Princeton University Computer Science Department

Computer Science 598C Advanced Topics in Computer Science: Current Topics in Computational Molecular Biology Mona Singh

Spring 2002

Course Summary

Administrative Information

Lectures: Tues 3:00-5:00, Room: CS 105

Professor: Mona Singh - 420 CS Building - 258-2087 msingh@cs.princeton.edu

Graduate Coordinator: Melissa Lawson - 310 CS Building - 258-5387 mml@cs.princeton.edu

• Introductory Materials on molecular biology.
• Lecture 1: Robert Osada
  • Luscombe NM, Laskowski RA, Thornton JM. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 2001 Jul 1;29(13):2860-74. pdf.
  • Benos PV, Lapedes AS, Fields DS, Stormo GD. SAMIE: statistical algorithm for modeling interaction energies. Pac Symp Biocomput 2001; 115-26. pdf.
  • Luscombe NM, Austin SE, Berman HM, Thornton J. An overview of the structures of protein-DNA complexes. Genome Biol 2000;1(1). html, pdf.
• Lecture 2: Elena Zaslavsky
  • GuhaThakurta D, Stormo GD. Identifying target sites for cooperatively binding factors. Bioinformatics 2001 Jul;17(7):608-21. pdf.
  • Stormo GD. DNA binding sites: representation and discovery. Bioinformatics 2000 Jan;16(1):16-23. pdf.
  • Sinha S, Tompa M. A Statistical Method for Finding Transcription Factor Binding Sites. Proc Int Conf Intell Syst Mol Biol. 2000;8:344-54. pdf.
• Lecture 3: Irene Pak
  • Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet. 2001 Oct;29(2):153-9. pdf.
  • Manson McGuire A, Church GM. Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res 2000 Nov 15;28(22):4523-30. pdf.
  • McGuire AM, Hughes JD, Church GM. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 2000 Jun;10(6):744-57. pdf.
• Lecture 4: Erich Schmidt
  • Gallet X, Charloteaux B, Thomas A, Brasseur R. A fast method to predict protein interaction sites from sequences. J Mol Biol 2000 Sep 29; 302(4): 917-26. pdf.
  • Sprinzak E, Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 2001 Aug 24; 311(4): 681-92. pdf.
  • Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. J Mol Biol 1997 Aug 29; 271(4): 511-23. pdf.
• Lecture 5: Devon Bush
  • Pollock D, Taylor W, Goldman N. Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol 1999 Mar 19;287(1):187-98. pdf.
  • Landgraf R, Xenarios I, Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol. 2001 Apr 13;307(5):1487-502. pdf.
  • Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000 Dec;18(12):1257-61. pdf. See also comment on article: Mayer M. and Hieter P. Protein networks--built by association. Nature Biotechnology 18, 1242 - 1243 (2000). pdf.
• Lecture 6: Catherine Cresson
  • Wang, Kollman, Kuntz. Flexible Ligand Docking: A Multistep Approach. Proteins 1999 Jul 1;36(1):1-19. pdf.
  • Palma PN, Krippahl L, Wampler JE, Moura JJ. BiGGER: A New(Soft) Docking Algorithm for Predicting Protein Interactions. Proteins 2000 Jun 1;39(4):372-84. pdf.
  • Budin N, Majeux N, Tenette-Souaille C, Caflisch A. Structure-Based Ligand Design by a Build-Up Approach and Genetic Algorithm. Journal of Computational Chemistry 2001 22(16): 1956-1970. pdf.
• Lecture 7: Jace Kohlmeier
  • Albert R, Barabasi AL. Statistical mechanics of complex networks. Chapter VI (small-world networks) and VII (scale-free model) pdf.
  • Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organization of metabolic networks. Nature 2000 Oct 5;407(6804):651-4. pdf.
  • Fell, D.A. and A. Wagner. The small world of metabolism. Nature Biotechnology 2000 18: 1121-1122. pdf.
  • Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001 May 3;411(6833):41-2. pdf.
• Lecture 8: Jessica Fong
  • Tong AH et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 2002 Jan 11; 295(5553): 321-324. pdf . See comment in Gerstein, Lan and Jansen. Proteomics. Integrating interactomes. Science. 2002 Jan 11;295(5553):284-7. pdf
  • Park J, Lappe M, Teichmann SA. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 2001 Mar 30;307(3):929-38. pdf
  • Taylor WR. A 'periodic table' for protein structures. Nature. 2002 Apr 11;416(6881):657-60. pdf.
• Lecture 9: Kam Jim
  • Liang, Fuhrman, Somogyi. Reveal: A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures. Pacific Symposium on Biocomputing 3: 18-29, 1998. pdf
  • Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian Networks to Analyze Expression Data. Journal of Computational Biology, 7:601--620, 2000. pdf
  • Segal, Barash, Simon, Friedman and Koller. From promoter sequence to expression. Recomb 2002. pdf
• Lecture 10: Carl Kingsford
  • Baker D, and Sali A. Protein structure prediction and structural genomics. Science Oct 5:294(5540):93--6, 2001. pdf
  • Dahiyat BI and Mayo SL. De Novo Protein Design: Fully Automated Sequence Selection. Science 278:82--7, 1997. pdf
  • Voigt CA, Gordon DB, Mayo SL. Trading Accuracy for Speed: A Quantitative Comparison of Search Algorithms in Protein Sequence Design. J. Mol. Biol. 299, 789--803 (2000) pdf
• Lecture 11: Brent Waters
  • Cedano J, Aloy P, Perez-Pons JA, Querol E. Relation between amino acid composition and cellular location of proteins. J Mol Biol 1997 Feb 28;266(3):594-600. pdf
  • Andrade MA, O'Donoghue SI, Rost B. Adaptation of protein surfaces to subcellular location. J Mol Biol 1998 Feb 20; 276(2):517-25.pdf
  • Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D. Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12115-20. pdf