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ISMB'96 Schedule; Conference on Computational Biology

Pankaj Agarwal agarwal at ibc.wustl.edu
Mon May 27 23:35:15 EST 1996

        The Fourth International Conference on Computational Biology:
                Intelligent Systems for Molecular Biology '96
                              ISMB'96 Schedule

The order of the keynote talks is not final yet.

                 Wednesday, June 12, 1996

9:00am - 10:00am: Continental breakfast
10:00am - 1:00pm: Morning Tutorials

  T-1 Intro to Molecular Biology (Roth)
  T-2 Intro to Machine Learning for Molecular Biology (Shavlik & Salzberg)
  T-3 Intro to Molecular Evolution and Phylogenic Reconstruction (McClure)
  T-4 Hidden Markov Models, Part 1: Using and understanding HMMs (UCSC group)

11:20am - 11:40am: Coffee break

1:00pm - 2:00pm: Lunch

2:00pm - 5:00pm: Afternoon Tutorials

  T-5 Automated Microbial Genome Analysis  (Gaasterland & Sensen)
  T-6 Computation with Metabolic Pathways (Ouzounis & Karp)
  T-7 Recurrent Processes in Genome Evolution (Sankoff)
  T-8 Hidden Markov Models, Part 2: Building HMMs (UCSC group)

3:20pm - 3:40pm: Coffee break

6:00pm - 8:00pm: Mixer
7:45pm - 8:00pm: Opening remarks
        David States
8:00pm - 9:00pm: Keynote
        Chris Sander, EMBL-EBI (not final)


                Thursday, June 13, 1996

8:00am - 9:00am : Continental breakfast
9:00am - 10:40am: Talks 1

  1. "Improving the Quality of Automatic DNA Sequence Assembly Using
     Fluorescent Trace-Data Classifications". Carolyn F. Allex, Schuyler F.
     Baldwin, Jude W. Shavlik, and Frederick R. Blattner.

  2. "The Megaprior Heuristic for Discovering Protein Sequence Patterns".
     Timothy L. Bailey and Michael Gribskov.

  3. "From Electron Density and Sequence to Structure: Integrating Protein
     Image Analysis and Threading for Structure Determination". Kim Baxter,
     Evan Steeg, Richard Lathrop, Janice Glasgow, and Suzanne Fortier.

  4. "Discovering Patterns and Subfamilies in Biosequences". Alvis Brazma,
     Inge Jonassen, Esko Ukkonen, and Jaak Vilo.

10:40am - 11:10am: Coffee break

11:10am - 12:30pm: Talks 2

  5. "A Sequence Similarity Search Algorithm Based on a Probabilistic
     Interpretation of an Alignment Scoring System". Philipp Bucher and Kay

  6. "The Mathematical Model of Subtractive Hybridization and its Practical
     Application". Olga D. Ermolaeva, Sergy A. Lukyanov and Eugene D.

  7. "Using Iterative Dynamic Programming to Obtain Accurate Pairwise and
     Multiple Alignments of Protein Structures". Mark Gerstein and Michael

12:30pm - 1:30pm: Lunch

1:30pm - 2:30pm: Contributed Posters

2:30pm - 3:20pm: Demos 1

D 1. "Java Genome Browser"
     Gregg Helt

D 2. "A Top-Down Approach to Whole Genome Visualization".
     Klaus Heumann, C. Harris, and H.W. Mewes.
     (proceedings paper)

3:20pm - 3:45pm: Coffee break

3:45pm - 5:00pm: Talks 3

  8. "A Generalized Hidden Markov Model for the Recognition of Human Genes
     in DNA". David Kulp, David Haussler, Martin G. Reese, and Frank H.

  9. "Good Maps are Straight". Eric Harley, Anthony J. Bonner, and Nathan

 10. "A Probabilistic Classification System for Predicting the Cellular
     Localization Sites of Proteins". Paul Horton and Kenta Nakai.

5:00pm - 8:00pm: Free time

8:00pm - 9:00pm: Keynote
        David Haussler, U. of California, Santa Cruz  (not final)
        Using Hidden Markov Models for Biosequence Analysis


                   Friday, June 14, 1996

8:00am - 9:00am: Continental breakfast
9:00am - 10:15am: Talks 4

 11. "HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways
     of H. influenzae". Peter D. Karp, Christos Ouzounis, and Suzanne Paley.

 12. "Inferring Relatedness of a Macromolecule to a Sequence Database
     Without Sequencing". Jin Kim, James R. Cole, Eric Torng, and Sakti

 13. "Compact Encoding Strategies for DNA Sequence Similarity Search".
     David J. States and Pankaj Agarwal.

10:15am - 10:45am: Coffee break

10:45am - 12:15pm: Talks 5

 14. "A Grammar-Based Unification of Several Alignment and Folding
     Algorithms". Fabrice Lefebvre.

 15. "Applications of GeneMark in Multispecies Environments". James D.
     McIninch, William S. Hayes and Mark Borodovsky.

 16. "Genome-Scale DNA Sequence Recognition by Hybridization to Short
     Oligomers". Aleksandar Milosavljevic, Suzana Savkovic, Radomir
     Crkvenjakov, David Salbego, Hope Serrato, Heidi Kreuzer, Anne Gemmell,
     Shawna Batus, Danica Grujic, Susan Carnahan, and Jovanka Tepavcevic.

12:15pm - 1:30pm: Lunch

1:30pm - 2:30pm: Posters

P 1. "Parameterization Studies for the SAM and HMMER Methods of Hidden Markov
     Model Generation".  Marcella A. McClure, Chris Smith, and Pete Elton.
     (proceedings paper, poster presentation by special request)

plus other contributed posters

2:30pm - 3:20pm: Demos 2

D 3. "Heterogeneous Information Sources for Cytokine Research",
     Gary K. Allen

D 4. "ParaMEME: Discovering Protein Sequence Patterns"
     William Grundy

3:20pm - 3:45pm: Coffee break

3:45pm - 5:00pm: Talks 6

 17. "Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden
     Markov Models". Anders Gorm Pedersen, Pierre Baldi, Soren Brunak, and
     Yves Chauvin.

 18. "Refining Neural Network Predictions for Helical Transmembrane Proteins
     by Dynamic Programming". Burkhard Rost, Rita Casadio, and Piero

 19. "Finding Genes in DNA Using Decision Trees and Dynamic Programming".
     Steven Salzberg, Xin Chen, John Henderson, and Kenneth Fasman.

5:00pm - 8:00pm: Free time

8:00pm - 9:00pm: Keynote
        Russell Doolitle, U. of California, San Diego (not final)


                    Saturday, June 15, 1996

8:00am - 9:00am: Continental breakfast
9:00am - 10:00am: Keynote
        Robert Waterston, Washington University (not final)

10:00am - 10:50pm: Talks 7

 20. "Ontological Foundations for Biology Knowledge Models". Carole D.
     Hafner and Natalya Fridman.

 21. "A Knowledge-Based Method for Protein Structure Refinement and
     Prediction". Shankar Subramaniam, David K. Tcheng and James M. Fenton.

10:50am - 11:10am: Coffee break

11:10am - 12:00pm: Demos 3

D 5. "Biocatalysis/Biodegradation Database"
     Lynda Ellis, Lawrence Wackett

D 6. "Genemark: Identification of Unnoticed Genes in Prokaryotes"
     William Hayes, James McIninch, Mark Borodovsky

12:00pm - 1:30pm: Lunch

1:30pm - 2:45pm: Demos 4

D 7. "GeneFisher - Software Support for the Detection of Postulated Genes".
     Robert Giegerich, Folker Meyer, and Chris Schleiermacher.
     (proceedings paper)

D 8. "MOOSE and WPDB: search engine and browser for the PDB"
     Ilya Shindyalov

D 9. "WWW-based Virtual Computing and Analysis Environment for Sequence"
     Shankar Subramaniam and Kurt Jamison

2:45pm - 3:15pm: Coffee break

3:15pm - 4:30pm: Talks 9

 22. "Discovering Empirically Conserved Amino Acid Substitution Groups in
     Databases of Protein Families". Thomas D. Wu and Douglas L. Brutlag.

 23. "Gene Recognition in Cyanobacterium Genomic Sequence Data Using the
     Hidden Markov Model". Tetsushi Yada and Makoto Hirosawa.

 24. "Gene Prediction by Pattern Recognition and Homology Search". Ying Xu
     and Edward C. Uberbacher.

6:00pm - 7:00pm: Cocktails
7:00pm - 9:00pm: Banquet
Pankaj Agarwal			
ISMB'96 Organizing Committee

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