| Comparative Genomics |
| A Local Chaining Algorithm and Its Applications in Comparative Genomics / M.I. Abouelhoda ; E. Ohlebusch |
| Common Intervals of Two Sequences / G. Didier |
| Database Searching |
| A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring / J. Colinge ; A. Masselot ; J. Magnin |
| Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity / B. Brejová ; D.G. Brown ; T. Vinař |
| Gene Finding and Expression |
| A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods / B. Hollas ; R. Schuler |
| A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence / P. Bonizzoni ; G. Pesole ; R. Rizzi |
| Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency |
| Genome Mapping |
| New Algorithm for the Simplified Partial Digest Problem / J. Błażewicz ; M. Jaroszewski |
| Noisy Data Make the Partial Digest Problem NP-hard / M. Cieliebak ; S. Eidenbenz ; P. Penna |
| Pattern and Motif Discovery |
| Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions / A. Mancheron ; I. Rusu |
| A Combinatorial Approach to Automatic Discovery of Cluster-Patterns / R. Eres ; G.M. Landau ; L. Parida |
| Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology / S. Rahmann |
| Phylogenetic Analysis |
| Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees / B. Holland ; V. Moulton |
| Efficient Generation of Uniform Samples from Phylogenetic Trees / P. Kearney ; J.I. Munro ; D. Phillips |
| New Efficient Algorithm for Detection of Horizontal Gene Transfer Events / A. Boc ; V. Makarenkov |
| Ancestral Maximum Likelihood of Evolutionary Trees Is Hard / L. Addario-Berry ; B. Chor ; M. Hallett ; J. Lagergren ; A. Panconesi ; T. Wareham |
| A Linear-Time Majority Tree Algorithm / N. Amenta ; F. Clarke ; K. St. John |
| Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model / G. Lunter ; I. Miklós ; A. Drummond ; J.L. Jensen ; J. Hein |
| Better Hill-Climbing Searches for Parsimony / G. Ganapathy ; V. Ramachandran ; T. Warnow |
| Computing Refined Buneman Trees in Cubic Time / G.S. Brodal ; R. Fagerberg ; A. Östlin ; C.N.S. Pedersen ; S.S. Rao |
| Distance Corrections on Recombinant Sequences / D. Bryant ; D. Huson ; T. Kloepper ; K. Nieselt-Struwe |
| Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks / Y.S. Song |
| Polymorphism |
| Identifying Blocks and Sub-populations in Noisy SNP Data / G. Kimmel ; R. Sharan ; R. Shamir |
| Designing Optimally Multiplexed SNP Genotyping Assays / Y. Aumann ; E. Manisterski ; Z. Yakhini |
| Minimum Recombinant Haplotype Configuration on Tree Pedigrees / K. Doi ; J. Li ; T. Jiang |
| Protein Structure |
| Efficient Energy Computation for Monte Carlo Simulation of Proteins / I. Lotan ; F. Schwarzer ; J.-C. Latombe |
| Speedup LP Approach to Protein Threading via Graph Reduction / J. Xu |
| Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment / J.C. Prasad ; M. Silberstein ; C.J. Camacho ; S. Vajda |
| Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power / J.A. Spriet |
| Sequence Alignment |
| A Large Version of the Small Parsimony Problem / J. Fredslund ; T. Scharling |
| Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree / B. Knudsen |
| Composition Alignment / G. Benson |
| String Algorithms |
| Match Chaining Algorithms for cDNA Mapping / T. Shibuya ; I. Kurochkin |
| Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt / S. Böcker |
| Bounds for Resequencing by Hybridization / D. Tsur |
| Selecting Degenerate Multiplex PCR Primers / R. Souvenir ; J. Buhler ; G. Stormo ; W. Zhang |
| Author Index |
| Comparative Genomics |
| A Local Chaining Algorithm and Its Applications in Comparative Genomics / M.I. Abouelhoda ; E. Ohlebusch |
| Common Intervals of Two Sequences / G. Didier |
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