Papers of the week

Dennis' paper of the week

My name is Dennis Lal, I am working on the genetics of rolandic epilepsy and idiopathic generalized epilepsies within the EuroEPINOMICS consortium. Like many scientists, I read a lot of publications, or well, at least the abstract. Roland and Ingo asked me repeatedly to write a post but I was afraid of losing too much time. But as a young and naive scientist you have to give things a try.That’s why I started commenting on my favorite papers of the week, collected here. This “experiment” is currently at 35 minutes (after several rounds of editing) and I aim to finish this blog post below 60 minutes.

  1. Have we identified “a significant” disease association? We geneticists increasingly face the question: “Is the variant pathogenic or is it just normal human variation?” Interpretation of the statistic results should be done carefully, especially if we use words like “functional”, “causative” or “pathogenic”. Here, a new paper in PNAS on revising statistical standards, which suggests trimming the “usual p-value” to 0.005 or 0.001.
  2. But what is the use of large variants lists and small p-values when you don’t know what to do with them? A recent review in the American Journal of Human Genetics guides the functional interpretation of noncoding variants identified through GWAS studies. This review will also be interesting for scientists working with whole genome data.
  3. These days a significant amount of reads cannot be mapped to the reference genome and will subsequently removed from the analysis. How much genomic variation will be discovered when de novo assemblies will become standard? Technically, these analyses will be feasible in the next years.
  4. More scores are more fun, right? Meet the “phenotypic relevance score“, computed from a large number of mouse exomes, which might help to shorten your long lists of variants. 

    PHIVE score

    Principal of the Exomiser combining human and mouse variation. Image from original publication licensed under CC-BY

  5. The commentary “So you want to be a computational biologist?” in Nature Biotechnology is fun to read, particularly  having our weekly telephone conferences in mind, when scientific disciplines have to talk to each other. Every new PhD student should read this commentary to be aware of how their work can look like. From my personal experience as a biologist, I was not aware about the skill set I should have developed. In my case, everything went fine because we collaborate closely.

That’s enough for my first post and I am at 55 minutes. I guess that’s an OK amount of time. With editing and this post has taken me 72 minutes.

One thought on “Papers of the week

  1. Pingback: 2013 in review: top three lists and the gene finding of the year | Beyond the Ion Channel

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