Shotgun Protein Sequencing (Keynote) / Pavel A. Pevzner |
Locality Kernels for Protein Classification / Evgeni Tsivtsivadze ; Jorma Boberg ; Tapio Salakoski |
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features / Roy Varshavsky ; Menachem Fromer ; Amit Man ; Michal Linial |
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps / Marco Vassura ; Luciano Margara ; Pietro Di Lena ; Filippo Medri ; Piero Fariselli ; Rita Casadio |
Bringing Folding Pathways into Strand Pairing Prediction / 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 / Loredana M. Genovese ; Filippo Geraci ; Marco Pellegrini |
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies / Phil Hyoun Lee ; Hagit Shatkay |
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity / Justin Kennedy ; Ion Mandoiu ; Bogdan Pasaniuc |
Haplotype Inference Via Hierarchical Genotype Parsing / Pasi Rastas ; Esko Ukkonen |
Seeded Tree Alignment and Planar Tanglegram Layout / 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) / Hadas Birin ; Zohar Gal-Or ; Isaac Elias ; Tamir Tuller |
An [Omega](n[superscript 2]/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem / Mukul S. Bansal ; Oliver Eulenstein |
Incremental Discovery of Irredundant Motif Bases in Time O([vertical bar Sigma vertical bar]n[superscript 2] log n) (Extended Abstract) / Alberto Apostolico ; Claudia Tagliacollo |
A Graph Clustering Approach to Weak Motif Recognition / Christina Boucher ; Daniel G. Brown ; Paul Church |
Informative Motifs in Protein Family Alignments / Hatice Gulcin Ozer ; William C. Ray |
Topology Independent Protein Structural Alignment / Joe Dundas ; T.A. Binkowski ; Bhaskar DasGupta ; Jie Liang |
Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction / Giuseppe Nicosia ; Giovanni Stracquadanio |
Alignment-Free Local Structural Search by Writhe Decomposition / Degui Zhi ; Maxim Shatsky ; Steven E. Brenner |
Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment / Xueyi Wang ; Jack Snoeyink |
Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding / Mihaela Pertea ; Steven L. Salzberg |
Genomic Signatures in De Bruijn Chains / Lenwood S. Heath ; Amrita Pati |
Fast Kernel Methods for SVM Sequence Classifiers / Pavel Kuksa ; Vladimir Pavlovic |
On-Line Viterbi Algorithm for Analysis of Long Biological Sequences / Rastislav Sramek ; Brona Brejova ; Tomas Vinar |
Predicting Protein Folding Kinetics Via Temporal Logic Model Checking (Extended Abstract) / Christopher James Langmead ; Sumit Kumar Jha |
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops / 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 / Vicky Choi ; Chunfang Zheng ; Qian Zhu ; David Sankoff |
Computability of Models for Sequence Assembly / Paul Medvedev ; Konstantinos Georgiou ; Gene Myers ; Michael Brudno |
Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data / Jaime Davila ; Sudha Balla ; Sanguthevar Rajasekaran |
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound / Chunmei Liu ; Yinglei Song ; Louis Shapiro |
HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding / Hosna Jabbari ; Anne Condon ; Ana Pop ; Cristina Pop ; Yinglei Zhao |
Homology Search with Fragmented Nucleic Acid Sequence Patterns / Axel Mosig ; Julian J.-L. Chen ; Peter F. Stadler |
Fast Computation of Good Multiple Spaced Seeds / Lucian Ilie ; Silvana Ilie |
Inverse Sequence Alignment from Partial Examples / Eagu Kim ; John Kececioglu |
Novel Approaches in Psychiatric Genomics (Keynote) / Maja Bucan |
The Point Placement Problem on a Line - Improved Bounds for Pairwise Distance Queries / 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 / Alexander Schliep ; Roland Krause |
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data / Yonghui Wu ; Prasanna Bhat ; Timothy J. Close ; Stefano Lonardi |
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence / Reka Albert ; Riccardo Dondi ; Sema Kachalo ; Eduardo Sontag ; Alexander Zelikovsky ; Kelly Westbrooks |
Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation / Geoffrey Koh ; Lisa Tucker-Kellogg ; David Hsu ; P.S. Thiagarajan |
Author Index |
Shotgun Protein Sequencing (Keynote) / Pavel A. Pevzner |
Locality Kernels for Protein Classification / Evgeni Tsivtsivadze ; Jorma Boberg ; Tapio Salakoski |
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features / Roy Varshavsky ; Menachem Fromer ; Amit Man ; Michal Linial |