Accepted Papers

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution
Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren and Bengt Sennblad

A Random Graph Approach to NMR Sequential Assignment
Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan

Interface Surfaces for Protein-Protein Complexes
Yih-En Andrew Ban, Herbert Edelsbrunner, Johannes Rudolph

Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation
Alexis Battle, Eran Segal, Daphne Koller

Learning Multiple Evolutionary Pathways from Cross-sectional Data
Niko Beerenwinkel, Jorg Rahnenfuhrer, Martin Daumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer

Multiple Organism Gene Finding by Collapsed Gibbs Sampling
Sourav Chatterji, Lior Pachter

Protein Similarity from Knot Theory and Geometric Convolution
Michael Erdmann

From Profiles to Patterns and Back Again: A Branch and Bound Algorithm for Finding Optimal Motif Profiles
Eleazar Eskin

Discovering temporal relations in molecular pathways using protein-protein interactions
Martin Farach-Colton, Yang Huang, John L. Woolford

Reconciliation problems for duplication, loss and horizontal gene transfer
Pawel Gorecki

Simultaneous Identification of Duplications and Lateral Transfers
M. Hallett, J. Lagergren, A. Tofigh

Perfect Phylogeny and Haplotype Assignment
Eran Halperin, Richard M. Karp

Identifying Conserved Gene Clusters in the Presence of Orthologous Groups
Xin He, Michael H. Goldwasser

Mining spatial motifs from protein structure graphs
Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alex Tropsha

Aligning alignments exactly
John Kececioglu, Dean Starrett

Maximum Likelihood Resolution of Multi-block Genotypes
Gad Kimmel, Ron Shamir

Checking homogeneity of motifs distribution in heterogenous sequences
Sabrina Ledent and Stephane Robin

Finding Motifs for Insufficient Number of Sequences with Strong Binding to Transcription Factor
Francis Y.L. Chin, Henry C.M. Leung, S.M. Yiu, T.W. Lam, Roni Rosenfeld, W.W. Tsang, David K. Smith, Y.Jiang

A Class of Edit Kernels for SVMs to Predict Translation Initiation Sites in Eukaryotic mRNAs
Haifeng Li, Tao Jiang

An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming
Jing Li, Tao Jiang

A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign, and its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme
Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce R. Donald

Finding anchors for genomic sequence comparison
Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail

Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Ap
plication to Recognizing Beta Trefoils

Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen

The Evolutionary Capacity of Protein Structures
Leonid Meyerguz, David Kempe, Jon Kleinberg, Ron Elber

Structured Motifs Search
Michele Morgante, Alberto Policriti, Nicola Vitacolonna, Andrea Zuccolo

Reconstructing Reticulate Evolution in Species - Theory and Practice
Luay Nakhleh, Tandy Warnow and C. Randal Linder

Hybrid-GMM-Matching toward Comparing Embryogenesis-Staining-Pattern- Images of Drosophila melanogaster and Finding Co-Regulated Genes
Hanchuan Peng, Eugene Myers

De novo Repeat Classification and Fragment Assembly
Pavel A. Pevzner, Haixu Tang, Glenn Tesler

Chromosomal breakpoint re-use in the inference of genome sequence rearrangement
David Sankoff, Phil Trinh

A Discriminative Model for Identifying Spatial Cis-Regulatory Modules
Eran Segal and Roded Sharan

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
Roded Sharan, Trey Ideker, Brian Kelley, Ron Shamir, Richard Karp

Computational identification of evolutionarily conserved exons
A. Siepel, D. Haussler

Designing multiple simultaneous seeds for DNA similarity search
Yanni Sun and Jeremy Buhler

Using Motion Planning to Study RNA Folding Kinetics
Xinyu Tang, Bonnie Kirkpatrick, Shawna Thomas, Guang Song, Nancy M. Amato

Faster genome annotation of non-coding RNA families without loss of accuracy
Zasha Weinberg, Walter L. Ruzzo

Finding Approximate Tandem Repeats in Genomic Sequences
Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger

Stochastic Models Based on Molecular Hybridization Theory for Short Oligonucleotide Microarrays
Zhijin Wu, Rafael A. Irizarry

Finding short DNA Motifs Using Permuted Markov Models
Xiaoyue Zhao, Haiyan Huang, Terence P. Speed