3. WABI 2003: Budapest, Hungary
Gary Benson, Roderic D. M. Page (Eds.): Algorithms in Bioinformatics, Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003, Proceedings. Springer 2003 Lecture Notes in Computer Science ISBN 3-540-20076-2
Comparative Genomics
- Mohamed Ibrahim Abouelhoda, Enno Ohlebusch: A Local Chaining Algorithm and Its Applications in Comparative Genomics. 1-16
- Gilles Didier: Common Intervals of Two Sequences. 17-24
Database Searching
- Jacques Colinge, Alexandre Masselot, Jérôme Magnin: A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring. 25-38
- Brona Brejová, Daniel G. Brown, Tomás Vinar: Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. 39-54
Gene Finding and Expression
- Boris Hollas, Rainer Schuler: A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods. 55-62
- Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi: A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence. 63-77
- Brona Brejová, Daniel G. Brown, Tomás Vinar: Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. 78-94
Genome Mapping
- Mark Cieliebak, Stephan Eidenbenz, Paolo Penna: Noisy Data Make the Partial Digest Problem NP-hard. 111-123
Pattern and Motif Discovery
- Alban Mancheron, Irena Rusu: Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions. 124-138
- Revital Eres, Gad M. Landau, Laxmi Parida: A Combinatorial Approach to Automatic Discovery of Cluster-Patterns. 139-150
- Sven Rahmann: Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology. 151-164
Phylogenetic Analysis
- Barbara Holland, Vincent Moulton: Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees. 165-176
- Paul E. Kearney, J. Ian Munro, Derek Phillips: Efficient Generation of Uniform Samples from Phylogenetic Trees. 177-189
- Alix Boc, Vladimir Makarenkov: New Efficient Algorithm for Detection of Horizontal Gene Transfer Events. 190-201
- Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham: Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. 202-215
- Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Jotun Hein: Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. 228-244
- Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy Warnow: Better Hill-Climbing Searches for Parsimony. 245-258
- Gerth Stølting Brodal, Rolf Fagerberg, Anna Östlin, Christian N. S. Pedersen, S. Srinivasa Rao: Computing Refined Buneman Trees in Cubic Time. 259-270
- David Bryant, Daniel H. Huson, Tobias H. Klöpper, Kay Nieselt-Struwe: Distance Corrections on Recombinant Sequences. 271-286
- Yun S. Song, Jotun Hein: Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. 287-302
Polymorphism
- Gad Kimmel, Roded Sharan, Ron Shamir: Identifying Blocks and Sub-populations in Noisy SNP Data. 303-319
- Yonatan Aumann, Efrat Manisterski, Zohar Yakhini: Designing Optimally Multiplexed SNP Genotyping Assays. 320-338
- Koichiro Doi, Jing Li, Tao Jiang: Minimum Recombiant Haplotype Configuration on Tree Pedigrees. 339-353
Protein Structure
- Itay Lotan, Fabian Schwarzer, Jean-Claude Latombe: Efficient Energy Computation for Monte Carlo Simulation of Proteins. 354-373
- Jinbo Xu: Speedup LP Approach to Protein Threading via Graph Reduction. 374-388
- Jahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda: Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. 389-401
- Jan A. Spriet: Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power. 402-416
Sequence Alignment
- Jakob Fredslund, Jotun Hein, Tejs Scharling: A Large Version of the Small Parsimony Problem. 417-432
- Bjarne Knudsen: Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree. 433-446
- Gary Benson: Composition Alignment. 447-461
String Algorithms
- Sebastian Böcker: Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt. 476-497
- Dekel Tsur: Bounds for Resquencing by Hybridization. 498-511
- Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang: Selecting Degenerate Multiplex PCR Primers. 512-526
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