Virginia Tech - CS6104 Student Talks

Student talks are scheduled below. Each student is allocated one and one-half class periods for his or her presentation. Each speaker is responsible for identifying appropriate source material and for providing copies of identified papers to the class, either electronically or on paper.

Links to copies of papers are accessible only from the vt.edu domain.

• Nick Allen: Shortest common superstring
  June 19-20, 2000
  

  References:

  • Avrim Blum, Tao Jiang, Ming Li, John Tromp, and Mihalis Yannakakis
    Linear Approximation of Shortest Superstrings
    Journal of the ACM 41, July 1994, 630-647.

  • S. Rao Kosaraju and Arthur L. Delcher
    Large-Scale Assembly of DNA Strings and Space-Efficient Construction of Suffix Trees
    ACM Symposium on Theory of Computing, 1995, 169-177.

• Jason Zwolak: Modeling the cell cycle
  June 20-21, 2000
  

  References:

  • John J. Tyson, Bela Novak, Kathy Chen, and John Val
    Checkpoints in the cell cycle from a modeler's perspective
    Progress in Cell Cycle Research 1, 1995, 1-8.

  • John J. Tyson, Bela Novak, Garrett M. Odell, Kathy Chen, and C. Dennis Thron
    Chemical kinetic theory: understanding cell-cycle regulation
    Trends in Biochemical Sciences 21, March 1996, 89-96.

• Dr. Alscher: Evolutionary Clocks and the Phylogeny of SODs
  June 23, 2000
  

  References:

  • § Francisco J. Ayala, Eladio Barrio, and Jan Kwiatowski
    Molecular clock or erratic evolution? A tale of two genes
    PNAS 93, October 1996, 11729-11734.

  • Francisco J. Ayala
    Vagaries of the molecular clock
    PNAS 97, July 1997, 7776-7783.

  • § Da-Fei Feng, Russell F. Doolittle
    Converting Amino Acid Alignment Scores into Measures of Evolutionary Time: A Simulation Study of Various Relationships
    Journal of Molecular Evolution 44, 997, 361-370.

  • Walter M. Fitch and Francicso J. Ayala
    Tempo and Mode in Evolution
    PNAS 91, July 19 1994, 6717-6720.

  • § Walter M. Fitch and Francicso J. Ayala
    The Superoxide Dismutase Molecular Clock Revisited
    PNAS 91, July 19 1994, 6802-6807.

  • § Jan Kwiatowski, Michal Krawczyk, Michal Jaworski, Douglas Skarecky, and Francisco J. Ayala
    Erratic Evolution of Glycerol-3-Phosphate Dehydrogenase in Drosophila, Chymomyza, and Ceratitis
    Journal of Molecular Evolution 44, 1997, 9-22.

  • Young Moo Lee, David J. Friedman, and Fracisco J. Ayala
    Superoxide Dismutase: An Evolutionary Puzzle
    PNAS 82, February 1 1985, 824-828.

  • Laurence Von Kalm, Jonna Weaver, Judy DeMarco, Ross J. MacIntyre, and David T. Sullivan
    Structural Characterization of the alpha-glycerol-3-phosphate Dehydrogenase-Encoding Gene of Drosophila melanogaster
    PNAS 86, July 1 1989, 5020-5024.

• Douglas Slotta: Phylogeny
  June 26, 2000
  

  References:

  • Joseph Felsenstein
    Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach
    Journal of Molecular Evolution 17, 1981, 368-376.

  • Junhyong Kim and Tandy Warnow
    Tutorial on Phylogenetic Tree Estimation
    Tutorial for ISMB 99.

• Subhag Oak: Sequence comparison
  June 26-27, 2000
  

  References:

  • S.F. Altschul, M.S. Boguski, W. Gish, and J.C. Wootton
    Issues in searching molecular sequence databases
    Nature Genetics 6, February 1994, 119-129.

  • H. Cantalloube, et al.
    Automat and BLAST: comparison of two protein sequence similarity search programs
    Comput Appl Biosci. 11, June 1995, 261-272.

  • T. Rognes and E. Seeberg
    SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments.
    Bioinformatics 14, 1998, 839-845.

• Chad Wingrave: Motif searching
  June 28-29, 2000
  

  References:

  • Steven Henikoft, Jorja G. Henikoft, and Shmuel Pietrovski
    Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations
    Bioinformatics 15, 1999, 471-479.

  • F. Corpet, J. Gouzy, and D. Kahn
    Recent improvements of the ProDom database of protein domain families
    Nucleic Acids Research 27, January 1 1999, 263-267.
    Also available locally as a PDF file.

  • T.K. Attwood, D.R. Flower, A.P. Lewis, J.E. Mabey, S.R. Morgan, P. Scordis, J.N. Selley, and W. Wright
    PRINTS prepares for the new millennium
    Nucleic Acids Research 27, January 1 1999, 220-225.
    Also available locally as a PDF file.

  • A. Bateman, E. Birney, R. Durbin, S.R. Eddy, R.D. Finn, and E.L. Sonnhammer
    Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
    Nucleic Acids Research 27, January 1 1999, 260-262.
    Also available locally as a PDF file.

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