nodalpoint.org - Bioinformatics paper of the month - Comments

Contributors

Neil — Tue, 29 Mar 2005 17:53:59 -0500

Gah, I set myself up for that one ;-)

I'll do my best. Next month...that'd be Friday.

So does that mean you're volu

Greg — Tue, 29 Mar 2005 10:16:40 -0500

So does that mean you're volunteering for next month ? If so my rough off-the-top-of-my-head guidelines would be: Regular contributors (i.e. the usual suspects) and/or anyone else who wants to take a turn contribute their entirely arbitrary choice for paper(s) of the month. By arbitrary I mean whatever you find interesting that month, and it can be more than on paper. Think of it as your "getting things done in the lab" excuse to review the literature each month. Further suggestions ?

Let's try to make this regular?

Neil — Mon, 28 Mar 2005 20:24:00 -0500

I like the idea of "paper of the month" - it requires effort from contributors of course, but I think Nodal has succeeded as a forum where we bring items of interest to the attention of others.

Nanopore sequencing is a fascinating idea - really, DNA sequencing technology has not progressed in terms of the basic chemistry for almost 30 years and has become the bottleneck in genome-scale projects. We need a breakthrough such as this to go to the next level.

Bioinformatics paper of the month

Greg — Fri, 25 Mar 2005 03:13:16 -0500

Once a month my Journal of Bioinformatics rss feed is updated with the latest research in the field. Herein I present my pick for bioinformatics paper of the month. Having spend many long hours pondering microarray data normalization I am thrilled to see it is still an issue for some people. However as fascinating as microarray data normalization is, my pick for bioinformatics paper of the month is:

A parallel graph decomposition algorithm for DNA sequencing with nanopores - Shahid H. Bokhari and Jon R. Sauer

That's right, a sequence assembly algorithm for a technology that doesn't exist yet. Still, it represents an interesting bioinformatics problem. How to assemble complete DNA sequence from variable read lengths up to 10^5 bases, where complementarity is unknown, the orientation is unknown and errors from the nanopore sequencer may also be unknown.