| Thursday, June 3 2004 | ||
| 12:00 - 13:00 | Registration | |
| 13:00 | Conference Opening | |
| Keynote (chair: Arne Elofsson) | ||
| 13:15 - 14:00 | Thomas Lengauer | Max Planck Institute |
| Analyzing HIV resistance phenomena with bioinformatics methods | ||
| Session: RNA (chair: Vincent Moulton) | ||
| 14:15 - 15:00 | Paul Higgs | McMaster University |
| RNA-based Phylogenetic Methods - Applications to Proteobacteria and to Animal Mitochondrial Genomes | ||
| 15:00 - 15:45 | Todd Lowe | University of California |
| Delving into Mammalian Genomes for non-coding RNAs | ||
| 15:45 - 16:15 | Coffee | |
| 16:15 - 17:00 | Peter Stadler | University of Leipzig |
| RNA in silico: The Computational Biology of RNA Secondary Structures | ||
| 17:00 - 17:45 | Michael Zuker | Rensselaer Polytechnic Institute |
| Predicting nucleic acid hybridization and melting profile | ||
| 18:00 | Welcome buffet | |
| Friday, June 4 2004 | ||
| Session: Databases and ontologies (chair: Patrick Lambrix) | ||
| 08:30 - 09:15 | Susan Davidson | University of Pennsylvania |
| Datalogical Biobases: an Oxymoron | ||
| 09:15 - 10:00 | Midori Harris | European Bioinformatics Institute |
| Ontologies for Biology: the Gene Ontology and OBO | ||
| 10:00 - 10:30 | Coffee | |
| 10:30 - 11:15 | Lynette Hirschman | MITRE |
| Naming, Describing, Classifying: Ontologies for Biological Databases | ||
| 11:15 - 12:00 | Robert Stevens | University of Manchester |
| Sequence Similarity Searching; Annotation Similarity Searching | ||
| 12:00 - 13:00 | Lunch | |
| Session: Posters I and companies | ||
| 13:00 - 14:00 | Posters (odd numbers) | |
| 13:30 - 14:00 | NBN meeting | |
| 14:00 - 15:00 | Company presentations | |
| 14:00 - 14:20 | Johan Gunnarsson | InNetics AB |
| PathwayLab - The Tool for Pathways and Simulation of Biochemical Reaction Networks | ||
| Excursion to Vadstena | ||
| 15:15 | Departure to Vadstena | |
| 16:15 | Individual sightseeing in the idyllic town Vadstena | |
| 18:15 | Banquet in Vadstena | |
| Saturday, June 5 2004 | ||
| Session: Systems Biology (chair: Jesper Tegnér) | ||
| 08:30 - 09:15 | John Quackenbush | The Institute for Genomic Research |
| From Expression to Biology | ||
| 09:15 - 10:00 | Nick Luscombe | Yale University |
| Transcription regulation: a genomic network | ||
| 10:00 - 10:30 | Coffee | |
| 10:30 - 11:15 | Avi Mayo | Weizmann Institute of Science |
| Design-principles of transcription networks, genetic gates and metabolic pathways | ||
| 11:15 - 12:00 | Jeff Hasty | University of California |
| Engineered Gene Circuits A Reductionist Approach to Systems Biology | ||
| 12:00 - 12:45 | John Jeremy Rice | IBM T. J. Watson Research Center |
| Analyzing and reconstructing gene regulatory networks | ||
| 12:45 - 13:45 | Lunch | |
| Session: Evolution of protein structure (chair: David Liberles) | ||
| 13:45 - 14:30 | Brian Golding | McMaster University |
| The relationships between three dimensional structure of proteins and the frequency and type of substitutions | ||
| 14:30 - 15:15 | Arthur Lesk | Penn State University |
| Evolution of the Globin Family | ||
| 15:15 - 15:45 | Coffee | |
| 15:45 - 16:30 | David Pollock | Louisiana State |
| Protein structure and evolution: context-dependence, modeling, and evolutionary inference | ||
| 16:30 - 17:15 | Boris Shakhnovich | Boston University |
| A graph theoretical treatment of Protein Evolution: Fitness characteristics and Natural Selection | ||
| Session: Posters II | ||
| 17:15 - 18:15 | Posters (even numbers) | |
| 18:15 - 19:15 | Oral poster presentations (chair: Arne Elofsson) | |
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Oriel Bergig, Danny Barash, Klara Kedem Searching for RNA motifs using computational geometry methods |
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Rodrigo Gouveia Oliveira, Anders Gorm Pedersen Extracting the phylogenetic signal from mutual information estimates |
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Gudmundur A. Thorisson, Lalitha Krishnan, Albert V. Smith, Lincoln D. Stein The International HapMap Project Data Coordination Center |
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Bairong Shen, Mauno Vihinen Structure and sequence based analysis of protein mutation |
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Dag Ahren, Christos Ouzounis Robustness of metabolic map reconstruction |
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| 19:15 - 19:45 | SocBiN meeting | |
| 20:00 | Dinner at Linköping Konsert & Kongress | |
| Sunday, June 6 2004 | ||
| Session: Comparative prokaryotic genomics (chair: David Ussery) | ||
| 08:30 - 09:15 | John Helmann | Cornell University |
| Predicting Function from Conserved Sequence Motifs: Networks of Gene Regulation in Bacillus subtilis | ||
| 09:15 - 10:00 | James McInerney | National University of Ireland Maynooth |
| The prokaryotic phylogeny: the curate's egg of the phylogeny world? | ||
| 10:00 - 10:30 | Coffee | |
| 10:30 - 11:15 | Dawn Field | Oxford University |
| <To be announced> | ||
| 11:15 - 12:00 | Nick Thomson | The Wellcome Trust Sanger Institute |
| Insights into the genome evolution of Human, Animal and Plant bacterial pathogens from comparative genomics | ||
| 12:00 | Concluding remarks | |