Peter Visscher and colleagues have recently published a flurry of papers employing a new software package called GCTA to estimate the heritability of traits using GWAS data (GCTA stands for Genome-wide Complex Trait Analysis -- clever acronymity!). The tool, supported (and presumably coded) by Jian Yang is remarkably easy to use, based in part on the familiar PLINK commandline interface.

I haven't posted much here recently, but here is a roundup of a few of the links I've shared on Twitter (@genetics_blog) over the last two weeks. Here is a nice tutorial on accessing high-throughput public data (from NCBI) using R and Bioconductor. Cloudnumbers.com , a startup that allows you to run high-performance computing (HPC) applications in the cloud, now supports the previously mentioned R IDE, RStudio.

Nucleic Acids Research just published its Web Server Issue, featuring new and updates to existing web servers and applications for genomics and proteomics research. In case you missed it, be sure to check out the Database Issue that came out earlier this year. This web server issue has lots of papers on tools for microRNA analysis, and protein/RNA secondary structure analysis and annotation.

DNA genotyping and sequencing are getting cheaper every day. As Oxford Nanopore CTO Clive Brown recently discussed at Genomes Unzipped, when the cost of a full DNA sequence begins to fall below $1000, the value of having that information far outweighs the cost of data generation.

I just read a helpful paper on pathway analysis and interactome reconstruction: Tieri, P., Fuente, A. D., Termanini, A., & Franceschi, C. (2011). Integrating Omics Data for Signaling Pathways, Interactome Reconstruction, and Functional Analysis. In Bioinformatics for Omics Data, Methods in Molecular Biology, vol.

After evaluating an unnamed bioinformatics core facility, a group of bioinformaticians in Europe wrote up a short list of basic guidelines for organizing a bioinformatics core facility in large research institutes.

Lately I haven't written as many full length posts as usual, but here's a quick roundup of a few links I've shared on Twitter (@genetics_blog) over the last week: First, 23andMe is having a big DNA Day Sale ($108) for the kit + 1 year of their personal genome subscription service https://www.23andme.com/. Previously mentioned R IDE RStudio released a new beta (version 0.93) that includes several new features and bugfixes.

When I have a question I usually ask the internet before bugging my neighbor.

Coming from the lineage of Jason Moore, I am obliged to occasionally remind everyone that biological systems are inherently complex, and to some degree, we should therefore expect statistical models involving those systems to be complex as well. With the development of GWAS, many approaches to examine epistasis are weighed down by the computational burden of exhaustively conducting billions of statistical tests.

While writing my thesis I came across this nice review by Rita Cantor, Kenneth Lange, and Janet Sinsheimer at UCLA, "Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application." Skip the introduction unless you're new to GWAS, in which case you'll probably want to start with this more recent review by Teri Manolio.