Workshop References

Introduction

• R.B. Altman, "A Curriculum for Bioinformatics: The Time is Ripe", Bioinformatics 14:549-550, 1998.
  
• D.B. Searls, "Grand challenges in computational biology," in Computation Methods in Molecular Biology, S.L. Saalzberg, D.B. Searls and S. Kasif (Eds.), Elsevier Science B.V. pages 3-10, 1998.
  
• S.L. Salzberg, "A Tutorial Introduction to Computaion for Biologists", in Computation Methods in Molecular Biology, S.L. Saalzberg, D.B. Searls and S. Kasif (Eds.), Elsevier Science B.V. pages 11-27, 1998.
  
• K.H. Fasman and S.L. Salzberg, "An Introduction to Biological Sequence Analysis" in Computation Methods in Molecular Biology, S.L. Saalzberg, D.B. Searls and S. Kasif (Eds.), Elsevier Science B.V. pages 11-27, 1998.

Molecular Evolution & Phylogeny

• J.L. Thorne, H. Kishino and J. Felsenstein, "An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences", Journal of Molecular Evolution 33:114-124, 1991.
  
• B. Labedan and M. Riley, "Gene Products of Escherichia coli: Sequence Comparisons and Common Ancestries", Molecular Biological Evolution 12:980-987, 1995.
  
• M.H. Saier, Jr. "Phylogenetic Approaches to the Identification and Characterization of Protein Families and Superfamilies", Microbial & Comparative Genomics 1:129-150, 1996.
  
• M. Nei, "Phylogenetic Analysis in Molecular Evolutionary Genetics", Annual Review of Genetics 30:371-403, 1996.
  
• A.G. Murzin, "How Far Divergent Evolution Goes in Proteins", Current Opinion in Structural Biology 8:380-387, 1998.

Metabolic Computing

• P. Karp, "What We Do Not Know About Sequence Analysis and Sequence Databases", Bioinformatics 14:753-754, 1998.

Nucleic Acid Informatics

• E.D. Uberbacher and R.J. Mural, "Locating Protein-Coding Regions in Huamn DNA Sequences by a Multiple Sensor-Neural Network Approach", Proceedings of the National Academy of Sciences USA 88:11261-11265, 1991.
  
• D.J. States, W. Gish and S.F. Altschul, "Improved Sensitivity of Nucleic Acid Database Searches Using Application-Specific Scoring Matrices", METHODS: A Companion to Methods in Enzymology 3:66-70, 1991.
  
• G.Sutton, O. White, M. Adams, A. Kerlavage, "TIGR Assembler, A New Tool for Assembling Large Shotgun Sequencing Projects", Geonome Science & Technology 1:9-19, 1995.
  
• J. Tamames, C. Ouzounis, C. Sander and A. Valencia, "Genomes with Distinct Function Composition", FEBS Letters 389:96-101, 1996.
  
• F.R. Blattner, G. Plunkett III, C.A. Bloch, N.T. Perna, V. Burland, M. Riley, J. Collado-Vides, J.D. Glasner, C.K. Rode, G.F. Mayhew, J. Gregor, N.W. Davis, H.A. Kirpatrick, M.A. Goeden, D.J. Rose, B. Mau and Y. Shao, "The Complete Genome Sequence of Escherichia coli K-12", Science 277:1453-1462, 1997.
  
• J.F. Tomb, O. White, A.R. Kerlavage, R.A. Clayton, G.G. Sutton, R.D. Fleischmann, K.A. Ketchum, H.P. Kleink, S. Gill, B.A. Dougherty, K. Nelson, J. Quackenbush, L. Zhou, E.F. Kirkness, S. Peterson, B. Loftus, D. Richardson, R. Dodson, H.G. Khalak, A. Glodek, K.McKenney, L.M. Fitzegerald, N. Lee, M.D. Adams, E.K. Hickey, D.E. Berg, J.D. Gocayne, T.R. Uttergack, J.D. Peterson, J.M. Kelley, M.D. Cotton, J.M. Weidman, C. Fujii, C. Bowman, L. Watthey, E. Wallin, W.S. Hayes, M. Borodovsky, P.D. Karp, H.O. Smith, C.M. Fraser and J.C. Venter, "The Complete Genome Sequence of the Gastric Pathogen Helicobacter pylori", Nature 388:539-547, 1997.
  
• D.B. Burge and S. Karlin, "Finding the Genes in Genomic DNA", Current Opinion in Structural Biology 8:346-354, 1998.
  
• P. Bucher, "Regulatory Elements and Expression Profiles", Current Opinion in Structural Biology 9:400-407, 1999.

Protein Informatics

Introduction to Sequence Analysis

• S.F. Altschul, M.S. Boguski, W. Gish and J.C. Wootton, "Issues in Searching Molecular Sequence Databases", Nature Genetics 6:119-129, 1994.

Algorithms & Related Issues

• W.M. Fitch and T.F. Smith, "Optimal Sequence Alignments", Proceedings of the National Academy of Sciences USA 80:1382-1386, 1983.
  
• W.R. Pearson and D.J. Lipman, "Improved Tools for Biological Sequence Comparison", Proceedings of the National Academy of Sciences USA 85:2444-2448, 1988.
  
• S. Karlin and S.F. Altschul, "Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes", Proceedings of the National Academy of Sciences USA 87:2264-2268, 1990.
  
• S.F. Altschul, W. Gish, W. Miller, E.W. Myers and D.J. Lipman, "Basic Local Alignment Search Tool", Journal of Molecular Biology 215:403-410, 1990.
  
• S.F. Altschul, "Amino Acid Substitution Matrices from an Information Theoretic Perspective", Journal of Molecular Biology 219:555-565, 1991
  
• J.W. Fickett and C.S. Tung, "Assessment of Protein Coding Measures," Nucleic Acids Research 20:6441-6451, 1992.
  
• S. Henikoff and J.G. Henikoff, "Amino Acid Substitution Matrices from Protein Blocks," Proceedings of the National Academy of Sciences USA 89:10915-10919, 1992.
  
• J.C. Wootton and S. Federhen, "Statistics of Local Complexity in Amino Acid Sequences and Sequence Databases," Computers & Chemistry 17:149-163, 1993.
  
• M.S. Waterman and M. Vingron, "Sequence Comparison Significance and Poisson Approximation", Statistical Sciences 9:367-381, 1994.
  
• W.R. Pearson, "Comparison of Methods for Searching Protein Sequence Databases", Protein Science 4:1145-1160, 1995.
  
• S.F. Altschul, T.L Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman, "Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs", Nucleic Acids Research 25:3389-3402, 1997.

Motifs & Multiple Alignment Methods

• D.L. Lipman, S.F. Altschul and J.D. Kececioglu, "A Tool for Multiple Sequence Alignment", Proceedings of the National Academy of Sciences USA 86:4412-4415, 1989.
  
• R.F. Smith and T.F. Smith, "Automatic Generation of Primary Sequence Patterns from Sets of Related Protein Sequences", Proceedings of the National Academy of Sciences USA 87:118-122, 1990.
  
• C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald and J.C. Wootton, "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment" Science 262:208-214, 1993.
  
• J.D. Thompson, D.G. Higgins and T.J. Gibson, "CLUSTALW:Improving the Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position-Specific Gap Penalities and Weight Matrix Choice", Nucleic Acids Research 22:4673-4680, 1994.
  
• M.A. McClure, T.K. Vasei and W.M. Fitch, "Comparative Analysis of Multiple Protein-Sequence Alignment Methods", Molecular Biology and Evolution 4:571-592, 1994.
  
• C. Notredame and D.G. Higgins, "SAGA: Sequence Alignment by Genetic Algorithm", Nucleic Acids Research 24:1515-1524, 1996.
  
• W.N. Grundy, T.L. Bailey and C.P. Elkan, "ParaMEME: A Parallel Implementation and a Web Interface for a DNA and Protein Motif Discovery Tool," Computer Applications in the Biosciences 12:303-310, 1996.
  
• S.R. Eddy, "Hidden Markov Models", Current Opinion in Structural Biology 6:361-365, 1996.
  
• A.F. Neuwald, J.S. Liu, D.J. Lipman and C.E. Lawrence, "Extracting Protein Alignment Models from the Sequence Database", Nucleic Acids Research 25:1655-1677, 1997.

Secondary & Tertiary Structure

• S. Pascarella and P. Argos, "Analysis of Insertions/Deletions in Protein Structures", Journal of Molecular Biology 224:461-471, 1992.
  
• C.A. Orengo, D.T. Jones and J.M Thornton, "Protein Superfamilies and Domain Superfolds", Nature 372:631-634, 1994.
  
• L. Holm and C. Sander, "Mapping the Protein Universe", Science 273:595-602, 1996.
  
• A. Marchler-Bauer and S.H. Bryant, "Measures of Threading Specificity and Accuracy", PROTEINS: Structure, Function and Genetics, Suppl. 1:74-82, 1997.
  
• R.A. Abagyan and S. Batalov, "Do Aligned Sequences Share the Same Fold?" Journal of Molecular Biology 273:355-368, 1997.
  
• M.J.E. Sternberg, P.A. Bates, L.A. Kelley and R. M. MacCallum, "Progress in Protein Structure Prediction: Assessment of CASP3", Current Opinion in Structural Biology 9:368-373, 1999

Transmembrane Segment Prediction

• DAS technique:
  Cserzo, M., Wallin, E., Simon, I., von Heijne, G., Elofsson, A., "Prediction of transmembrane alpha-helices in procariotic membrane proteins: the Dense Alignment Surface method", Prot. Engineering 10(6):673-676, 1997.
• HMMTOP technique:
  Tusnady, G.E., Simon, I., "Principles Governing Amino Acid Composition of Membrane Proteins: Applications to Topology Prediction", J. Mol. Biol. 283:489-506, 1998.
• Memsat technique:
  Jones, D.T., Taylor, W.R. and Thornton, J.M., "A model recognition approach to the prediction of all-helical membrane protein structure and topology", Biochemistry 33:3038-3049, 1994.
• PHDhtm technique:
  Rost, B., Casadio, R., Fariselli, P. & Sanders, C., "Transmembrane helices predicted at 95% accuracy", Prot. Science 4:521-533, 1995.
• PRED-TMR technique:
  Pasquier C, Promponas VJ, Palaios GA, Hamodrakas JS, Hamodrakas SJ, "A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm", Protein Eng 12(5):381-5, 1999.
• SOSUI technique:
  Hirokawa, T., Boon-Chieng, S. & Mitaku, S., "SOSUI: classification and secondary structure prediction system for membrane proteins", Bioinformatics 14(4):378-379, 1998.
• SPLIT technique:
  Juretic, D., Jeroncic, A. and Zucic, D. "Sequence analysis of membrane proteins with the web server SPLIT", Croatica Chemica Acta 72(4):975-997 1999.
• Tmap techinque:
  Persson, B. & Argos, P., "Prediction of transmembrane segments in proteins utilising multiple sequence alignments", J. Mol. Biol. 237:182-192, 1994.

  Persson, B. & Argos, P., "Topology prediction of membrane proteins", Prot. Science 5:363-371, 1996.

• TMHMM technique:
  Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L.L., "Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes", Journal of Molecular Biology 305(3):567-580, 2001.

  Sonnhammer, E.L.L, von Heijne, G., Krogh, A. "A hidden Markov model for predicting transmembrane helices in protein sequences", Proc Sixth Int. Conf. on Intelligent Systems for Molecular Biology, 175-182, AAAI Press, 1998.

• Tmpred technique:
  Based on K. Hofmann, K. and Stoffel, W., "TMbase - A database of membrane spanning proteins segments", Biol. Chem. Hoppe-Seyler 347,166, 1993 (meeting abstract).
• TopPred2 technique:
  von Heijne, G., "Membrane Protein Structure Prediction: Hydrophobicity Analysis and the 'Positive Inside' Rule", J. Mol. Biol. 225:487-494, 1992.

  Claros, M.G., and von Heijne, G.,"TopPred II: An Improved Software For Membrane Protein Structure Predictions", CABIOS 10:685-686, 1994.

• TSEG technique:
  Kirara, D., Shimizu, T. & Kanehisa, M., "Prediction of Membrane Proteins Based on Classification of Transmembrane Segments", Prot. Engineering 11(11):961-970, 1998.

Linking Structure to Function

• P. Green, D. Lipman, L. Hillier, R. Waterston, D. States and J.-M. Claverie, "Ancient Conserved Regions in New Gene Sequences and the Protein Databases", Science 259:1711-1716, 1993.
  
• P.C. Babbitt and J.A. Gerlt, "Understanding Enzyme Superfamilies", Journal of Biological Chemistry 272:30591-30594, 1997.
  
• A. Sali, "100,000 Protein Structure for the Biologist", Nature Structural Biology 5:1029-1032, 1998.
  
• P. Bork and E.V. Koonin, "Predicting Function from Protein Sequences - Where are the Bottlenecks?", Nature Genetics 18:313-318, 1998.
  
• L. Holm, "Unification of Protein Families", Current Opinion in Structural Biology 8:372-379, 1998.
  
• B. Kuster and M. Mann, "Identifying Proteins and Post-Translational Modification by Mass Spectrometry", Current Opinion in Structural Biology 8:393-400, 1998.
  
• A. Danchin, "From Protein Sequence to Function", Current Opinion in Structural Biology 9:374-382, 1999.
  
• S.A.Teichmann, C. Chothia and M. Gerstein, "Advances in Structural Genomics", Current Opinion in Structural Biology 9:390-399, 1999
  
• R.R. Copley, J. Schultz, C.P. Ponting and P. Bork, "Protein Families in Multicellular Organisms", Current Opinion in Structural Biology 9:408-415, 1999.
  
• R. L. Tatusov, E.V. Koonin and D.J. Lipman, "A Perspective on Protein Families", Science 278:631-637, 1997.
  
• A.G. Murzin and L. Patthy, "Sequences and Topology From Sequence to Structure to Function", Current Opinion in Structural Biology 9:359-362, 1999.
  
• O. Lichtarge, H.R. Bourne and F.E. Cohen, "An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families", Journal of Molecular Biology 257:342-358, 1996.