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 in systems biology#

• NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-12.

• H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein (2004). Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 14: 1107-18.

• J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Global analysis of protein phosphorylation in yeast. Nature 438: 679-84.

• 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.

• Han J-DJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, Cusick ME, Roth FP, and Vidal M. Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 2004;430:88–93.

• Rual J-F, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S,Rosenberg J, Goldberg DS, ZhangLV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas e,Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-8, 2005.

• Yildirim MA, Goh K-I, Cusick ME, Barabási A-L, Vidal M. Drug-target network. Nat Biotechnol 2007; 25:1119-26.

• Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL. The human disease network. Proc Natl Acad Sci USA 2007; 104:8685-90.

• Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, Lin C, Hao T, Fan C, Milstein S, Dupuy D, Brasseur R, Hill DE, Cusick ME, Vidal M. Edgetic perturbation models of human inherited disorders. Mol Syst Biol 2009; 3:321.

• Brehme M, Vidal M. A global protein-lipid interactome map. Mol Syst Biol 2010; 6:443.

• Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller D, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science 330:1385-1389 (2010)

• Chuang, HY, Lee, E, Liu, YT, Lee, D, and Ideker, T. Network-based classification of breast cancer metastasis.MolSyst Biol. 3:140 (2007).

• Konig, R., Zhou, Y., Elleder, D., Diamond, T.L., Bonamy, G.M., Irelan, J.T., Chiang, C.Y., Tu, B.P., De Jesus, P.D., Lilley, C.E., Seidel, S., Opaluch, A.M., Caldwell, J.S., Weitzman, M.D., Kuhen, K.L., Bandyopadhyay, S., Ideker, T., Orth, A.P., Miraglia, L.J., Bushman, F.D., Young, J.A., Chanda, S.K. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135(1):49-60 (2008).

• Kelley, B. P., Sharan, R., Karp, R., Sittler, E. T., Root, D. E., Stockwell, B. R., and Ideker, T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. ProcNatlAcadSci U S A 100, 11394-9 (2003).

• Workman, CT., Mak, HC.,McCuine, S., Tagne, JB., Agarwal, M., Ozier, O., Begley, TJ., Samson, LD., Ideker, T. A Systems Approach to Mapping DNA Damage Response Pathways.Science. 312 (5776):1054-1059 (2006)

• Lee I, Date SV, Adai AT, Marcotte EM, A probabilistic functional network of yeast genes, Science, 306(5701):1555-8 (2004)

• Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D, Detecting protein function and protein-protein interactions from genome sequences, Science, 285(5428):751-3 (1999)

• W. Ma, A. Trusina, H. El-Samad, W. Lim and C. Tang, "Defining Network Topologies that Can Achieve Biochemical Adaptation," Cell 138(4), 760 (2009).

• H. Li, R. Helling, C. Tang, and N. Wingreen, "Emergence of Preferred Structures in a Simple Model of Protein Folding," Science 273, 666 (1996).

• X Wu, R Jiang, MQ Zhang, S.Li - Network-based global inference of human disease genes. Molecular Systems Biology, 2008

• Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, et al. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol. 2009;5:294.

• Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003).

• Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ and Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology 5(1): e8 (2007).

• Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000).