Biology Reference
In-Depth Information
development and metabolism (35), comparative and evolutionary analysis (6),
funding agency management (4), physical and genetic mapping (12), ribo-
somal RNA genes and related retrotransposable elements (4), gene prediction
and consensus set (20), honeybee disease and immunity (18), BAC/fosmid
library construction and analysis (9), G
C content (5), transposable elements
(2), gene regulation (30), superscaffold assembly (6), data management (14),
chromosome structure (6), population genetics and SNPs (13), genome as-
sembly (7), (A
+
T)-rich DNA generation (6), tiling arrays (6), anti-xenobiotic
defense mechanisms (11), and DNA sequencing (26). Honeybee Genome
Sequencing Consortium, “Insights into Social Insects.” Of course, the physics
community has been used to working in large interdisciplinary groups since
the fi rst large-scale particle accelerator experiments in the 1950s. Some biolo-
gists I spoke to said that biology was just “catching up” with physics in terms
of its attitudes toward management and interdisciplinarity.
6. Interview with Charles DeLisi, February 12, 2008, Boston
Massachusetts.
7. Interview with Richard J. Roberts, February 25, 2008, Ipswich,
Massachusetts.
8. Very recently a third group has begun to emerge from dedicated bio-
informatics and computational biology PhD programs, like the CSB (Compu-
tational and Systems Biology) program at MIT. Many of these individuals have
had signifi cant training in and exposure to
both
computer science and biology.
9. Those trained in biology would be more inclined to publish in
Cell
or
the
Journal of Molecular Biology
, while those with training in other fi elds
might look to
Bioinformatics
,
Journal of Computational Biology
, or even
Machine Learning
.
10. Burge encouraged his students to spend time doing both wet-lab and
dry-lab work, often giving them problems that would require them to en-
gage in both. However, he made sure that students spent a minimum of three
months on one side before switching; in his experience, any less would lead to
less than satisfactory work.
11. This description is based on a paper from the Burge lab: Yeo et al.,
“Identifi cation and Analysis of Alternative Splicing Events.” The supplemen-
tary material contains a detailed description of the experimental procedures.
12. This is a description (based on the interview) of the project under-
taken by the computer science graduate student working in the Burge lab, as
described above.
13. According to Burks, as of 2008, approximately 2
+
10
11
bases had
been sequenced. The genomes of one hundred representatives of all species
would amount to 3
×
×
10
18
bases, or about 10 million times more sequence
than the 2008 fi gure.
14. Stark et al., “Discovery of Functional Elements.”
15. For a recent example of this kind of argument, see Stein, “The Case for
Cloud Computing.” In fact, Charles DeLisi fi rst pointed out this possibility in
1988: DeLisi, “Computers in Molecular Biology.”
16. For instance, the cover headline for the BioIT World issue of April
2008 was “Weathering the Next-Gen Data Deluge.” The story it referred to
