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History & Philosophy of Computational & Genome Biology

The National Center for Biotechnology Information (1990) |PubMed|PDF| An article describing the background and launch of the NCBI. See the first issue of "NCBI News" at bottom right. My colleagues and I, plus some guest lecturers, gave the first NIH course in computational biology in the Fall of 1990. I am in the process of posting excerpts on YouTube and you can view the first of these at http://www.youtube.com/profile_videos?user=markbmd
A Molecular Biologist Visits Jurassic Park (1992) |PubMed|PDF| This case of molecular archaeology turned out to be a popular and widely-used example for pedagogical purposes, for example. Back in the day, it was customary to send reprints to colleagues and so with the hubris and naiveté of a young postdoc, I sent reprints to Michael Crichton and the late Stephen J. Gould. I got back some amusing replies.
I Think, Therefore I Publish (1994) |PubMed|PDF| If a tree falls in the woods and nobody hears it, does it make a sound?
The Turning Point in Genome Research (1995) |PubMed|PDF|
The End of the Beginning: The Race to Begin Human Genome Sequencing (1996) |PubMed|PDF|
Genomes and Evolution (1996) |PubMed|PDF|
Genome Horizons (1997) |PubMed|PDF|
Bioinformatics - a New Era (1998) |PubMed|PDF| This Special Issue of the Trends journal also contained an extensive glossary of genomics and bioinformatics terms.
Late-Night Thoughts on the Sequence Annotation Problem (1998) |PubMed|PDF| This article, written somewhat tongue-in-cheek, made a "modest proposal" of stripping sequence databases of all their annotation and re-computing it on demand based on the latest available algorithms and sources. No one seemed to get the allusion to Jonathan Swift.
Biosequence Exegesis (1999) |PubMed|PDF| A consideration of the epistemology and teleology of the genome era and origins of systems biology.
Connecting the Dots (1999) |PubMed|PDF|
An Effective Approach for Analyzing "Prefinished" Genomic Sequence Data (1999) |PubMed|PDF| I don't remember what the difference was between "prefinished" and "draft" sequence data but see next bullet.
Database Divisions and Homology Search Files: A Guide for the Perplexed (1997) |PubMed|PDF| Different purposes and strategies of DNA sequencing created a large variety of qualitatively different data types that needed to be analyzed with various caveats.
Comparative Genomics: The Mouse That Roared (2002) |PubMed|PDF|
The Only Thing Permanent Is Change (2003) |PubMed|PDF| This was my inaugural editorial when I became Editor-in-Chief of GENOMICS. It talks about the history of the name, the journal and its influence on the field.
Encode and Chip-Chip in the Genome Era (2004) |PubMed|PDF| Now that we have the sequence of the human genome, how will we analyze, annotate and interpret it?

An interesting historical 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.

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What an enticing title -- this book, first published in 1983 was reissued in 1999. I read it when I was in graduate school, along with Knuth, to get started in computational biology and computer programming.