Monday, January 19, 2009

Draft of our first paper: Shotgun DNA Mapping!


Today, Larry, Anthony, Linh, and I hunkered down and created a draft of our first paper that will come out of our lab. We had been really struggling to write this paper collaboratively in bits and pieces on the wiki, and so we decided to just block off a bunch of time and try to write it together using Word, an overhead projector, and a whiteboard. This took us about 9 hours and worked fantastically. Pats on the back for all of us.

You can find a draft of our paper on Scribd. We welcome any comments or criticisms on this draft!

The work we are describing was done by Larry at the end of last year (2008, August and on) and we believe it presents really promising evidence that shotgun DNA mapping (SMD) by unzipping single DNA molecules will work in a variety of applications. We've been discussing the idea for over a year, particularly during Diego Ramallo Pardo's work towards single-molecule chromatin mapping in collaboration with the Osley laboratory. We had been thinking that SDM would enable single-molecule mapping of native chromatin molecules (we'll call that "shotgun chromatin mapping"), but we now envision other areas of high impact. One area would be in structural genome mapping. We cite the paper by Kidd et al. (2008) which described the amount of structural genome variation between 8 human individuals. Due to the nature of this kind of variation, it would be very well suited for detection by single-molecule DNA unzipping. Furthermore, we envision in the future shotgun DNA mapping of DNA from tumor cells, which (if someone made the method suitably high-throughput) could be a way of typing tumors based on structural genome variety. Another possibility is a genome could be scanned for protein binding sites by shotgun DNA mapping in the presence of purified protein (e.g. finding new binding sites for a newly purified protein of interest).

We're currently planning on submitting our paper to Biophysical Journal. This is a very good journal that we often read. However, we're still wondering whether we may be able to publish in a higher impact journal and reach more biologists if we can better explain the potential applications of our work. We're hoping our biologist friends will have some suggestions about this after reading our draft. And please do let us know your opinion!

(You can read more of Steve's comments about the writing process on his research blog.)

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