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Frontiers in Bioinformatics: Unsolved Problems and Challenges

Organized by Samuel Karlin, David Eisenberg and Russ Altman

October 15-17, 2004
Irvine, CA

Meeting Overview:
The Sackler Colloquium Frontiers of Bioinformatics held October 16 and 17, 2004, provided a forum for discussing concepts and methods emerging in bioinformatics concomitant with recent advances in theory and experiment across the biological and medical sciences. The deluge of genome data in the last two decades has driven the emergence of bioinformatics as an important discipline. The first wave of genome sequence data created a demand for tools for search, comparison, and analysis of nucleic acid protein sequences and macromolecular structures. The second wave of expression data has similarly created a demand for tools that allowed the data to be understood and reduced. Future waves promise to bring innovations in proteomics research, including protein structure, interactions, compartmentalization, and turnover. In addition, experimental biologists are likely to create other new technologies that will further enable high throughput collection of useful biological data. These sources of cellular data will also be correlated with higher levels of phenotypic data, based on observations of the nature of cells, organs and organisms.

Our understanding of basic biology will be facilitated through the comparison of organisms at different evolutionary distances, in order to reconstruct both the tree of life and the emergence of important phenotypic traits. Also, there is a growing expectation that bioinformatics will help fuel the creation of computational models (both qualitative and quantitative) which will allow us to capture, store and maintain biological models that help explain experimental observations.

Algorithms in bioinformatics cover research in all aspects of computational biology. The emphasis is on discrete algorithms that address important problems in molecular biology, genomics, and proteomics, that are computationally efficient, that have been implemented and tested in simulations and on real datasets, and that provide new biological results and insights. Exact and approximate algorithms pertain to genomics, sequence analysis, gene and signal recognition, alignment, molecular evolution, phylogenetics, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design. In particular, bioinformatics tools include the BLAST program (homology searching), GENSCAN, GENIE (gene-finding), SAPS (statistical analysis of protein sequences), CLUSTAL, ITERALIGN, (multiple sequence alignment), r-SCAN STATISTICS (target array clustering, overdispersion), etc. These programs, are used by thousands of researchers every day in molecular biology and medicine. The BLAST protocol currently serves more than 100 000 queries per day at the National Center for Biotechnology Information (NCBI) in Washington, DC.

Opening Remarks
Samuel Karlin, Stanford University

Session I: Informatics of the Human Genome
Samuel Karlin, Stanford University, Chair

Biological and Clinical Challenges for Bioinformatics
George Miklos, Human Genetic Signatures

Human Genome Annotation
Mark Gerstein, Yale University

Using Evolution to Explore the Human Genome
David Haussler, University of California at Santa Cruz

Transforming Men into Mice (and into Cats, Dogs, Cows, Rats, Chimpanzees, etc.): Evolutionary Lessons from Mammalian Sequencing and Comparative Mapping Projects
Pavel Pevzner, University of California at San Diego

Session II: Motifs and Genomics
Russ Altman, Stanford University, Chair

Genome Evolution and Protein Networks
Peer Bork, European Molecular Biology Laboratory, Heidelberg

Signal and Noise in Genome Sequences
Phil Green, University of Washington

Session III: Protein-Protein Interactions
Valerie Daggett, University of Washington, Chair

Protein Interactions
David Eisenberg, University of California at Los Angeles

From Cellular Networks to Molecular Interactions and Back
Hanah Margalit, Hebrew University

Prediction of Protein-Protein Interactions: Evolution Rescues Energetics
Shoshana Wodak, Free University of Brussels

After Dinner Speaker
Introduced by David Eisenberg, University of California at Los Angeles

Regarding Irreducible Complexities
Russ Doolittle, University of California at San Diego

Session IV: Regulation with RNA and Aspects of Splicing
David Eisenberg, University of California at Los Angeles, Chair

The Modern RNA World: Computational Screens for Noncoding RNA Genes
Sean Eddy, Washington University of St. Louis

Toward an RNA Splicing Code
Chris Burge, Massachusetts Institute of Technology

RNA Splicing as an Evolutionary Strategy
Chris Lee, University of California at Los Angeles

Session V: Protein Structure
Valerie Daggett, University of Washington, Chair

Probing the PDB
Helen Berman, Rutgers University

Structural Alignment and Classification of all Known Protein Structure
Michael Levitt, Stanford University

Session VI: Transcriiption and Translation of Eukaryotic Genomes
George Mikolos, Human Genetic Signatures, Chair

Comparative Plant Genomics: Evaluation of the Model Genome Concept
Volker Brendel, Iowa State

Lessons from the Arabidopsis Genome: Decoding Evidence for Novel Transcription
Terry Gaasterland, Rockefeller University

Building Genotype Phenotype Data Resources
Russ Altman, Stanford University

Protein Expression Analysis Based on Codon Usage and 2D Gels with Emphasis on Archaeal and Eukaryotics Genomes
Samuel Karlin, Stanford University

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