References 409
Schaffer, A.A., L. Aravind, T.L. Madden, S. Shavirin, J.L. Spouge, Y.I. Wolf, E.V.
Koonin, and S.F. Altschul. 2001. Improving the accuracy of PSI-BLAST protein
database searches with composition-based statistics and other refinements.Nucleic
Acids Res.29:2994–3005.
Schofield, P.N., J.B. Bard, C. Booth, J. Boniver, V. Covelli, P. Delvenne, M. Ellender,
W. Engstrom, W. Goessner, M. Gruenberger, H. Hoefler, J. Hopewell, M. Mancuso,
C. Mothersill, C.S. Potten, L. Quintanilla-Fend, B. Rozell, H. Sariola, J.P. Sundberg,
and A. Ward. 2004. Pathbase: a database of mutant mouse pathology.Nucleic Acids
Res.32:D512–D515. Database issue.
Servant, F., C. Bru, S. Carrere, E. Courcelle, J. Gouzy, D. Peyruc, and D. Kahn. 2002.
ProDom: automated clustering of homologous domains.Brief Bioinform.3:246–251.
Shafer, G. 1976.A Mathematical Theory of Evidence. Princeton, NJ: Princeton University
Press.
Sherry, S.T., M.H. Ward, M. Kholodov, J. Baker, L. Phan, E.M. Smigielski, and
K. Sirotkin. 2001. dbSNP: the NCBI database of genetic variation.Nucleic Acids
Res.29:308–311.
Shipley, B. 2000.Cause and Correlation in Biology. Cambridge, UK: Cambridge Uni-
versity Press.
Shortliffe, E. 1976.Computer-Based Medical Consultation: MYCIN. New York: Elsevier.
Sigrist, C.J., L. Cerutti, N. Hulo, A. Gattiker, L. Falquet, M. Pagni, A. Bairoch, and
P. Bucher. 2002. PROSITE: a documented database using patterns and profiles as
motif descriptors.Brief Bioinform.3:265–274.
Smith, T.F., and M.S. Waterman. 1981. Identification of common molecular subse-
quences.J. Mol. Biol.147:195–197.
Software, Hit, 2004. Hit Software XML utilities.www.hitsw.com/xml_utilites/.
Spellman, P.T., M. Miller, J. Stewart, C. Troup, U. Sarkans, S. Chervitz, D. Bernhart,
G. Sherlock, C. Ball, M. Lepage, M. Swiatek, W.L. Marks, J. Goncalves, S. Markel,
D. Iordan, M. Shojatalab, A. Pizarro, J. White, R. Hubley, E. Deutsch, M. Senger, B.J.
Aronow, A. Robinson, D. Bassett, C.J. Stoeckert, Jr., and A. Brazma. 2002. Design
and implementation of microarray gene expression markup language (MAGE-
ML).Genome Biol.3:RESEARCH0046.
Spinoza, B. 1998.The Ethics (1677). Translated by R. Elwes. McLean, VA: IndyPub-
lish.com.
Spirtes, P., C. Glymour, and R. Scheines. 2001.Causation, Prediction and Search.Cam-
bridge, MA: MIT Press.
States, D.J., and W. Gish. 1994. Combined use of sequence similarity and codon bias
for coding region identification.J. Comput. Biol.1:39–50.