Dagstuhl-Seminar 9528
Molecular Bioinformatics
( 10. Jul – 14. Jul, 1995 )
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Organisatoren
- C. Sander
- D. Gustfield
- T. Lengauer
Kontakt
The seminar was a sequel to the first Dagstuhl Seminar on Molecular Bioinformatics which took place from Sep 7 to Sep 11, 1992 and brought together computer scientists and applied mathematicians with biochemists and molecular biologists in order to discuss possibilities of cooperation in the field of computer-aided design of biomolecular sequences and structures. Since that time, several developments have taken place in Germany and internationally. In Germany, BMBF (the Science Ministry) has funded a program on Molecular Bioinformatics. Within this program, eight large interdisciplinary projects are working on topics such as protein structure prediction, biomolecular docking, genomic databases, and RNA secondary and tertiary structure prediction. Internationally, efforts in computer science applications in molecular biology have increased significantly. Countries such as U. S. and Japan witness lively activity in these fields, albeit somewhat more concentrated on the genome itself than on genomic products such as proteins. Interaction between computer scientists and molecular biologists is intensifying, and a growing number of results are obtained with involvement of computer scientists. The topic of the seminar included research on both the genome and its products, with somewhat of a emphasis on genomic products and on the relationship between those two kinds of research than on the genome itself. As the previous seminar, this seminar concentrated on algorithmic issues and touch issues such as data handling technology, computer graphics etc. only insofar as they relate to algorithmic issues. In addition to the presentations, there was an evening tutorial on protein structures, a round of discussion on traditional and network-based teaching forms for bioinformatics, and a software demonstration. The general feelings of the participants were that after the ground-breaking character of the first seminar, this seminar was marked by an increased understanding and depth of communication between the CS and the molecular biology side. It was clearly evident that the two communities came to understand each other and began to develop a common feeling of identity.
The facilities and procedures at Dagstuhl as well as the unique concept of the Dagstuhl seminars were praised by many participants. The participants expressed the hope that this seminar be succeeded with another seminar on bioinformatics in due time. While a few of the participants expressed the wish to have future workshops more strongly focussed, say, just on alignment of sequences and structures, the majority of the participants welcomed the broadness of the workshop and felt that this width of scope should be maintained of some more time.
Monday, July 10 | |
Tom Lengauer | Welcome |
Morning Session | Chair: Tom Lengauer |
John Kececioglu | Genome Rearrangements |
Gene Myers | Developments in DNA Sequencing |
Dan Gusfield | Parametric Alignment |
Afternoon Session | Chair: Dan Gusfield |
Ralf Zimmer | Parametric Alignment |
Kevin Karplus | Using Simple Markov Models |
Tandy Warnow | Reconsidering the Construction of Evolutionary Trees |
Steve Altschul | Aspects of the Statistics of Local Sequence Comparison |
Andreas Dress | Visualization Procedures Related to Abstract Similarity Analysis, Quasi-Crystals and the Traveling Salesman Problem, Part I: Pictures |
Evening Session | Chair: Chris Sander |
Chris Sander | Tutorial on Protein Structures |
Tuesday, July 11 | |
Morning Session | Chair: Steve Bryant |
Andreas Dress | Visualization Procedures Related to Abstract Similarity Analysis, Quasi-Crystals and the Traveling Salesman Problem, Part II: Proofs |
Volker Brendel | Application of Scoring in Sequence Comparison for Evolutionary Studies and Motif Recognition |
Dalit Naor | Amino-Acid Pair Interchanges at Spatially Conserved Locations |
Joachim Selbig | Clustering of Protein Structures on the Basis of Hexapeptides |
Georg Casari | Specific Functional Regions in Protein Families |
Afternoon Session | Chair: Chris Sander |
Russ Altman | Probabilistic Representations and Algorithms for Analysis of Structure |
Liisa Holm | Protein Structure Database Searches |
Steve Bryant | Finding the Most Surprising Structural Similarities |
Ralf Thiele | Threading by Recursive Dynamic Programming |
Steve Bryant | An Alignment Model and Fast Algorithms for Protein Threading |
Evening Session | Chair: Robert Giegerich |
Giegerich, Shamir | Teaching Computational Biology |
Altman, Karplus | - |
Vingron, Myers | - |
Wednesday, July 12 | |
Morning Session | Chair: John Kececioglu |
Mike Steel | Generating New Phylogenetic Information from a Collection of Trees |
Ron Shamir | Physical Maps and Interval Graphs |
Michael Gribskov | An Evolutionary Mixture Model for Describing Protein Sequence Families |
Ina Koch | An Algorithm for Finding All Maximal Common Substructures and Its Application to Protein Structures |
Thursday, July 13 | |
Morning Session | Chair: Martin Vingron |
Norbert Blum | On the Prediction of RNA Secondary Structure |
Russ Altman | Constraint Satisfaction Methods for Modeling the Complete 30S Ribosomal Subunit and its Interaction with Transfer DNA |
Robert Giegerich | Representing Large RNA Folding Landscapes |
Dannie Durand | Ultraselfish Genes in Mice | Hans-Peter Lenhof | Protein-Protein Docking |
Afternoon Session | Chair: Dalit Naor |
Matthias Rarey | Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins |
Thomas Seidl | A Database System for Protein Docking |
John Kececioglu | Multiple Sequence Alignment |
Gene Myers | Rapid Similarity Search |
Satoru Miyano | BONSAI Garden: Parallel Knowledge Discovery System for Sequences |
Matthias Rarey | Demonstration: Docking |
Friday, July 14 | |
Morning Session | Chair: Tandy Warnow |
Thure Etzold | Integration of Biological Flat File Databanks into an Object-Oriented Retrieval System |
Jürgen Kleffe | Loglinear Models for Splice Site Recognition |
Martin Vingron | Sequence Alignment and Phylogeny |
Dan Gusfield | How to Think About Repetitive Structures |
Tom Lengauer | Close and Goodbye |
- C. Sander
- D. Gustfield
- T. Lengauer