Another Word For It Patrick Durusau on Topic Maps and Semantic Diversity

December 17, 2014

History & Philosophy of Computational and Genome Biology

Filed under: Bioinformatics,Biology,Genome — Patrick Durusau @ 8:35 pm

History & Philosophy of Computational and Genome Biology by Mark Boguski.

A nice collection of books and articles on computational and genome biology. It concludes with this anecdote:

Despite all of the recent books and biographies that have come out about the Human Genome Project, I think there are still many good stories to be told. One of them is the origin of the idea for whole-genome shotgun and assembly. I recall a GRRC (Genome Research Review Committee) review that took place in late 1996 or early 1997 where Jim Weber proposed a whole-genome shotgun approach. The review panel, at first, wanted to unceremoniously “NeRF” (Not Recommend for Funding) the grant but I convinced them that it deserved to be formally reviewed and scored, based on Jim’s pioneering reputation in the area of genetic polymorphism mapping and its impact on the positional cloning of human disease genes and the origins of whole-genome genotyping. After due deliberation, the GRRC gave the Weber application a non-fundable score (around 350 as I recall) largely on the basis of Weber’s inability to demonstrate that the “shotgun” data could be assembled effectively.

Some time later, I was giving a ride to Jim Weber who was in Bethesda for a meeting. He told me why his grant got a low score and asked me if I knew any computer scientists that could help him address the assembly problem. I suggested he talk with Gene Myers (I knew Gene and his interests well since, as one of the five authors of the BLAST algorithm, he was a not infrequent visitor to NCBI).

The following May, Weber and Myers submitted a “perspective” for publication in Genome Research entitled “Human whole-genome shotgun sequencing“. This article described computer simulations which showed that assembly was possible and was essentially a rebuttal to the negative review and low priority score that came out of the GRRC. The editors of Genome Research (including me at the time) sent the Weber/Myers article to Phil Green (a well-known critic of shotgun sequencing) for review. Phil’s review was extremely detailed and actually longer that the Weber/Myers paper itself! The editors convinced Phil to allow us to publish his critique entitled “Against a whole-genome shotgun” as a point-counterpoint feature alongside the Weber-Myers article in the journal.

The rest, as they say, is history, because only a short time later, Craig Venter (whose office at TIGR had requested FAX copies of both the point and counterpoint as soon as they were published) and Mike Hunkapiller announced their shotgun sequencing and assembly project and formed Celera. They hired Gene Myers to build the computational capabilities and assemble their shotgun data which was first applied to the Drosophila genome as practice for tackling a human genome which, as is now known, was Venter’s own. Three of my graduate students (Peter Kuehl, Jiong Zhang and Oxana Pickeral) and I participated in the Drosophila annotation “jamboree” (organized by Mark Adams of Celera and Gerry Rubin) working specifically on an analysis of the counterparts of human disease genes in the Drosophila genome. Other aspects of the Jamboree are described in a short book by one of the other participants, Michael Ashburner.

The same type of stories exist not only from the early days of computer science but since then as well. Stories that will capture the imaginations of potential CS majors as well as illuminate areas where computer science can or can’t be useful.

How many of those stories have you captured?

I first saw this in a tweet by Neil Saunders.

No Comments

No comments yet.

RSS feed for comments on this post.

Sorry, the comment form is closed at this time.

Powered by WordPress