List of accepted papers for WABI 2006

The program committee of WABI'06 received 100 submissions and was able to accept 36 of them, listed below in no particular order.

Christian Blum and Mateu Yábar Vallès. New constructive heuristics for DNA sequencing by hybridization

Laxmi Parida. Gapped Permutation Patterns for Comparative Genomics

Anne Bergeron, Julia Mixtacki and Jens Stoye. A unifying view of genome rearrangements

Daniel Huson, Mike Steel and Jim Whitfield. Reducing Distortion in Phylogenetic Networks

Barbara Holland, Glenn Conner, Katharina T. Huber and Vincent Moulton. Imputing supertrees and supernetworks from quartets

Mee Yee Chan, Wun-Tat Chan, Francis Chin, Stanley Fung and Ming-Yang Kao. Linear-Time Haplotype Inference on Pedigree without Recombinations

Geir Kjetil Sandve, Magnar Nedland, Oyvind Bo Syrstad, Lars Andreas Eidsheim, Osman Abul and Finn Drablos. Accelerating Motif Discovery: Motif Matching on Parallel Hardware

Jeff M. Phillips, Johannes Rudolph and Pankaj K. Agarwal. Segmenting Motifs in Protein-Protein Interface Surfaces

Marco Terzer and Joerg Stelling. Accelerating the Computation of Elementary Modes Using Pattern Trees

Eun-Jong Hong and Tomas Lozano-Perez. Protein Side-chain Placement through MAP Estimation and Problem-Size Reduction

Shuai Cheng Li and Ming Li. On the Complexity of the Crossing Contact Map Pattern Matching Problem

Lusheng Wang, Yu Lin and Xiaowen Liu. Approximation Algorithms for Bi-clustering Problems

Dandan Song and Zhidong Deng. A Fuzzy Dynamic Programming Approach to Predict RNA Secondary Structure

István Miklós, Timothy Brooks Paige and Péter Ligeti. Efficient Sampling of transpositions and inverted transpositions for Bayesian MCMC

Hongmei Zhu, Jiaxin Wang, Zehong Yang and Yixu Song. A Method to Design Standard HMMs with Desired Length Distribution for Biological Sequence Analysis

Marta Łuksza, Bogusław Kluge, Jerzy Ostrowski, Jakub Karczmarski and Anna Gambin. Efficient Model-Based Clustering for LC-MS Data

Kathleen Steinhöfel, Alexandros Skaliotis and Andreas A. Albrecht. Landscape Analysis for Protein Folding Simulation in the H-P Model

Jens Gramm, Tzvika Hartman, Till Neirhoff, Roded Sharan and Till Tantau. On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model

Jieping Ye, Ivaylo Ilinkin, Ravi Janardan and Adam Isom. Multiple structure alignment and consensus identification for proteins

Sebastian Böcker, Zsuzsanna Lipták and Anton Pervukhin. Decomposing metabolomic isotope patterns

Jizhen Zhao, Russell Malmberg and Liming Cai. Rapid ab initio RNA Folding Including Pseudoknots via Graph Tree Decomposition

Pedro Gonnet, Yves Barral, Nicol N. Schraudolph, Markus Friberg and Gaston H. Gonnet. Pairwise Codon Bias Suggests Context-Dependent DNA Repair in Saccharomyces cerevisiae

Dekel Tsur. Optimal Probing Patterns for Sequencing By Hybridization

Paul Jenkins, Rune Lyngsoe and Jotun Hein. How Many Transcripts does it Take to Reconstruct the Splice Graph?

Yinglei Song, Chunmei Liu, Russell Malmberg and Liming Cai. Phylogenetic Network Inferences through Efficient Haplotyping

Aaron Darling, Todd Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer and Nicole Perna. Procrastination leads to efficient filtration for local multiple alignment

Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin and Ron Pinter. Flux Based vs. Topology Based Similarity of Metabolic Genes

Miklos Csuros, Ming-Te Cheng, Andreas Grimm, Amine Halawani and Perrine Landreau. Segmentation with an isochore distribution

Lukas Burger and Erik van Nimwegen. A Bayesian algorithm for reconstructing bacterial signaling networks

Dumitru Brinza and Alexander Zelikovsky. Combinatorial Methods for Disease Association Search and Susceptibility Prediction

Leo van Iersel, Judith Keijsper, Steven Kelk and Leen Stougie. Beaches of islands of tractability: Algorithms for parsimony and minimum perfect phylogeny haplotyping problems

Nikola Stojanovic and Piotr Berman. A linear-time algorithm for studying genetic variation

Augusto Vellozo, Carlos Eduardo Alves and Alair do Lago. Alignment with non-overlapping inversions in cubic time

Minmei Hou, Piotr Berman, Louxin Zhang and Webb Miller. Controlling size when aligning multiple genomic sequences with duplications

Sven Rahmann and Gunnar Klau. Integer Linear Programs for Discovering Approximate Gene Clusters

Sven Rahmann and Sergio A. de Carvalho Jr.. Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning