| 2006 | A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks. Lukas Burger, Erik van Nimwegen |
| 2006 | A Fuzzy Dynamic Programming Approach to Predict RNA Secondary Structure. Dandan Song, Zhidong Deng |
| 2006 | A Linear-Time Algorithm for Studying Genetic Variation. Nikola Stojanovic, Piotr Berman |
| 2006 | A Method to Design Standard HMMs with Desired Length Distribution for Biological Sequence Analysis. Hongmei Zhu, Jiaxin Wang, Zehong Yang, Yixu Song |
| 2006 | A Unifying View of Genome Rearrangements. Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2006 | Accelerating Motif Discovery: Motif Matching on Parallel Hardware. Geir Kjetil Sandve, Magnar Nedland, Øyvind Bø Syrstad, Lars Andreas Eidsheim, Osman Abul, Finn Drabløs |
| 2006 | Accelerating the Computation of Elementary Modes Using Pattern Trees. Marco Terzer, Jörg Stelling |
| 2006 | Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings Philipp Bucher, Bernard M. E. Moret |
| 2006 | Alignment with Non-overlapping Inversions in Augusto F. Vellozo, Carlos E. R. Alves, Alair Pereira do Lago |
| 2006 | Approximation Algorithms for Bi-clustering Problems. Lusheng Wang, Yu Lin, Xiaowen Liu |
| 2006 | Beaches of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems. Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie |
| 2006 | Combinatorial Methods for Disease Association Search and Susceptibility Prediction. Dumitru Brinza, Alexander Zelikovsky |
| 2006 | Controlling Size When Aligning Multiple Genomic Sequences with Duplications. Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller |
| 2006 | Decomposing Metabolomic Isotope Patterns. Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin |
| 2006 | Efficient Model-Based Clustering for LC-MS Data. Marta Luksza, Boguslaw Kluge, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin |
| 2006 | Efficient Sampling of Transpositions and Inverted Transpositions for Bayesian MCMC. István Miklós, Timothy Brooks Paige, Péter Ligeti |
| 2006 | Flux-Based Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter |
| 2006 | Gapped Permutation Patterns for Comparative Genomics. Laxmi Parida |
| 2006 | How Many Transcripts Does It Take to Reconstruct the Splice Graph? Paul A. Jenkins, Rune B. Lyngsø, Jotun Hein |
| 2006 | Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning. Sérgio A. de Carvalho, Sven Rahmann |
| 2006 | Imputing Supertrees and Supernetworks from Quartets. Barbara R. Holland, Glenn Conner, Katharina T. Huber, Vincent Moulton |
| 2006 | Integer Linear Programs for Discovering Approximate Gene Clusters. Sven Rahmann, Gunnar W. Klau |
| 2006 | Landscape Analysis for Protein-Folding Simulation in the H-P Model. Kathleen Steinhöfel, Alexandros Skaliotis, Andreas Alexander Albrecht |
| 2006 | Linear-Time Haplotype Inference on Pedigrees Without Recombinations. Bethany Man-Yee Chan, Joseph Wun-Tat Chan, Francis Y. L. Chin, Stanley P. Y. Fung, Ming-Yang Kao |
| 2006 | Measures of Codon Bias in Yeast, the tRNA Pairing Index and Possible DNA Repair Mechanisms. Markus T. Friberg, Pedro Gonnet, Yves Barral, Nicol N. Schraudolph, Gaston H. Gonnet |
| 2006 | Multiple Structure Alignment and Consensus Identification for Proteins. Jieping Ye, Ivaylo Ilinkin, Ravi Janardan, Adam Isom |
| 2006 | New Constructive Heuristics for DNA Sequencing by Hybridization. Christian Blum, Mateu Yábar Vallès |
| 2006 | On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model. Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau |
| 2006 | On the Complexity of the Crossing Contact Map Pattern Matching Problem. Shuai Cheng Li, Ming Li |
| 2006 | Optimal Probing Patterns for Sequencing by Hybridization. Dekel Tsur |
| 2006 | Phylogenetic Network Inferences Through Efficient Haplotyping. Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai |
| 2006 | Procrastination Leads to Efficient Filtration for Local Multiple Alignment. Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna |
| 2006 | Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction. Eun-Jong Hong, Tomás Lozano-Pérez |
| 2006 | Rapid Jizhen Zhao, Russell L. Malmberg, Liming Cai |
| 2006 | Reducing Distortion in Phylogenetic Networks. Daniel H. Huson, Mike A. Steel, Jim Whitfield |
| 2006 | Segmentation with an Isochore Distribution. Miklós Csürös, Ming-Te Cheng, Andreas Grimm, Amine Halawani, Perrine Landreau |
| 2006 | Segmenting Motifs in Protein-Protein Interface Surfaces. Jeff M. Phillips, Johannes Rudolph, Pankaj K. Agarwal |