Further Information and References

Entrez Genomes:

• Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. 2007. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35(Database issue):D5-12 (January 1).
• Tatusova TA, Karsch-Mizrachi I, and Ostell JA (1999) Complete genomes in WWW Entrez: data representation and analysis. Bioinformatics 15:536-543

Genes, RNA:

• Baxevanis AD and Ouellette FBF (2001) Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Chapter 10, Wiley- Interscience
• Davuluri RV, Grosse I, Zhang MQ (2001) Computational identification of promoters and first exons in the human genome. Nature Genetics 29:412-417
• Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007 Jun;17(6):669-81.17567988
• The RNA revolution: Biology's Big Bang. The Economist, Jun 14th 2007. http://www.economist.com/opinion/displaystory.cfm?story_id=9339752. The article above also includes a link to: RNA: Really New Advances. The Economist, Jun 14th 2007 http://www.economist.com/opinion/displaystory.cfm?story_id=9333471

COGs:

• Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova, ND, Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29(1):22-8
• Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28(1):33-6
• Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics. Sep 11;4(1):41.
• Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-7

Genome Resources

• Model Organisms (2003) The Scientist Supplement 1, June 2, 2003. http://www.the-scientist.com/supplement/2003-6-2/
• Drosophila Genome Sequence (2000) Science 287:2185
• Howard J. Jacob and Anne E.Kwitek (2002) Rat Genetics: Attaching Physiology and Pharmacology to the Genome. Nature Reviews/Genetic 1:33-42

HomoloGene

• Zhang, Schwartz, Wagner, and Miller (2000) A Greedy Algorithm for Aligning DNA Sequences, J. Comp. Biol. 7(1-2):203-14