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E-grāmata: Algorithms in Bioinformatics: 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings

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  • Formāts: PDF+DRM
  • Sērija : Lecture Notes in Bioinformatics 3692
  • Izdošanas datums: 21-Oct-2005
  • Izdevniecība: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • Valoda: eng
  • ISBN-13: 9783540318125
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  • Formāts: PDF+DRM
  • Sērija : Lecture Notes in Bioinformatics 3692
  • Izdošanas datums: 21-Oct-2005
  • Izdevniecība: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • Valoda: eng
  • ISBN-13: 9783540318125

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We are pleased to present the proceedings of the 5th Workshop on Algorithms in Bioinformatics (WABI 2005) which took place in Mallorca, Spain, October 3-6, 2005. The WABI 2005 workshop was part of the ?ve ALGO 2005 conf- ence meetings, which, in addition to WABI, included ESA, WAOA, IWPEC, and ATMOS. WABI 2005 was sponsored by EATCS (the European Assoc- tion for Theoretical Computer Science), the ISCB (the International Society for Computational Biology), the Universitat Polit' ecnica de Catalunya, the U- versitat de les Illes Balears, and the Ministerio de Educaci' on y Ciencia. See http://www.lsi.upc.edu/"wabi05/ for more details. The Workshop on Algorithms in Bioinformatics highlights research work speci cally developed to address algorithmic problems in biosequence analysis. Theemphasisisthereforeonstatisticalandprobabilisticalgorithmsthataddress important problems in the ?eld of molecular and structural biology. At present, given the enormous scienti c and technical e orts in functional and structural genomics, the relevance of the problem is therefore constrained by the need for sound, e cient and specialized algorithms, capable of achieving solutions that can be tested by the biological community. Indeed the ultimate goal is to - plement algorithms capable of extracting real features from real biological data sets. Therefore the workshop aims to present recent research results, including signi cant work in progress, and to identify and explore directions of future research.
Expression
Hybrid Methods
Spectral Clustering Gene Ontology Terms to Group Genes by Function
1(12)
Nora Speer
Christian Spieth
Andreas Zell
Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression
13(14)
Chaya Ben-Zaken Zilberstein
Michal Ziv-Ukelson
Time Patterns
Clustering Gene Expression Series with Prior Knowledge
27(12)
Laurent Brehelin
A Linear Time Biclustering Algorithm for Time Series Gene Expression Data
39(14)
Sara C. Madeira
Arlindo L. Oliveira
Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds
53(12)
Tamir Tuller
Efrat Oron
Erez Makavy
Daniel A. Chamovitz
Benny Chor
Phylogeny
Quartets
A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem
65(12)
Gang Wu
Jia-Huai You
Guohui Lin
Computing the Quartet Distance Between Trees of Arbitrary Degree
77(12)
Chris Christiansen
Thomas Mailund
Christian N.S. Pedersen
Martin Randers
Tree Reconciliation
Using Semi-definite Programming to Enhance Supertree Resolvability
89(15)
Shlomo Moran
Satish Rao
Sagi Snir
An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree
104(12)
Z.S. Peng
H.F. Ting
Clades and Haplotypes
Pattern Identification in Biogeography
116(12)
Ganeshkumar Ganapathy
Barbara Goodson
Robert Jansen
Vijaya Ramachandran
Tandy Warnow
On the Complexity of Several Haplotyping Problems
128(12)
Rudi Cilibrasi
Leo van Iersel
Steven Kelk
John Tromp
A Hidden Markov Technique for Haplotype Reconstruction
140(12)
Pasi Rastas
Mikko Koivisto
Heikki Mannila
Esko Ukkonen
Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event
152(13)
Yun S. Song
Yufeng Wu
Dan Gusfield
Networks
A Faster Algorithm for Detecting Network Motifs
165(13)
Sebastian Wernicke
Reaction Motifs in Metabolic Networks
178(14)
Vincent Lacroix
Cristina G. Fernandes
Marie-France Sagot
Reconstructing Metabolic Networks Using Interval Analysis
192(12)
Warwick Tucker
Vincent Moulton
Genome Rearrangements
Trasposition Model
1.375-Approximation Algorithm for Sorting by Transpositions
204(12)
Isaac Elias
Tzvika Hartman
A New Tight Upper Bound on the Transposition Distance
216(12)
Anthony Labarre
Other Models
Perfect Sorting by Reversals Is Not Always Difficult
228(11)
Severine Berard
Anne Bergeron
Cedric Chauve
Christophe Paul
Minimum Recombination Histories by Branch and Bound
239(12)
Rune B. Lyngso
Yun S. Song
Jotun Hein
Sequences
Strings
A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds
251(13)
Gregory Kucherov
Laurent Noe
Mikhail Roytberg
Generalized Planted (l,d)-Motif Problem with Negative Set
264(12)
Henry C.M. Leung
Francis Y.L. Chin
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
276(15)
Michael Sammeth
Thomas Weniger
Dag Harmsen
Jens Stoye
The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
291(12)
Daniel Dalevi
Devdatt Dubhashi
Multi-alignment and Clustering
Multiple Structural RNA Alignment with Lagrangian Relaxation
303(12)
Markus Bauer
Gunnar W. Klau
Knut Reinert
Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons
315(13)
Pankaj K. Agarwal
Yonatan Bilu
Rachel Kolodny
Ortholog Clustering on a Multipartite Graph
328(13)
Akshay Vashist
Casimir Kulikowski
Ilya Muchnik
Clustering and Representation
Linear Time Algorithm for Parsing RNA Secondary Structure
341(12)
Baharak Rastegari
Anne Condon
A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance
353(12)
Robert S. Boyer
Warren A. Hunt Jr
Serita M. Nelesen
Structure
Threading
Optimal Protein Threading by Cost-Splitting
365(11)
Philippe Veber
Nicola Yanev
Rumen Andonov
Vincent Poirriez
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment
376(13)
Yinglei Song
Chunmei Liu
Xiuzhen Huang
Russell L. Malmberg
Ying Xu
Liming Cai
Folding
Rotamer-Pair Energy Calculations Using a Trie Data Structure
389(12)
Andrew Leaver-Fay
Brian Kuhlman
Jack Snoeyink
Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity
401(13)
Eran Eyal
Dan Halperin
The Main Structural Regularities of the Sandwich Proteins
414(9)
Alexander Kister
Discovery of Protein Substructures in EM Maps
423(12)
Keren Lasker
Oranit Dror
Ruth Nussinov
Haim Wolfson
Author Index 435