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Algorithms in Bioinformatics

6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006. Proceedings

  • Philipp Bücher
  • Bernard M. E. Moret
Conference proceedings WABI 2006

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 4175)

Table of contents

  1. Front Matter
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  2. Measures of Codon Bias in Yeast, the tRNA Pairing Index and Possible DNA Repair Mechanisms
    Markus T. Friberg, Pedro Gonnet, Yves Barral, Nicol N. Schraudolph, Gaston H. Gonnet
    Pages 1-11
  3. Decomposing Metabolomic Isotope Patterns
    Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin
    Pages 12-23
  4. A Method to Design Standard HMMs with Desired Length Distribution for Biological Sequence Analysis
    Hongmei Zhu, Jiaxin Wang, Zehong Yang, Yixu Song
    Pages 24-31
  5. Efficient Model-Based Clustering for LC-MS Data
    Marta Łuksza, Bogusław Kluge, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin
    Pages 32-43
  6. A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks
    Lukas Burger, Erik van Nimwegen
    Pages 44-55
  7. Linear-Time Haplotype Inference on Pedigrees Without Recombinations
    M. Y. Chan, Wun-Tat Chan, Francis Y. L. Chin, Stanley P. Y. Fung, Ming-Yang Kao
    Pages 56-67
  8. Phylogenetic Network Inferences Through Efficient Haplotyping
    Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai
    Pages 68-79
  9. Beaches of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems
    Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie
    Pages 80-91
  10. On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model
    Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau
    Pages 92-102
  11. How Many Transcripts Does It Take to Reconstruct the Splice Graph?
    Paul Jenkins, Rune Lyngsø, Jotun Hein
    Pages 103-114
  12. Multiple Structure Alignment and Consensus Identification for Proteins
    Jieping Ye, Ivaylo Ilinkin, Ravi Janardan, Adam Isom
    Pages 115-125
  13. Procrastination Leads to Efficient Filtration for Local Multiple Alignment
    Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna
    Pages 126-137
  14. Controlling Size When Aligning Multiple Genomic Sequences with Duplications
    Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller
    Pages 138-149
  15. Reducing Distortion in Phylogenetic Networks
    Daniel H. Huson, Mike A. Steel, Jim Whitfield
    Pages 150-161
  16. Imputing Supertrees and Supernetworks from Quartets
    Barbara Hollan, Glenn Conner, Katharina T. Huber, Vincent Moulton
    Pages 162-162
  17. A Unifying View of Genome Rearrangements
    Anne Bergeron, Julia Mixtacki, Jens Stoye
    Pages 163-173
  18. Efficient Sampling of Transpositions and Inverted Transpositions for Bayesian MCMC
    István Miklós, Timothy Brooks Paige, Péter Ligeti
    Pages 174-185
  19. Alignment with Non-overlapping Inversions in O(n3)-Time
    Augusto F. Vellozo, Carlos E. R. Alves, Alair Pereira do Lago
    Pages 186-196
  20. Accelerating Motif Discovery: Motif Matching on Parallel Hardware
    Geir Kjetil Sandve, Magnar Nedland, Øyvind Bø Syrstad, Lars Andreas Eidsheim, Osman Abul, Finn Drabløs
    Pages 197-206
  21. Segmenting Motifs in Protein-Protein Interface Surfaces
    Jeff M. Phillips, Johannes Rudolph, Pankaj K. Agarwal
    Pages 207-218
  22. Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction
    Eun-Jong Hong, Tomás Lozano-Pérez
    Pages 219-230
  23. On the Complexity of the Crossing Contact Map Pattern Matching Problem
    Shuai Cheng Li, Ming Li
    Pages 231-241
  24. A Fuzzy Dynamic Programming Approach to Predict RNA Secondary Structure
    Dandan Song, Zhidong Deng
    Pages 242-251
  25. Landscape Analysis for Protein-Folding Simulation in the H-P Model
    Kathleen Steinhöfel, Alexandros Skaliotis, Andreas A. Albrecht
    Pages 252-261
  26. Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition
    Jizhen Zhao, Russell L. Malmberg, Liming Cai
    Pages 262-273
  27. Flux-Based vs. Topology-Based Similarity of Metabolic Genes
    Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter
    Pages 274-285
  28. Combinatorial Methods for Disease Association Search and Susceptibility Prediction
    Dumitru Brinza, Alexander Zelikovsky
    Pages 286-297
  29. Integer Linear Programs for Discovering Approximate Gene Clusters
    Sven Rahmann, Gunnar W. Klau
    Pages 298-309
  30. Approximation Algorithms for Bi-clustering Problems
    Lusheng Wang, Yu Lin, Xiaowen Liu
    Pages 310-320
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  31. Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning
    Sérgio A. de Carvalho Jr., Sven Rahmann
    Pages 321-332
  32. Accelerating the Computation of Elementary Modes Using Pattern Trees
    Marco Terzer, Jörg Stelling
    Pages 333-343
  33. A Linear-Time Algorithm for Studying Genetic Variation
    Nikola Stojanovic, Piotr Berman
    Pages 344-354
  34. New Constructive Heuristics for DNA Sequencing by Hybridization
    Christian Blum, Mateu Yábar Vallès
    Pages 355-365
  35. Optimal Probing Patterns for Sequencing by Hybridization
    Dekel Tsur
    Pages 366-375
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  36. Gapped Permutation Patterns for Comparative Genomics
    Laxmi Parida
    Pages 376-387
  37. Segmentation with an Isochore Distribution
    Miklós Csűrös, Ming-Te Cheng, Andreas Grimm, Amine Halawani, Perrine Landreau
    Pages 388-399
  38. Back Matter
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About these proceedings

Keywords

Alignment algorithm algorithms bioinformatics combinatorial optimization genome optimization sequence analysis

Editors and affiliations

  • Philipp Bücher
    • 1
  • Bernard M. E. Moret
    • 2
  1. 1.Ecole Polytechnique Fédérale de LausanneSwitzerland
  2. 2.Laboratory for Computational Biology and BioinformaticsEPFL (Ecole Polytechnique Fédérale de Lausanne), Swiss Institute of BioinformaticsLausanneSwitzerland

Bibliographic information

  • DOI https://doi.org/10.1007/11851561
  • Copyright Information Springer-Verlag Berlin Heidelberg 2006
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-39583-6
  • Online ISBN 978-3-540-39584-3
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site