Front matter
1-10
An Improved Model for Statistical Alignment
István Miklós and Zoltán Toroczkai
11-26
Improving Profile-Profile Alignments via Log Average Scoring
Niklas von Ohsen and Ralf Zimmer
27-40
False Positives in Genomic Map Assembly and Sequence Validation
Thomas Anantharaman and Bud Mishra
41-51
Boosting EM for Radiation Hybrid and Genetic Mapping
Thomas Schiex, Patrick Chabrier, Martin Bouchez and Denis Milan
52-68
Placing Probes along the Genome Using Pairwise Distance Data
Will Casey, Bud Mishra and Mike Wigler
69-84
Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar
Arun Jagota, Rune B. Lyngsø and Christian N. S. Pedersen
85-97
Assessing the Statistical Significance of Overrepresented Oligonucleotides
Alain Denise, Mireille Régnier and Mathias Vandenbogaert
98-111
Pattern Matching and Pattern Discovery Algorithms for Protein Topologies
Juris Víksna and David Gilbert
112-127
Computing Linking Numbers of a Filtration
Herbert Edelsbrunner and Afra Zomorodian
128-141
Side Chain-Positioning as an Integer Programming Problem
Olivia Eriksson, Yishao Zhou and Arne Elofsson
142-155
A Chemical-Distance-Based Test for Positive Darwinian Selection
Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir and Dan Graur
156-163
Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time
Ganeshkumar Ganapathysaravanabavan and Tandy Warnow
164-174
Experiments in Computing Sequences of Reversals
Anne Bergeron and François Strasbourg
175-188
Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes
Li-San Wang
189-203
Finding an Optimal Inversion Median: Experimental Results
Adam C. Siepel and Bernard M. E. Moret
204-213
Analytic Solutions for Three-Taxon MLMC Trees with Variable Rates Across Sites
Benny Chor, Michael Hendy and David Penny
214-226
The Performance of Phylogenetic Methods on Trees of Bounded Diameter
Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun and Tandy Warnow
227-237
(1+ε)-Approximation of Sorting by Reversals and Transpositions
Niklas Eriksen
238-251
On the Practical Solution of the Reversal Median Problem
Alberto Caprara
252-263
Algorithms for Finding Gene Clusters
Steffen Heber and Jens Stoye
264-277
Determination of Binding Amino Acids Based on Random Peptide Array Screening Data
Peter J. van der Veen, L. F. A. Wessels, J. W. Slootstra, R. H. Meloen and M. J. T. Reinders, et al.
278-293
A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
Yoseph Barash, Gill Bejerano and Nir Friedman
294-306
Comparing Assemblies Using Fragments and Mate-Pairs
Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers and Knut Reinert, et al.
Back matter