| 2005 | Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets. | Shiri Dori, Gad M. Landau |
| 2005 | Faster Algorithms for delta, gamma-Matching and Related Problems. | Peter Clifford, Raphal Clifford, Costas S. Iliopoulos |
| 2005 | An Optimal Algorithm for Online Square Detection. | Gen-Huey Chen, Jin-Ju Hong, Hsueh-I Lu |
| 2005 | Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. | Brona Brejov, Daniel G. Brown, Ian M. Harrower, Alejandro Lpez-Ortiz, Toms Vinar |
| 2005 | Assessing the Significance of Sets of Words. | Valentina Boeva, Julien Clment, Mireille Rgnier, Mathias Vandenbogaert |
| 2005 | Mass Spectra Alignments and Their Significance. | Sebastian Bcker, Hans-Michael Kaltenbach |
| 2005 | Identifying Similar Surface Patches on Proteins Using a Spin-Image Surface Representation. | Mary Ellen Bock, Guido Maria Cortelazzo, Carlo Ferrari, Concettina Guerra |
| 2005 | DNA Compression Challenge Revisited: A Dynamic Programming Approach. | Behshad Behzadi, Fabrice Le Fessant |
| 2005 | Regular Expression Constrained Sequence Alignment. | Abdullah N. Arslan |
| 2005 | Approximate Matching in the L | Amihood Amir, Ohad Lipsky, Ely Porat, Julia Umanski |
| 2005 | Inferring a Graph from Path Frequency. | Tatsuya Akutsu, Daiji Fukagawa |
| 2005 | A Polynomial Time Matching Algorithm of Ordered Tree Patterns Having Height-Constrained Variables. | Kazuhide Aikou, Yusuke Suzuki, Takayoshi Shoudai, Tomoyuki Uchida, Tetsuhiro Miyahara |
| 2004 | Optimizing Multiple Spaced Seeds for Homology Search. | Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma |
| 2004 | Sorting by Reversals in Subquadratic Time. | Eric Tannier, Marie-France Sagot |
| 2004 | Sorting by Length-Weighted Reversals: Dealing with Signs and Circularity. | Firas Swidan, Michael A. Bender, Dongdong Ge, Simai He, Haodong Hu, Ron Y. Pinter |
| 2004 | Approximate Point Set Pattern Matching on Sequences and Planes. | Tomoaki Suga, Shinichi Shimozono |
| 2004 | Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. | Thomas Schmidt, Jens Stoye |
| 2004 | Approximate Labelled Subtree Homeomorphism. | Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson |
| 2004 | Compressed Compact Suffix Arrays. | Veli Mkinen, Gonzalo Navarro |
| 2004 | Average-Case Analysis of Approximate Trie Search (Extended Abstract). | Moritz G. Maa |
| 2004 | Finding Biclusters by Random Projections. | Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang |
| 2004 | A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes. | Guojun Li, Xingqin Qi, Xiaoli Wang, Binhai Zhu |
| 2004 | Two Algorithms for LCS Consecutive Suffix Alignment. | Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson |
| 2004 | Multi-seed Lossless Filtration (Extended Abstract). | Gregory Kucherov, Laurent No, Mikhail A. Roytberg |
| 2004 | On the k-Closest Substring and k-Consensus Pattern Problems. | Yishan Jiao, Jingyi Xu, Ming Li |