Front matter
1-9
Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces
L. R. Grate, C. Bhattacharyya, M. I. Jordan and I. S. Mian
10-28
Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design
Miklós Csűrös and Aleksandar Milosavljevic
29-43
Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem
Romeo Rizzi, Vineet Bafna, Sorin Istrail and Giuseppe Lancia
44-59
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
The Haplotype Coloring Problem
Russell Schwartz, Andrew G. Clark and Sorin Istrail
60-67
Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks
Martin Reczko, Petko Fiziev, Eike Staub and Artemis Hatzigeorgiou
68-81
Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry
Nathan Edwards and Ross Lippert
82-96
Improved Approximation Algorithms for NMR Spectral Peak Assignment
Chen Zhi-Zhong, Tao Jiang, Guohui Lin, Jianjun Wen and Dong Xu, et al.
97-111
Efficient Methods for Inferring Tandem Duplication History
Louxin Zhang, Bin Ma and Lusheng Wang
112-125
Genome Rearrangement Phylogeny Using Weighbor
Wang Li-San
126-139
Segment Match Refinement and Applications
Aaron L. Halpern, Daniel H. Huson and Knut Reinert
140-156
Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation
Ezekiel F. Adebiyi and Michael Kaufmann
157-171
Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics
Michael H. Goldwasser, Ming-Yang Kao and Hsueh-I Lu
172-184
FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures
Mariusz Milik, Sandor Szalma and Krzysztof A. Olszewski
185-200
Efficient Unbound Docking of Rigid Molecules
Dina Duhovny, Ruth Nussinov and Haim J. Wolfson
201-209
A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants
Raymond Wheeler
210-219
A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding
Mihaela Pertea and Steven L. Salzberg
220-234
Comparative Methods for Gene Structure Prediction in Homologous Sequences
Christian N.S. Pedersen and Tejs Scharling
235-250
MultiProt — A Multiple Protein Structural Alignment Algorithm
Maxim Shatsky, Ruth Nussinov and Haim J. Wolfson
251-262
A Hybrid Scoring Function for Protein Multiple Alignment
Emily Rocke
263-276
Functional Consequences in Metabolic Pathways from Phylogenetic Profiles
Yonatan Bilu and Michal Linial
277-286
Finding Founder Sequences from a Set of Recombinants
Esko Ukkonen
287-299
Estimating the Deviation from a Molecular Clock
Luay Nakhleh, Usman Roshan, Lisa Vawter and Tandy Warnow
300-315
Exploring the Set of All Minimal Sequences of Reversals — An Application to Test the Replication-Directed Reversal Hypothesis
Yasmine Ajana, Lefebvre Jean-François, Elisabeth R.M. Tillier and Nadia El-Mabrouk
316-330
Approximating the Expected Number of Inversions Given the Number of Breakpoints
Niklas Eriksen
331-342
Invited Lecture — Accelerating Smith-Waterman Searches
Gene Myers and Richard Durbin
343-356
Sequence-Length Requirements for Phylogenetic Methods
Bernard M.E. Moret, Usman Roshan and Tandy Warnow
357-374
Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle
Richard Desper and Olivier Gascuel
375-391
NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks
David Bryant and Vincent Moulton
392-403
On the Control of Hybridization Noise in DNA Sequencing-by-Hybridization
H.-W. Leong, F. P. Preparata, W.-K. Sung and H. Willy
404-417
Restricting SBH Ambiguity via Restriction Enzymes
Steven Skiena and Sagi Snir
418
Invited Lecture — Molecule as Computation: Towards an Abstraction of Biomolecular Systems
Ehud Shapiro
419-433
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search
Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein and Ming-Yang Kao, et al.
434
Rapid Large-Scale Oligonucleotide Selection for Microarrays
Sven Rahmann
435-448
Border Length Minimization in DNA Array Design*
A. B. Kahng, I. I. Măndoiu, P. A. Pevzner, S. Reda and A. Z. Zelikovsky
449-463
The Enhanced Suffix Array and Its Applications to Genome Analysis
Mohamed Ibrahim Abouelhoda, Stefan Kurtz and Enno Ohlebusch
464-476
The Algorithmic of Gene Teams
Anne Bergeron, Sylvie Corteel and Mathieu Raffinot
477-490
Combinatorial Use of Short Probes for Differential Gene Expression Profiling
Liling L. Warren and Ben Hui Liu
491-505
Designing Specific Oligonucleotide Probes for the Entire
S. cerevisiae
Transcriptome
Doron Lipson, Peter Webb and Zohar Yakhini
506-520
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data
Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel and Tommi S. Jaakkola, et al.
521-536
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
Bernard M. E. Moret, Adam C. Siepel, Jijun Tang and Tao Liu
537-551
Modified Mincut Supertrees
Roderic D.M. Page
Back matter