Algorithms in Bioinformatics

We are very pleased to present the proceedings of the First Workshop on Bio- formatics (WABI 2001), which took place in Aarhus on August 28{31, 2001, under the auspices of the European Association for Theoretical Computer S- ence (EATCS) and the Danish Center for Basic Research in Computer Science (BRICS). TheWorkshop onAlgorithmsinBioinformatics coversresearch onallaspects of algorithmic work in bioinformatics. The emphasis is on discrete algorithms that address important problems in molecular biology. These are founded on sound models, are computationally e cient, and have been implemented and tested in simulationsand on real datasets. The goal is to present recent research results, including signi cant work-in-progress, and to identify and explore dir- tions of future research. Speci c topics of interest include, but are not limited to: { Exactandapproximatealgorithmsforgenomics,sequence analysis,gene and signal recognition, alignment, molecular evolution, structure determination or prediction, gene expression and gene networks, proteomics, functional genomics, and drug design. { Methods, software and dataset repositories for development and testing of such algorithms and their underlying models. { High-performance approaches to computationallyhardproblems inbioinf- matics, particularly optimization problems.

Includes supplementary material: sn.pub/extras

Inhalt
An Improved Model for Statistical Alignment.- Improving Profile-Profile Alignments via Log Average Scoring.- False Positives in Genomic Map Assembly and Sequence Validation.- Boosting EM for Radiation Hybrid and Genetic Mapping.- Placing Probes along the Genome Using Pairwise Distance Data.- Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar.- Assessing the Statistical Significance of Overrepresented Oligonucleotides.- Pattern Matching and Pattern Discovery Algorithms for Protein Topologies.- Computing Linking Numbers of a Filtration.- Side Chain-Positioning as an Integer Programming Problem.- A Chemical-Distance-Based Test for Positive Darwinian Selection.- Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time.- Experiments in Computing Sequences of Reversals.- Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes.- Finding an Optimal Inversion Median: Experimental Results.- Analytic Solutions for Three-Taxon MLMC Trees with Variable Rates Across Sites.- The Performance of Phylogenetic Methods on Trees of Bounded Diameter.- (1+?)-Approximation of Sorting by Reversals and Transpositions.- On the Practical Solution of the Reversal Median Problem.- Algorithms for Finding Gene Clusters.- Determination of Binding Amino Acids Based on Random Peptide Array Screening Data.- A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites.- Comparing Assemblies Using Fragments and Mate-Pairs.