Chapter 01

A glimpse of the future?

Blumberg, B.S. (1996). Medical research for the next millennium. The Cambridge Review, 117, 3-8. A fascinating prediction of things to come, some of which are already here.

The intellectual setting

Mayr, E. (2004). What Makes Biology Unique? Considerations on the Autonomy of a Scientific Discipline. Cambridge University Press, Cambridge. Perspectives, from a self-described 'dirty-fingernails biologist' with an unequalled clarity of mind.

The overall biological context

Doolittle, W.F. (2000). Uprooting the tree of life. Scientific American, 282(2), 90-95. Implications of analysis of sequences for our understanding of the relationships between living things. [PubMed: 10710791]

Genomic sequence determination

Green, E.D. (2001). Strategies for systematic sequencing of complex organisms. Nature Reviews Genetics, 2, 573-583. A clear discussion of possible approaches to large-scale sequencing projects. Includes list of, and links to, ongoing projects for sequencing of multicellular organisms. [PubMed: 11483982] [DOI: 10.1038/35084503]

Sulston, J. and Ferry, G. (2002). The Common Thread: A Story of Science, Politics, Ethics and the Human Genome. Bantam, New York In: A first-hand account.

Discussions of databases and information retrieval

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402. [PubMed: 9254694] [DOI: 10.1093/nar/25.17.3389]

Frishman, D., Heumann, K., Lesk, A. and Mewes, H.-W. (1998). Comprehensive, comprehensible, distributed and intelligent databases: current status. Bioinformatics, 14, 551-561. [PubMed: 9730920] [DOI: 10.1093/bioinformatics/14.7.551]

Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Geer, L.Y., Kapustin, Y., Khovayko, O., Landsman, D., Lipman, D.J., Madden, T.L., Maglott, D.R., Ostell, J., Miller, V., Pruitt, K.D., Schuler, G.D., Sequeira, E., Sherry, S.T., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusov, R.L., Tatusova, T.A., Wagner, L. and Yaschenko, E. (2007). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 35, D5-D12. [PubMed: 17170002] [DOI: 10.1093/nar/gkl1031]

Ouzounis, C.A. and Karp, P.D. (2002). The past, present and future of genome-wide re-annotation. Genome Biology, comment2001.1-comment2001.6. Discussion of how to improve the quality of annotation in databanks, making use of the growth in relevant data.

Valencia, A. (2002). Search and retrieve. EMBO Reports, 3, 396-400. Examination of what information-retrieval tools we have and what tools we will need. [PubMed: 11991940] [DOI: 10.1093/embo-reports/kvf104]

Proteins

Branden, C. I. and Tooze, J. (1999). Introduction to Protein Structure, 2nd edn. Garland, New York. A fine introductory text.

Lesk, A. M. (2001). Introduction to Protein Architecture: The Structural Biology of Proteins. Oxford University Press, Oxford.

Lesk, A. M. (2004). Introduction to Protein Science: Architecture, Function and Genomics. Oxford University Press, Oxford. Companion volumes to Introduction to Bioinformatics, with a focus on protein structure, function and evolution.

The transition to electronic publishing

Berners-Lee, T. and Hendler, J. (2001). Publishing on the semantic web. Nature, 410, 1023-1024. From the inventor of the Web. [DOI: 10.1038/35074206]

Legal aspects

Human Genome Project Information Website: Genetics and Patenting. www.ornl.gov/hgmis/elsi/patents.html.

Bobrow, M. and Thomas, S. (2002). Patenting DNA. Current Opinion in Molecular Therapy, 4, 542-547.

Kieff, F.S., ed. (2003). Perspectives on properties of the Human Genome Project. Advances in Genetics, vol. 50. A collection of articles, discussing legal aspects of genomics and bioinformatics. [PubMed: 14714707,14714689]

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