| 2006 | Obtaining Provably Good Performance from Suffix Trees in Secondary Storage. | Pang Ko, Srinivas Aluru |
| 2006 | A Compact Mathematical Programming Formulation for DNA Motif Finding. | Carl Kingsford, Elena Zaslavsky, Mona Singh |
| 2006 | A Simpler Analysis of Burrows-Wheeler Based Compression. | Haim Kaplan, Shir Landau, Elad Verbin |
| 2006 | Algorithms for Finding a Most Similar Subforest. | Jesper Jansson, Zeshan Peng |
| 2006 | On-Line Linear-Time Construction of Word Suffix Trees. | Shunsuke Inenaga, Masayuki Takeda |
| 2006 | SNP and Haplotype Analysis - Algorithms and Applications. | Eran Halperin |
| 2006 | Solving the Maximum Agreement SubTree and the Maximum Compatible Tree Problems on Many Bounded Degree Trees. | Sylvain Guillemot, Franois Nicolas |
| 2006 | Statistical Encoding of Succinct Data Structures. | Rodrigo Gonzlez, Gonzalo Navarro |
| 2006 | Theoretical and Practical Improvements on the RMQ-Problem, with Applications to LCA and LCE. | Johannes Fischer, Volker Heun |
| 2006 | Finding Common RNA Pseudoknot Structures in Polynomial Time. | Patricia A. Evans |
| 2006 | Efficient Algorithms for Regular Expression Constrained Sequence Alignment. | Yun Sheng Chung, Chin Lung Lu, Chuan Yi Tang |
| 2006 | A Linear Size Index for Approximate Pattern Matching. | Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong |
| 2006 | Faster Algorithms for Computing Longest Common Increasing Subsequences. | Gerth Stlting Brodal, Kanela Kaligosi, Irit Katriel, Martin Kutz |
| 2006 | New Bounds for Motif Finding in Strong Instances. | Brona Brejov, Daniel G. Brown, Ian M. Harrower, Toms Vinar |
| 2006 | Fingerprint Clustering with Bounded Number of Missing Values. | Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri |
| 2006 | Tiling an Interval of the Discrete Line. | Olivier Bodini, Eric Rivals |
| 2006 | Common Substrings in Random Strings. | Eric Blais, Mathieu Blanchette |
| 2006 | An Improved Algorithm for the Macro-evolutionary Phylogeny Problem. | Behshad Behzadi, Martin Vingron |
| 2006 | Adaptive Searching in Succinctly Encoded Binary Relations and Tree-Structured Documents. | Jrmy Barbay, Alexander Golynski, J. Ian Munro, S. Srinivasa Rao |
| 2006 | Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. | Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann |
| 2006 | Reducing the Space Requirement of LZ-Index. | Diego Arroyuelo, Gonzalo Navarro, Kunihiko Sadakane |
| 2006 | Approximate Matching in Weighted Sequences. | Amihood Amir, Costas S. Iliopoulos, Oren Kapah, Ely Porat |
| 2006 | Property Matching and Weighted Matching. | Amihood Amir, Eran Chencinski, Costas S. Iliopoulos, Tsvi Kopelowitz, Hui Zhang |
| 2006 | Faster Two Dimensional Scaled Matching. | Amihood Amir, Eran Chencinski |
| 2006 | Asynchronous Pattern Matching. | Amihood Amir |