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C.3 Journal Articles

  1. Altschul, S.F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.

  2. Altschul, S.F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389-3402.

  3. Bailey, Timothy L., and Charles Elkan. 1994 Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology 28-36. Menlo Park: AAAI Press.

  4. Bailey, Timothy L., and Michael Gribskov. 1998. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14:48-54.

  5. Bairoch, A., and R. Apweiler. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28:45-48.

  6. Bateman, A., E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, and E. L. L. Sonnhammer. 2002. The Pfam Protein Families Database. Nucleic Acids Research 30 (1):275-280.

  7. Benson, D.A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler. 2002. GenBank. Nucleic Acids Research 30 (1):17-20.

  8. Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJA, Hofmann K, Bairoch A. 2002. The PROSITE database, its status in 2002. Nucleic Acids Research. Jan 1;30(1):235-8.

  9. Gilbert, D. G. 1999. Readseq version 2, an improved biosequence conversion tool, written in the Java language. Bionet.Software (August).

  10. Gish, W., and D. J. States. 1993. Identification of protein coding regions by database similarity search. Nature Genet. 3:266-272.

  11. Higgins, D., J. Thompson, T. Gibson, J. D. Thompson, D. G. Higgins, T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673-4680.

  12. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.

  13. Kent, W. James. 2002. BLAT - The BLAST-Like Alignment Tool. Genome Research 12 (4):656-664.

  14. Pearson, W.R., and D. J. Lipman. 1988. Improved Tools for Biological Sequence Analysis. Proceedings of the National Academy of Sciences 85:2444-2448.

  15. Rice, P., I. Longden, and A. Bleasby. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16 (6):276-277.

  16. Sigrist CJA, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P. 2002. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 3(3):265-74.

  17. Stoesser, G., W. Baker, A. van den Broek, E. Camon, M. Garcia-Pastor, C. Kanz, T. Kulikova, R. Leinonen, Q. Lin, V. Lombard, R. Lopez, N. Redaschi, P. Stoehr, M. A. Tuli, K. Tzouvara, and R. Vaughan. 2002. The EMBL Nucleotide Sequence Database. Nucleic Acids Research 30 (1):21-26.

  18. Tateno, Y., T. Imanishi, S. Miyazaki, K. Fukami-Kobayashi, N. Saitou, H. Sugawara, and T. Gojobori. 2002. DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Research 30 (1):27-30.

  19. Venter, J. Craig, et al. 2001. The Sequence of the Human Genome. Science 291:1304-1351.
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