref_id = g.display_xref_id ...
written 5.6 years ago by Giulietta - Ensembl Helpdesk1.2k
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Answer: A: How To Convert Chromosome Names Of Ensembl Annotation To The Ones Of Ucsc Refseq
... A few more tips that might help: The INSDC coordinates are visible on Ensembl gene summary pages like this one http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32889611-32973805 For the primary assembly, chromosome synonyms are here: ftp://ftp.ncbi.nlm.nih.gov/genbank/genome ...
written 5.9 years ago by Giulietta - Ensembl Helpdesk1.2k
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Answer: A: How To Convert Chromosome Names Of Ensembl Annotation To The Ones Of Ucsc Refseq
... Hi Ning-Yi Shao, I have a little more information about this for you. UCSC probably do this because the names that they use are not the officially accepted names. In most cases, Ensembl does use the official accession.version in the seq_region table. When they don't (for example - all chromosomes ...
written 5.9 years ago by Giulietta - Ensembl Helpdesk1.2k
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Answer: A: How To Get All Ensembl Repeatfeatures From Biomart Or The Ensembl Rest Api?
... Just to add to this, it is possible through the Ensembl REST, but you have to specify a region: http://beta.rest.ensembl.org/feature/region/human/3:1000-200000.gff3?feature=repeat Cheers, Giulietta ...
written 5.9 years ago by Giulietta - Ensembl Helpdesk1.2k
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Answer: A: Functional Annotation With Ensembl Gene Ids
... BioMart is a useful tool for this, as mentioned. The Ensembl Core Perl API can also be used to retrieve GO terms. Installation instructions are here: http://www.ensembl.org/info/docs/api/api_installation.html Modules are here: http://www.ensembl.org/info/docs/Doxygen/core-api/index.html Specif ...
written 6.7 years ago by Giulietta - Ensembl Helpdesk1.2k
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Forum: Ensembl Tutorials Youtube Channel
... Ensembl's latest video on our YouTube channel provides a quick guide to installing our APIs. http://www.youtube.com/watch?v=l6a9Exe6Bsc&feature=share&list=UUKGzTZIXfs2HX44X3HqBtDA Check out over 20 videos on Ensembl data and how to access it, including BioMart. http://www.youtube.com/user ...
ensembl biomart forum written 6.7 years ago by Giulietta - Ensembl Helpdesk1.2k • updated 6.7 years ago by Istvan Albert ♦♦ 80k
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Answer: A: Refseq From Ensembl?
... See the table at the bottom of this view for RefSeqs mapped to Ensembl transcripts: http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000139618;r=13:32889611-32973805 Using the Perl API, you can find these as 'Xrefs' or External References. If you want to use the browser, have a look at the v ...
written 7.1 years ago by Giulietta - Ensembl Helpdesk1.2k

Latest awards to Giulietta - Ensembl Helpdesk

Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: Source Of Predicted Genes In Ensembl
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Synonymous And Non-Synonymous Snps
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Source Of Predicted Genes In Ensembl
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: 53893 Genes In Ensembl?
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Ensembl-Ids Vs. Entrez-Ids
Appreciated 5.4 years ago, created a post with more than 5 votes. For Ensembl Tutorials Youtube Channel
Good Answer 5.4 years ago, created an answer that was upvoted at least 5 times. For A: Source Of Predicted Genes In Ensembl
Good Answer 5.4 years ago, created an answer that was upvoted at least 5 times. For A: 53893 Genes In Ensembl?
Good Answer 5.4 years ago, created an answer that was upvoted at least 5 times. For A: What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
Good Answer 5.4 years ago, created an answer that was upvoted at least 5 times. For A: Ensembl-Ids Vs. Entrez-Ids
Guru 5.4 years ago, received more than 100 upvotes.
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Refseq From Ensembl?
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: How To Measure Gene Enrichement (Go, Kegg) Using R And Ensembl Ids ?
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: What Is Ivsi Number Of A Mutation?
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: How To Retrieve A Protein Sequence Given An Ensembl Gene Id Using Perl
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: How To Map Ensembl Exon Ids To Gene Ids?
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Synonymous And Non-Synonymous Snps
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: How To Retrieve Gene Name And Species Associated With A Ensembl Protein Id In R
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Ensembl Perl Api Translateable_Seq Returns Sequences That Aren'T Multiples Of 3
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Api Variation Tools And 1000Genomes Dbsnp132
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Phylogenetic Tree And Ensembl
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Source Of Predicted Genes In Ensembl
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: 53893 Genes In Ensembl?

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