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| 2005 | A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance. Robert S. Boyer, Warren A. Hunt Jr., Serita M. Nelesen |
| 2005 | A Faster Algorithm for Detecting Network Motifs. Sebastian Wernicke |
| 2005 | A Hidden Markov Technique for Haplotype Reconstruction. Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen |
| 2005 | A Linear Time Biclustering Algorithm for Time Series Gene Expression Data. Sara C. Madeira, Arlindo L. Oliveira |
| 2005 | A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem. Gang Wu, Jia-Huai You, Guohui Lin |
| 2005 | A New Tight Upper Bound on the Transposition Distance. Anthony Labarre |
| 2005 | A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds. Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg |
| 2005 | Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. Yun S. Song, Yufeng Wu, Dan Gusfield |
| 2005 | Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings Rita Casadio, Gene Myers |
| 2005 | Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye |
| 2005 | An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree. Zeshan Peng, H. F. Ting |
| 2005 | Clustering Gene Expression Series with Prior Knowledge. Laurent Bréhélin |
| 2005 | Computing the Quartet Distance Between Trees of Arbitrary Degree. Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers |
| 2005 | Discovery of Protein Substructures in EM Maps. Keren Lasker, Oranit Dror, Ruth Nussinov, Haim J. Wolfson |
| 2005 | Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression. Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson |
| 2005 | Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment. Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai |
| 2005 | Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons. Pankaj K. Agarwal, Yonatan Bilu, Rachel Kolodny |
| 2005 | Generalized Planted ( Henry C. M. Leung, Francis Y. L. Chin |
| 2005 | Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity. Eran Eyal, Dan Halperin |
| 2005 | Linear Time Algorithm for Parsing RNA Secondary Structure. Baharak Rastegari, Anne Condon |
| 2005 | Minimum Recombination Histories by Branch and Bound. Rune B. Lyngsø, Yun S. Song, Jotun Hein |
| 2005 | Multiple Structural RNA Alignment with Lagrangian Relaxation. Markus Bauer, Gunnar W. Klau, Knut Reinert |
| 2005 | On the Complexity of Several Haplotyping Problems. Rudi Cilibrasi, Leo van Iersel, Steven Kelk, John Tromp |
| 2005 | Optimal Protein Threading by Cost-Splitting. Philippe Veber, Nicola Yanev, Rumen Andonov, Vincent Poirriez |
| 2005 | Ortholog Clustering on a Multipartite Graph. Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik |
| 2005 | Pattern Identification in Biogeography. Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Vijaya Ramachandran, Tandy J. Warnow |
| 2005 | Perfect Sorting by Reversals Is Not Always Difficult. Sèverine Bérard, Anne Bergeron, Cédric Chauve, Christophe Paul |
| 2005 | Reaction Motifs in Metabolic Networks. Vincent Lacroix, Cristina G. Fernandes, Marie-France Sagot |
| 2005 | Reconstructing Metabolic Networks Using Interval Analysis. Warwick Tucker, Vincent Moulton |
| 2005 | Rotamer-Pair Energy Calculations Using a Trie Data Structure. Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink |
| 2005 | Spectral Clustering Gene Ontology Terms to Group Genes by Function. Nora Speer, Christian Spieth, Andreas Zell |
| 2005 | The Main Structural Regularities of the Sandwich Proteins. Alexander Kister |
| 2005 | The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity. Daniel Dalevi, Devdatt P. Dubhashi |
| 2005 | Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor |
| 2005 | Using Semi-definite Programming to Enhance Supertree Resolvability. Shlomo Moran, Satish Rao, Sagi Snir |