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ORCID5. WABI 2005: Mallorca, Spain
- Rita Casadio, Gene Myers:
Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings. Lecture Notes in Computer Science 3692, Springer 2005, ISBN 3-540-29008-7
Expression
Hybrid Methods
- Nora Speer, Christian Spieth, Andreas Zell:
Spectral Clustering Gene Ontology Terms to Group Genes by Function. 1-12 - Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression. 13-26
Time Patterns
- Laurent Bréhélin:
Clustering Gene Expression Series with Prior Knowledge. 27-38 - Sara C. Madeira
, Arlindo L. Oliveira:
A Linear Time Biclustering Algorithm for Time Series Gene Expression Data. 39-52 - Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor:
Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. 53-64
Phylogeny
Quartets
- Gang Wu, Jia-Huai You, Guohui Lin:
A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem. 65-76 - Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers:
Computing the Quartet Distance Between Trees of Arbitrary Degree. 77-88
Tree Reconciliation
- Shlomo Moran, Satish Rao, Sagi Snir:
Using Semi-definite Programming to Enhance Supertree Resolvability. 89-103 - Zeshan Peng, H. F. Ting:
An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree. 104-115
Clades and Haplotypes
- Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Vijaya Ramachandran, Tandy J. Warnow:
Pattern Identification in Biogeography. 116-127 - Rudi Cilibrasi, Leo van Iersel, Steven Kelk, John Tromp:
On the Complexity of Several Haplotyping Problems. 128-139 - Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen:
A Hidden Markov Technique for Haplotype Reconstruction. 140-151 - Yun S. Song, Yufeng Wu, Dan Gusfield:
Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. 152-164
Networks
- Sebastian Wernicke:
A Faster Algorithm for Detecting Network Motifs. 165-177 - Vincent Lacroix, Cristina G. Fernandes, Marie-France Sagot:
Reaction Motifs in Metabolic Networks. 178-191 - Warwick Tucker, Vincent Moulton:
Reconstructing Metabolic Networks Using Interval Analysis. 192-203
Genome Rearrangements
Transposition Model
- Isaac Elias, Tzvika Hartman:
A 1.375-Approximation Algorithm for Sorting by Transpositions. 204-215 - Anthony Labarre:
A New Tight Upper Bound on the Transposition Distance. 216-227
Other Models
- Sèverine Bérard, Anne Bergeron, Cédric Chauve, Christophe Paul:
Perfect Sorting by Reversals Is Not Always Difficult. 228-238 - Rune B. Lyngsø, Yun S. Song, Jotun Hein:
Minimum Recombination Histories by Branch and Bound. 239-250
Sequences
Strings
- Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg:
A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds. 251-263 - Henry C. M. Leung, Francis Y. L. Chin:
Generalized Planted (l, d)-Motif Problem with Negative Set. 264-275 - Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye:
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). 276-290 - Daniel Dalevi, Devdatt P. Dubhashi:
The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity. 291-302
Multi-alignment and Clustering
- Markus Bauer, Gunnar W. Klau, Knut Reinert:
Multiple Structural RNA Alignment with Lagrangian Relaxation. 303-314 - Pankaj K. Agarwal, Yonatan Bilu, Rachel Kolodny:
Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons. 315-327 - Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik:
Ortholog Clustering on a Multipartite Graph. 328-340
Clustering and Representation
- Baharak Rastegari, Anne Condon:
Linear Time Algorithm for Parsing RNA Secondary Structure. 341-352 - Robert S. Boyer, Warren A. Hunt Jr., Serita M. Nelesen:
A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance. 353-364
Structure
Threading
- Philippe Veber, Nicola Yanev, Rumen Andonov, Vincent Poirriez:
Optimal Protein Threading by Cost-Splitting. 365-375 - Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai:
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment. 376-388
Folding
- Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink:
Rotamer-Pair Energy Calculations Using a Trie Data Structure. 389-400 - Eran Eyal, Dan Halperin:
Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity. 401-413 - Alexander Kister:
The Main Structural Regularities of the Sandwich Proteins. 414-422 - Keren Lasker, Oranit Dror, Ruth Nussinov, Haim J. Wolfson:
Discovery of Protein Substructures in EM Maps. 423-434
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