User: Treylathe

gravatar for Treylathe
Treylathe940
Reputation:
940
Status:
New User
Location:
San Francisco
Website:
http://blog.openhelix.com
Last seen:
3 years, 9 months ago
Joined:
7 years, 3 months ago
Email:
w*****@openhelix.com

I was a postdoc for nearly 4 years at the European Molecular Biology Laboratory (EMBL) in the Bork group. Research topics ranged from the evolution and regulation of bacterial genes to mapping Human SNPs to 3D protein structures. I've had extensive lecturing experience at several colleges and universities including the University of Rochester, City College of San Francisco and University of Heidelberg. I have a Ph.D. from the University of Rochester in Molecular and Evolutionary Biology and completed my undergraduate studies at Brigham Young University in Zoology and Art History.

Currently CSO at OpenHelix, training scientists on the use of publicly available databases and resources and keeping a blog up-to-date.

I live in San Francisco with my husband, 2 daughters and various other living organisms... some wanted, some unwanted.

Interests in biology include evolutionary biology, personal genomics and comparative genomics. Outside of biology include history (Asian), knitting, gardening, cooking, hiking and an eclectic mix of whatever catches my interest hour by hour.

Posts by Treylathe

<prev • 42 results • page 1 of 5 • next >
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Answer: A: Find Out The Genes That Correspond To My Coordinates
... A simple Table Browser search of these regions do the trick, unless you need something more robust and for larger sets of data (NM_ is the refseq as mentioned above)? table browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start choose species and assembly choose genes and gene prediction c ...
written 5.4 years ago by Treylathe940
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Answer: A: Major Bioinformatics Website Usage Statistics
... UCSC Genome Browser: http://genome.ucsc.edu/admin/stats/ I'd like to know the others also. NCBI has database stats, but the only usage stats I see are for PubMed: http://www.ncbi.nlm.nih.gov/Sitemap/Summary/statistics.html#GenomeStats ...
written 5.8 years ago by Treylathe940
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Answer: A: Retrieve Sequences Flanking Ends Of A List Of Genes
... You can also do this in the ucsc table browser and also galaxy, we have a quick on how to do this in galaxy here: http://blog.openhelix.eu/?p=9808F ...
written 5.9 years ago by Treylathe940
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Answer: A: Know Of Any Human Metabolomics Databases?
... HMDB is a good one of course These also might help,there's PathCase: http://nashua.case.edu/PathwaysMAW/Web/ which allows a user to browse and search by metabolites, view in pathways, etc. Polysearch isn't particularly a metabolomics database, but you can search several databases by metabolite of ...
written 6.2 years ago by Treylathe940
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Answer: A: How To Do Multiple Whole Genomes Alignments?
... If they are three species that are sequenced and complete, you can get an pre-computed alignment of specific regions of the species of choice from UCSC: http://screencast.com/t/JCb3UpsfvSf I'd also check out Vista for pre-computed whole genome alignments. http://pipeline.lbl.gov/cgi-bin/gateway2 If ...
written 6.3 years ago by Treylathe940
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Comment: C: Gene Network Construction... Web Based Tool
... just wanted to point out, if it's not out-of-line, GeneMania has a (publicly-available) tutorial (GeneMania funds tutorial, we provide): http://www.openhelix.com/genemania ...
written 6.5 years ago by Treylathe940
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Comment: C: What Are Not The Popular Sites For Asking Bioinformatics Questions?
... Yeah, I have to agree. There are some very large groups with lots of funding have some not-so-great responsiveness. Other small groups are amazing. ...
written 6.6 years ago by Treylathe940
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Answer: A: How Do I Get A Neandertal Sequence?
... I know Ensembl has a neanderthal browser: http://projects.ensembl.org/neandertal/ (but I can't get it to work right now, so can't remember) You could also try the UCSC browser (there are tracks under Neanderthal group). If you just want the sequences of neanderthal that align with a particular regio ...
written 6.6 years ago by Treylathe940
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Answer: A: What Is The Best Method To Find Orthologous Genes Of A Species?
... Agreed with the above, not sure it would be easy to assess which is best, but the ones you named are good: You might want to try out MetaPhOrs. I did a blog tip (video) on it a couple weeks ago. ...
written 6.6 years ago by Treylathe940
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Answer: A: Database Of Databases?
... Id say my favorites are the nar database listed above. OBRC is great too: http://www.hsls.pitt.edu/obrc/ We have a curated one at http://www.openhelix.com that is publicly available. It has almost 700 and growing. The search ranks by several relevant criteria (keyword context), usage, etc. ...
written 6.6 years ago by Treylathe940

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