Princeton University Computer Science Department

Computer Science 598B AdTopCS: Topics in Computational Molecular Biology Mona Singh

Spring 2003

Course Summary

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Administrative Information

Lectures: Thursday 12:30--2:30, Room: CS105

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

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

• Introductory Materials on molecular biology.
• Lecture 1: Mona Singh
  • Minghua Deng, Shipra Mehta, Fengzhu Sun, and Ting Chen. Inferring Domain-Domain Interactions From Protein-Protein Interactions. Genome Res. 2002 12: 1540-1548. pdf
• Lecture 2: Elena Nabieva
  • S.M. Gomez and A. Rzhetsky. Towards the Prediction of Complete Protein-Protein Interaction Networks. Pacific Symposium on Biocomputing 7:413-424 (2002). pdf
  • Joel R. Bock and David A. Gough. Whole-proteome interaction mining. Bioinformatics 2003 19: 125-134. pdf
• Lecture 3: Carl Kingsford
  • R. Singh, M. Saha. Identifying Structural Motifs in Proteins. Pacific Symposium on Biocomputing 8:228-239 (2003). pdf
  • M. P. Liang, D. L. Brutlag, R. B. Altman. Automated Construction of Structural Motifs for Predicting Functional Sites on Protein Structures. Pacific Symposium Biocomputing 8:204-215 (2003). paper
  • Bradley, P. S. Kim, B. Berger. TRILOGY: Discovery of sequence-structure patterns across diverse proteins. Proc. Natl. Acad. Sci. USA 99:8500-8505 (2002). pdf
• Lecture 4: Robert Osada
  • Yoseph Barash, Gal Elidan, Nir Friedman and Tommy Kaplan. Modeling dependencies in protein-DNA binding sites. In: Recomb 2003. pdf
  • Lee Ann McCue, William Thompson, C. Steven Carmack, and Charles E. Lawrence. Factors Influencing the Identification of Transcription Factor Binding Sites by Cross-Species Comparison. Genome Res. 2002 12: 1523-1532.pdf
• Lecture 5: Elena Zaslavsky
  • Mathieu Blanchette and Martin Tompa. Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting. Genome Res. 2002 12: 739-748. pdf
  • U. Keich and P.A. Pevzner. Finding motifs in the twilight zone. Bioinformatics 2002 18: 1374-1381. pdf
• Lecture 6: Joe Barillari
  • Phil Bradley, Lenore Cowen, Matt Menke, Jonathan King, Bonnie Berger. BETAWRAP: successful prediction of parallel beta-helices from primary sequence reveals an association with many microbial pathogens. Proc Natl Acad Sci U S A 2001 Dec 18;98(26):14819-24 pdf
  • Yufeng Zhai and Milton H. Saier, JR. The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes Protein Sci 2002 11: 2196-2207. pdf
• Lecture 7: Subhayu Basu
  • Bulyk, M. L., Johnson, P. and Church, G. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 2002 30: 1255-1261. pdf
  • Benos, Bulyk, and Stormo. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res. 2002 Oct 15 30(20): 4442. pdf
  • Benos, Lapedes, and Stormo. Is there a code for protein-DNA recognition? Probab(ilistical)ly... Bioessays 2002 May 24(5): 466-475. pdf
• Lecture 8: DJ Halliday
  • Kaur, H., Raghava, G.P.S. An evaluation of beta-turn prediction methods. Bioinformatics. 2002 18: 1508-1514. pdf
  • Kaur, H., Raghava, G.P.S Prediction of beta-turns in proteins from multiple alignment using neural networks. Protein Sci. 2003 12(3): 627-634. pdf
• Lecture 9: Hanno Hinsch
  • Korber BT, Farber RM, Wolpert DH, Lapedes AS. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc Natl Acad Sci U S A 1993 Aug 1;90(15):7176-80 pdf
  • Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 1999 Oct 8;286(5438):295-9. pdf
  • Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol. 2003 Jan;10(1):59-69. pdf
• Lecture 10: Saby Guharay
  • Li, Wentian. The Study of Correlation Structures of DNA Sequences: A Critical Review. Computers and Chemistry (1997) 21(4): 257--271. pdf
  • H. Herzel, O. Weiss and E.N. Trifonov. 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics (1999) 15(3):187--193. pdf
• Lecture 11: Jessica Fong
  • Ramani AK, Marcotte EM. Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol 2003 Mar 14;327(1):273-84. pdf
  • Mirny LA, Gelfand MS. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 2002 Aug 2;321(1):7-20. pdf
• Lecture 12: Kam Jim
  • Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW. PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics. 2003 Mar 27;4(1):11. pdf
  • Ding, J. et. al. Mining MEDLINE: Abstracts, sentences, or phrases? Pacific Symposium on Biocomputing, 326-337, 2002. pdf
  • B. Stapley and G. Benoit. Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in medline asbtracts. Pacific Symposium on Biocomputing, 529--540, 2000 pdf from here