Classic Articles in Computational Biology: A collection of publications assembled by Stanford Professor of Genetics and Medicine Russ B. Altman.#

Altman, R.B. A Probabilistic Approach to Determining Biological Structure: Integrating Uncertain Data Sources. Int. J. Human-Computer Studies, 42, pp. 593-616, 1995.

Altschul, S.F. Amino Acid Substitution Matrices from an Information Theoretic Perspective. J. Mol. Bio. , 219, pp. 555-565, 1991.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. Basic Local Alignment Search Tool. J. Mol. Biol., 215, pp. 403-410, 1990.

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Research, 25(17), pp. 3389-3402, 1997., pp. 698-700, 1987.

Bagley, S.C. and Altman, R.B. Characterizing the Microenvironment Surrounding Protein Sites. Protein Science, 4, pp. 622 -635, 1995.

Bork, P., Dandekar, T., Diaz -Lazcoz, Y., Eisenhaber, F., Huynen, M., and Yuan, Y. Predicting Function: From Genes to Genomes and Back. J. Mol. Biol., 283, pp. 707-725, 1998.

Bowie, J.U., Luthy, R., and Eisenberg, D. A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure. Science, 253, pp. 164 -170, 1991.

Brown, M.P.S., Grundy, W.N., Lin, D., Cristianini, N., Sugent, C.W., Furey, T.S., Ares Jr., M., and Haussler, D. Knowledge-based Analysis of Microarray Gene Expression Data by Using Support Vector Machines. PNAS, 97(1), pp. 262-267, 2000.

Bryant, S.H. and Altschul, S.F. Statistics of Sequence-structure Threading. Current Opinion in Structural Biology, 5, pp. 236-244, 1995.

Burge, C. and Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA. J. Mol. Biol., 268, pp. 78-94, 1997.

Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. A Model of Evolutionary Change in Proteins. Atlas of Protein Sequence and Structure, v. 5 suppl. 3, pp. 345-352, 1978.

Doolittle, R.F., Feng, D-F, Tsang, S., Cho, G., and Little, E. Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock. Science, 271, pp. 470-477, 1996.

Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. Cluster Analysis and Display of Genome-wide Expression Patterns. Proc. Natl. Acad. Sci. USA, 95, pp. 12863-14868, 1998.

Gerstein, M. and Levitt, M. Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. Proc. of ISMB-96, pp. 59-67, 1996.

Gotoh, O. An Improved Algorithm for Matching Biological Sequences. J. Mol. Biol., 162, pp. 705-708, 1982.

Gribskov, M., McLachlan, A.D., and Eisenberg, D. Prot ein Analysis: Detection of Distantly Related Proteins. Proc. Natl. Acad. Sci. USA, 84, pp. 4355-4358, 1987.

Gribskov, M. and Devereux, J. Dynamic Programming Methods. In Sequence Analysis Primer. W.H. Freeman and Company, NY, pp. 123 -137, 1994.

Henikoff, S. and Henikoff, Jorja G. Amino Acid Substitution Matrices from Protein Blocks. Proc. Natl. Acad. Sci. USA, 89, pp. 10915-10919, 1992.

Karlin, S. and Altshcul, S.F. Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes. Proc. Natl. Acad. Sci. USA, 87, pp. 2264-2268, 1990.

Karp, P.D. and Riley, M. EcoCyc: The Resource and the Lessons Learned. SRI Report, January 21, 1999.

Koza, J.R. Evolution of a Computer Program for Classifying Protein Segments as Transmembrane Domains Using Genetic Programming. Proc. of ISMB-94, pp. 244-252, 1994.

Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. Hidden Markov Models in Computational Biology. J. Mol. Biol., 235. pp. 1501-1531, 1994.

Lathrop, R.H. The Protein Threading Problem with Sequence Amino Acid Interaction Preferences is NP -Complete. Protein Engineering, 7:9, pp. 1059-1068, 1994.

Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F., Wootton, J.C. Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science, 262, pp. 208-214, 1993.

Lipman, D.J., Altschul, S.F., and Kececioglu, J.D. A Tool for Multiple Sequence Alignment. Proc. Natl. Acad. Sci. USA, Vol. 86, pp. 4412-4415, 1989.

Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O., and Eisenberg, D. A Combined Algorithm for Genome-wide Prediction of Protein Function. Nature, Vol. 402, pp. 83-86, 1999.

McClure, M.A., Vasi, T.K., and Fitch, W.M. Comparative Analysis of Multiple Protein-Sequence Alignment Methods. Mol. Biol. Evol., 11:4, pp. 571-592, 1994.

Needleman, S.B. and Wunsch, C.D. A General Method Applicable to the Search for Similarities in Amino Acid Sequence of Two Proteins. J. Mol. Biol., 48, pp. 443 -453, 1970.

Nei, M. Phylogenetic Analysis in Molecular Evolutionary Genetics. Annu. Rev. Genet., 30, pp. 371-403, 1996.

Nussinov, R. and Wolfson, H.J. Efficient Detection of Three -dimensional Structural Motifs in Biological Macromolecules by Computer Vision Techniques. Proc. Natl. Acad. Sci. USA, 88, pp. 10495-10499, 1991.

Orengo, C.A. and Taylor, W.R. SSAP: Sequential Structure Alignment Program for Protein Structure Comparison. Methods in Enzymology, 266, pp. 617-635, 1996.

Pedersen, J.T. and Moult, J. Protein Folding Simulations with Genetic Algorithms and a Detailed Molecular Description. J. Mol. Biol., 269, pp. 240 -259, 1997.

Prevelige, P. and Fasman, G.D. Chou-Fasman Prediction of the Secondary Structure of Proteins: The Chou-Fasman-Prevelige Algorithm. In Prediction of Protein Structure and the Principles of Protein Conformation (G.D. Fasman, ed.) Plenum Publishing, N.Y., pp. 391 -416, 1989.

Richards, F.M. Calculation of Molecular Volumes and Areas for Structures of Known Geometry. Methods in Enzymology, 115, pp. 440 -464, 1996.

Richards, F.M. The Protein Folding Problem. Scientific American, pp. 54-63, January 1991. Sippl, M.J. Knowledge-based Potentials for Proteins. Current Opinion in Structural Biology, 5, pp. 229-235, 1995.

Smith, T.F. The History of the Genetic Sequence Databases. Genomics, 6, pp. 701-707, 1990. Smith, T.F. and Waterman, M.S. Identification of Common Molecular Subsequences. J. Mol. Biol., 147, pp. 195-197, 1981.

Subbiah, S., Laurents, D.V., and Levitt, M. Structural Similarity of DNA -binding Domains of Bacteriophage Repressors and the Globin Core. Current Biology, 3:3, pp. 141-148, 1993.

Thompson, J.D., Higgins, D.G., and Gibson, T.J. CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-specific Gap Penalties and Weight Matrix Choice. Nucleic Acids Research, 22(22), pp. 4673-4680, 1994.

Thorne, J.L., Kishino, H., and Felsenstein, J. An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences. J. Mol. Evol., 33, pp. 114-124, 1991.

Unger, R. and Moult, J. Genetic Algorithms for Protein Folding Simulations. J. Mol. Biol., 231, pp. 75-81, 1993.

Zuker, M. On Finding All Suboptimal Foldings of an RNA Molecule. Science, 244, pp. 48-52, 1989.

Recent papers#