5. WABI 2005: Mallorca, Spain

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
  
• Z. S. 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 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, Cedric 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
  

Last update Tue Feb 14 04:12:50 2012 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page