7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings
Omschrijving
This book constitutes the refereed proceedings of the 7th International Workshop on Algorithms in Bioinformatics, WABI 2007, held in Philadelphia, PA, USA in September 2007.
The 38 revised full papers presented together with the abstract of a keynote talk were carefully reviewed and selected from 133 submissions. All current issues of algorithms in bioinformatics are addressed, ranging from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. Numerous biological problems are dealt with, including genetic mapping, sequence alignment and sequence analysis, phylogeny, comparative genomics, and protein structure. Furthermore the papers feature high-performance computing approaches to computationally hard learning and optimization problems in bioinformatics and cover methods, software and dataset repositories for development and testing of such algorithms and their underlying models. The refereed proceedings from the 7th International Workshop on Algorithms in Bioinformatics are provided in this volume. Papers address current issues in algorithms in bioinformatics, ranging from mathematical tools to experimental studies of approximation algorithms to significant computational analyses. Biological problems examined include genetic mapping, sequence alignment and analysis, phylogeny, comparative genomics, and protein structure. Shotgun Protein Sequencing (Keynote)
1(1)
Pavel A. Pevzner
Locality Kernels for Protein Classification
2(10)
Evgeni Tsivtsivadze
Jorma Boberg
Tapio Salakoski
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features
12(13)
Roy Varshavsky
Menachem Fromer
Amit Man
Michal Linial
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps
25(13)
Marco Vassura
Luciano Margara
Pietro Di Lena
Filippo Medri
Piero Fariselli
Rita Casadio
Bringing Folding Pathways into Strand Pairing Prediction
38(11)
Jieun K. Jeong
Piotr Berman
Teresa M. Przytycka
A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
49(12)
Loredana M. Genovese
Filippo Geraci
Marco Pellegrini
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies
61(12)
Phil Hyoun Lee
Hagit Shatkay
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity
73(12)
Justin Kennedy
Ion Mandoiu
Bogdan Pasaniuc
Haplotype Inference Via Hierarchical Genotype Parsing
85(13)
Pasi Rastas
Esko Ukkonen
Seeded Tree Alignment and Planar Tanglegram Layout
98(13)
Antoni Lozano
Ron Y. Pinter
Oleg Rokhlenko
Gabriel Valiente
Michal Ziv-Ukelson
Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion (Extended Abstract)
111(13)
Hadas Birin
Zohar Gal-Or
Isaac Elias
Tamir Tuller
An ?(n2 / log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem
124(12)
Mukul S. Bansal
Oliver Eulenstein
Incremental Discovery of Irredundant Motif Bases in Time O (|?|n2 log n) (Extended Abstract)
136(13)
Alberto Apostolico
Claudia Tagliacollo
A Graph Clustering Approach to Weak Motif Recognition
149(12)
Christina Boucher
Daniel G. Brown
Paul Church
Informative Motifs in Protein Family Alignments
161(10)
Hatice Gulcin Ozer
William C. Ray
Topology Independent Protein Structural Alignment
171(12)
Joe Dundas
T.A. Binkowski
Bhaskar DasGupta
Jie Liang
Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction
183(11)
Giuseppe Nicosia
Giovanni Stracquadanio
Alignment-Free Local Structural Search by Writhe Decomposition
194(2)
Degui Zhi
Maxim Shatsky
Steven E. Brenner
Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment
196(12)
Xueyi Wang
Jack Snoeyink
Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding
208(8)
Mihaela Pertea
Steven L. Salzberg
Genomic Signatures in De Bruijn Chains
216(12)
Lenwood S. Heath
Amrita Pati
Fast Kernel Methods for SVM Sequence Classifiers
228(12)
Pavel Kuksa
Vladimir Pavlovic
On-Line Viterbi Algorithm for Analysis of Long Biological Sequences
240(12)
Rastislav Sramek
Brona Brejova
Tomas Vinar
Predicting Protein Folding Kinetics Via Temporal Logic Model Checking (Extended Abstract)
252(13)
Christopher James Langmead
Sumit Kumar Jha
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops
265(12)
Ankur Dhanik
Peggy Yao
Nathan Marz
Ryan Propper
Charles Kou
Guanfeng Liu
Henry van den Bedem
Jean-Claude Latombe
Algorithms for the Extraction of Synteny Blocks from Comparative Maps
277(12)
Vicky Choi
Chunfang Zheng
Qian Zhu
David Sankoff
Computability of Models for Sequence Assembly
289(13)
Paul Medvedev
Konstantinos Georgiou
Gene Myers
Michael Brudno
Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data
302(8)
Jaime Davila
Sudha Balla
Sanguthevar Rajasekaran
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound
310(13)
Chunmei Liu
Yinglei Song
Louis Shapiro
HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding
323(12)
Hosna Jabbari
Anne Condon
Ana Pop
Cristina Pop
Yinglei Zhao
Homology Search with Fragmented Nucleic Acid Sequence Patterns
335(11)
Axel Mosig
Julian J.-L. Chen
Peter F. Stadler
Fast Computation of Good Multiple Spaced Seeds
346(13)
Lucian Ilie
Silvana Ilie
Inverse Sequence Alignment from Partial Examples
359(12)
Eagu Kim
John Kececioglu
Novel Approaches in Psychiatric Genomics (Keynote)
371(1)
Maja Bucan
The Point Placement Problem on a Line -- Improved Bounds for Pairwise Distance Queries
372(11)
Francis Y.L. Chin
Henry C.M. Leung
W.K. Sung
S.M. Yiu
Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach
383(12)
Alexander Schliep
Roland Krause
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data
395(12)
Yonghui Wu
Prasanna Bhat
Timothy J. Close
Stefano Lonardi
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence
407(13)
Reka Albert
Bhaskar DasGupta
Riccardo Dondi
Sema Kachalo
Eduardo Sontag
Alexander Zelikovsky
Kelly Westbrooks
Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation
420(11)
Geoffrey Koh
Lisa Tucker-Kellogg
David Hsu
P.S. Thiagarajan
Author Index
431