| 2005 | A Fast Algorithm for Approximate String Matching on Gene Sequences. Zheng Liu, Xin Chen, James Borneman, Tao Jiang |
| 2005 | A Linear Tree Edit Distance Algorithm for Similar Ordered Trees. Hélène Touzet |
| 2005 | A New Compressed Suffix Tree Supporting Fast Search and Its Construction Algorithm Using Optimal Working Space. Dong Kyue Kim, Heejin Park |
| 2005 | A New Periodicity Lemma. Kangmin Fan, William F. Smyth, R. J. Simpson |
| 2005 | A Polynomial Time Matching Algorithm of Ordered Tree Patterns Having Height-Constrained Variables. Kazuhide Aikou, Yusuke Suzuki, Takayoshi Shoudai, Tomoyuki Uchida, Tetsuhiro Miyahara |
| 2005 | A Simple Fast Hybrid Pattern-Matching Algorithm. Frantisek Franek, Christopher G. Jennings, William F. Smyth |
| 2005 | An Efficient Algorithm for Generating Super Condensed Neighborhoods. Luís M. S. Russo, Arlindo L. Oliveira |
| 2005 | An Extension of the Burrows Wheeler Transform and Applications to Sequence Comparison and Data Compression. Sabrina Mantaci, Antonio Restivo, Giovanna Rosone, Marinella Sciortino |
| 2005 | An Optimal Algorithm for Online Square Detection. Gen-Huey Chen, Jin-Ju Hong, Hsueh-I Lu |
| 2005 | An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery. Paul Horton, Wataru Fujibuchi |
| 2005 | Approximate Matching in the L Amihood Amir, Ohad Lipsky, Ely Porat, Julia Umanski |
| 2005 | Assessing the Significance of Sets of Words. Valentina Boeva, Julien Clément, Mireille Régnier, Mathias Vandenbogaert |
| 2005 | Combinatorial Pattern Matching, 16th Annual Symposium, CPM 2005, Jeju Island, Korea, June 19-22, 2005, Proceedings Alberto Apostolico, Maxime Crochemore, Kunsoo Park |
| 2005 | Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets. Shiri Dori, Gad M. Landau |
| 2005 | DNA Compression Challenge Revisited: A Dynamic Programming Approach. Behshad Behzadi, Fabrice Le Fessant |
| 2005 | Exact and Approximation Algorithms for DNA Tag Set Design. Ion I. Mandoiu, Dragos Trinca |
| 2005 | Faster Algorithms for delta, gamma-Matching and Related Problems. Peter Clifford, Raphaël Clifford, Costas S. Iliopoulos |
| 2005 | Hardness of Optimal Spaced Seed Design. François Nicolas, Eric Rivals |
| 2005 | Identifying Similar Surface Patches on Proteins Using a Spin-Image Surface Representation. Mary Ellen Bock, Guido Maria Cortelazzo, Carlo Ferrari, Concettina Guerra |
| 2005 | Incremental Inference of Relational Motifs with a Degenerate Alphabet. Nadia Pisanti, Henry Soldano, Mathilde Carpentier |
| 2005 | Inferring a Graph from Path Frequency. Tatsuya Akutsu, Daiji Fukagawa |
| 2005 | Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements. Jijun Tang, Bernard M. E. Moret |
| 2005 | Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets. Joong Chae Na |
| 2005 | Mass Spectra Alignments and Their Significance. Sebastian Böcker, Hans-Michael Kaltenbach |
| 2005 | On the Complexity of Sparse Exon Assembly. Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson |
| 2005 | On the Longest Common Rigid Subsequence Problem. Bin Ma, Kaizhong Zhang |
| 2005 | Parametric Analysis for Ungapped Markov Models of Evolution. David Fernández-Baca, Balaji Venkatachalam |
| 2005 | Prefix-Free Regular-Expression Matching. Yo-Sub Han, Yajun Wang, Derick Wood |
| 2005 | Reducing the Size of NFAs by Using Equivalences and Preorders. Lucian Ilie, Roberto Solis-Oba, Sheng Yu |
| 2005 | Regular Expression Constrained Sequence Alignment. Abdullah N. Arslan |
| 2005 | Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. Brona Brejová, Daniel G. Brown, Ian M. Harrower, Alejandro López-Ortiz, Tomás Vinar |
| 2005 | Speeding up Parsing of Biological Context-Free Grammars. Daniel Fredouille, Christopher H. Bryant |
| 2005 | Succinct Suffix Arrays Based on Run-Length Encoding. Veli Mäkinen, Gonzalo Navarro |
| 2005 | Text Indexing with Errors. Moritz G. Maaß, Johannes Nowak |
| 2005 | The Median Problem for the Reversal Distance in Circular Bacterial Genomes. Enno Ohlebusch, Mohamed Ibrahim Abouelhoda, Kathrin Hockel, Jan Stallkamp |
| 2005 | Two Dimensional Parameterized Matching. Carmit Hazay, Moshe Lewenstein, Dekel Tsur |
| 2005 | Using PQ Trees for Comparative Genomics. Gad M. Landau, Laxmi Parida, Oren Weimann |
| 2005 | Weighted Directed Word Graph. Meng Zhang, Liang Hu, Qiang Li, Jiubin Ju |