I direct the Bioinformatics Core at the University of Virginia, and I'm hiring. Visit this link on the UVA Jobs website for more information. Here's the description: I'm Hiring - Bioinformatics Analyst in the UVA Bioinformatics CoreGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

I'm updating my CV and biosketch for a few grant applications, and for some time now, NIH has required you to include the PubMed Central ID for each article you publish that arose from NIH support. I only have a dozen or so papers indexed in PubMed, but I still wanted a way to do this automatically. If you have scores of publications, looking up all the PMCIDs could easily become a hassle. First, create an account at My NCBI.

Kevin White from the University of Chicago will be giving a special guest lecture at NCI next week on systems biology approaches to mine genomics data for biomarkers and therapeutic targets. The lecture will be available online as a videocast.

Title: A Backstage Tour of ggplot2 with Hadley Wickham Date: Wednesday, February 8, 2012 Time: 11:00AM - 12:00PM Pacific Presenter: Hadley Wickham, Professor of Statistics, Rice University Register here.

The winter Joint Techs meeting is next week in Baton Rouge. I'm not going, but I plan on participating via a netcast to see what's going on. Jim Bottum, Clemson's CIO, is moderating an entire day devoted to the topic Enhancing Infrastructure Support for Data Intensive Science. Of particular interest to me are the talks from 9:30-11am Tuesday January 24 from researchers and those supporting climatology, genomics, and the XSEDE projects.

Lately I've been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resulting ExpressionSet won't contain any featureData annotation. Consequentially, when I run topTable to get a list of differentially expressed genes, there's no annotation information other than the Affymetrix probeset IDs or transcript cluster IDs.

Farhad Manjoo at Slate has a good article on why you need to learn how to program. Chances are, if you're reading this post here you're already fairly adept at some form of programming. But if you're not, you should give it some serious thought.

I use this all the time, and the setup is dead simple. Follow the code below to load the RMySQL package, connect to a database (here the UCSC genome browser's public MySQL instance), set up a function to make querying easier, and query the database to return results as a data frame. Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

The Galaxy Project started using CiteULike to organize papers that are about, use, or reference Galaxy. The Galaxy CiteULike group is open to any CUL user, and once you join, you can add papers to the group, assign tags, and rate papers.

I just got this announcement from EMBL-EBI about an RNA-seq/ChIP-seq analysis hands-on course. Find the full details, schedule, and speaker list here.

I found the slides below on the education page from Bioinformatics & Research Computing at the Whitehead Institute. The first set (PDF) gives an overview of the methods and software available for quality assessment of microarray and RNA-seq experiments using the FastX toolkit and FastQC. The second set (PDF)  gives an example RNA-seq workflow using TopHat, SAMtools, Python/HTseq, and R/DEseq.