| 2006 | A Compact Mathematical Programming Formulation for DNA Motif Finding. Carl Kingsford, Elena Zaslavsky, Mona Singh |
| 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 | A Simpler Analysis of Burrows-Wheeler Based Compression. Haim Kaplan, Shir Landau, Elad Verbin |
| 2006 | Adaptive Searching in Succinctly Encoded Binary Relations and Tree-Structured Documents. Jérémy Barbay, Alexander Golynski, J. Ian Munro, S. Srinivasa Rao |
| 2006 | Algorithms for Finding a Most Similar Subforest. Jesper Jansson, Zeshan Peng |
| 2006 | An Improved Algorithm for the Macro-evolutionary Phylogeny Problem. Behshad Behzadi, Martin Vingron |
| 2006 | An O(n Michal Ozery-Flato, Ron Shamir |
| 2006 | Approximate Matching in Weighted Sequences. Amihood Amir, Costas S. Iliopoulos, Oren Kapah, Ely Porat |
| 2006 | Approximation of RNA Multiple Structural Alignment. Marcin Kubica, Romeo Rizzi, Stéphane Vialette, Tomasz Walen |
| 2006 | Asynchronous Pattern Matching. Amihood Amir |
| 2006 | Combinatorial Pattern Matching, 17th Annual Symposium, CPM 2006, Barcelona, Spain, July 5-7, 2006, Proceedings Moshe Lewenstein, Gabriel Valiente |
| 2006 | Common Substrings in Random Strings. Eric Blais, Mathieu Blanchette |
| 2006 | Dynamic Entropy-Compressed Sequences and Full-Text Indexes. Veli Mäkinen, Gonzalo Navarro |
| 2006 | Efficient Algorithms for Regular Expression Constrained Sequence Alignment. Yun Sheng Chung, Chin Lung Lu, Chuan Yi Tang |
| 2006 | Faster Algorithms for Computing Longest Common Increasing Subsequences. Gerth Stølting Brodal, Kanela Kaligosi, Irit Katriel, Martin Kutz |
| 2006 | Faster Two Dimensional Scaled Matching. Amihood Amir, Eran Chencinski |
| 2006 | Finding Common RNA Pseudoknot Structures in Polynomial Time. Patricia A. Evans |
| 2006 | Fingerprint Clustering with Bounded Number of Missing Values. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri |
| 2006 | Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures. Tetsuo Shibuya |
| 2006 | Identifying Co-referential Names Across Large Corpora. Levon Lloyd, Andrew Mehler, Steven Skiena |
| 2006 | Large Scale Matching for Position Weight Matrices. Aude Liefooghe, Hélène Touzet, Jean-Stéphane Varré |
| 2006 | Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann |
| 2006 | Longest Common Subsequences in Permutations and Maximum Cliques in Circle Graphs. Alexandre Tiskin |
| 2006 | New Algorithms for Text Fingerprinting. Roman Kolpakov, Mathieu Raffinot |
| 2006 | New Bounds for Motif Finding in Strong Instances. Brona Brejová, Daniel G. Brown, Ian M. Harrower, Tomás Vinar |
| 2006 | Obtaining Provably Good Performance from Suffix Trees in Secondary Storage. Pang Ko, Srinivas Aluru |
| 2006 | On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter |
| 2006 | On-Line Linear-Time Construction of Word Suffix Trees. Shunsuke Inenaga, Masayuki Takeda |
| 2006 | Property Matching and Weighted Matching. Amihood Amir, Eran Chencinski, Costas S. Iliopoulos, Tsvi Kopelowitz, Hui Zhang |
| 2006 | Reducing the Space Requirement of LZ-Index. Diego Arroyuelo, Gonzalo Navarro, Kunihiko Sadakane |
| 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, François Nicolas |
| 2006 | Statistical Encoding of Succinct Data Structures. Rodrigo González, Gonzalo Navarro |
| 2006 | Sublinear Algorithms for Parameterized Matching. Leena Salmela, Jorma Tarhio |
| 2006 | Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms. Sven Rahmann |
| 2006 | Theoretical and Practical Improvements on the RMQ-Problem, with Applications to LCA and LCE. Johannes Fischer, Volker Heun |
| 2006 | Tiling an Interval of the Discrete Line. Olivier Bodini, Eric Rivals |