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* Altman, R.B. A Probabilistic Approach to Determining Biological Structure: Integrating Uncertain Data Sources. Int. J. Human-Computer Studies, 42, pp. 593-616, 1995. [getPDF |altman1995.pdf]
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* Altschul, S.F. Amino Acid Substitution Matrices from an Information Theoretic Perspective. J. Mol. Bio. , 219, pp. 555-565, 1991. [getPDF |altschul1991.pdf]
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!! Recent papers
* 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. [getPDF |altschuletal1990.pdf]
* 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. [getPDF |altschuletal1997.pdf]
* Bagley, S.C. and Altman, R.B. Characterizing the Microenvironment Surrounding Protein Sites. Protein Science, 4, pp. 622 -635, 1995. [getPDF | bagleyandaltman1995.pdf]
* 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. [getPDF | borketal1998.pdf]
* 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. [getPDF | bowieetal1991.pdf]
* 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. [getPDF | brownetal2000.pdf]
* Bryant, S.H. and Altschul, S.F. Statistics of Sequence-structure Threading. Current Opinion in Structural Biology, 5, pp. 236-244, 1995. [getPDF | bryantandaltschul1995.pdf]
* Burge, C. and Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA. J. Mol. Biol., 268, pp. 78-94, 1997. [getPDF | burgeandkarlin1997.pdf]
* 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. [getPDF | dayhoffetal1978.pdf]
* 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. [getPDF | doolittleetal1996.pdf]
* 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. [getPDF | eisenetal1998.pdf]
* 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. [getPDF | gersteinandlevitt1996.pdf]
* Gotoh, O. An Improved Algorithm for Matching Biological Sequences. J. Mol. Biol., 162, pp. 705-708, 1982. [getPDF | gotoh1982.pdf]
* 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. [getPDF | gribshovetal1987.pdf]
* Gribskov, M. and Devereux, J. Dynamic Programming Methods. In Sequence Analysis Primer. W.H. Freeman and Company, NY, pp. 123 -137, 1994. [getPDF | gribskovanddevereux1994.pdf]
* Henikoff, S. and Henikoff, Jorja G. Amino Acid Substitution Matrices from Protein Blocks. Proc. Natl. Acad. Sci. USA, 89, pp. 10915-10919, 1992. [getPDF | henikoffandhenikoff1992.pdf]
* 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. [getPDF | karlinandatlschul1990.pdf]
* Karp, P.D. and Riley, M. EcoCyc: The Resource and the Lessons Learned. SRI Report, January 21, 1999. [getPDF | karpandriley1999.pdf]
* 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. [getPDF | koza1994.pdf]
* 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. [getPDF | kroghetal1994.pdf]
* Lathrop, R.H. The Protein Threading Problem with Sequence Amino Acid Interaction Preferences is NP -Complete. Protein Engineering, 7:9, pp. 1059-1068, 1994. [getPDF |lathrop1994.pdf ]
* 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. [getPDF | lawrence1993.pdf]
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* Orengo, C.A. and Taylor, W.R. SSAP: Sequential Structure Alignment Program for Protein Structure Comparison. Methods in Enzymology, 266, pp. 617-635, 1996. [getPDF | orengoandtaylor1996.pdf]
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!! Recent papers in systems biology
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* NJ Krogan, G Cagney, H Yu, G Zhong, X Guo, A Ignatchenko, J Li, S Pu, N Datta, AP Tikuisis, T Punna, JM Peregrín-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-43. [getPDF | Kroganetal2006.pdf]
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