Accepted Papers

De Novo Peptide Sequencing for Mass Spectra Based on Multi-Charge Strong Tags
by Kang Ning, Ket Fah Chong, Hon Wai Leong

Metagenome Analysis using Megan
by Daniel Huson, Alexander Auch, Ji Qi, Stephan Schuster

An Effiective Promoter Detection Method using the Adaboost Algorithm
by Xudong Xie, Shuanhu Wu, Kin-Man Lam, Hong Yan

Infering Gene Regulatory Networks by Machine Learning Methods
by Jochen Supper, Holger Fröhlich, Christian Spieth, Andreas Dräger, Andreas Zell

Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments
by Tatsuya Akutsu, Daiji Fukagawa

A Novel Clustering Method for Analysis of Biological Networks Using Maximal Components of Graphs
by Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi

A New Strategy of Geometrical Biclustering for Microarray Data Analysis
by Hongya Zhao, Alan W. C. Liew, Hong Yan

Subtle Motif Discovery for Detection of DNA Regulatory Sites
by Matteo Comin, Laxmi Parida

Algorithmic Approaches to Selecting Control Clonesin DNA Array Hybridization Experiments
by Qi Fu, Elizabeth Bent, James Borneman, Marek Chrobak, Neal Young

Gene Regulatory Network Inference via Regression Based Topological Refinement
by Jochen Supper, Holger Fröhlich, Andreas Zell

Selecting Genes with Dissimilar Discrimination Strength for Sample Class Prediction
by Zhipeng Cai, Randy Goebel, Mohammad Salavatipour, Yi Shi, Lizhe Xu, Guohui Lin

All Hits All The Time: Parameter Free Calculation of Seed Sensitivity
by Denise Mak, Gary Benson

The Distance Between Randomly Constructed Genomes
by Wei Xu

A Probabilistic Method to Identify Compensatory Substitutions for Pathogenic Mutations
by Brett Easton, Peter Maxwell, Alexander Isaev, Gavin Huttley

Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees
by Martin Stissing, Thomas Mailund, Christian N. S. Pedersen, Gerth S. Brodal, Rolf Fagerberg

Computing the Quartet Distance Between Evolutionary Trees of Bounded Degree
by Martin Stissing, Christian N. S. Pedersen, Thomas Mailund, Gerth S. Brodal, Rolf Fagerberg

Simple and Fast Alignment of Metabolic Pathways by Exploiting Local Dissimilarity
by Sebastian Wernicke, Florian Rasche

Fast Structural Similarity Search Based on Topology String Matching
by Sung Hee Park, David Gilbert, Keun Ho Ryu

Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway Detection
by Falk Hüffner, Sebastian Wernicke, Thomas Zichner

Protein Structure-Structure Alignment with Discrete Frechet Distance
by Minghui Jiang, Ying Xu, Binhai Zhu

Using Formal Concept Analysis for Microarray Data Comparison
by Vicky Choi, Yang Huang, Vy Lam, Dustin Potter, Reinhard Laubenbacher, Karen Duca

Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry
by Baozhen Shan, Bin Ma, Kaizhong Zhang, Gilles Lajoie

Exact and Heuristic Approaches for Identifying Disease-Associated SNP Motifs
by Gaofeng Huang, Peter Jeavons, and Dominic Kwiatkowski

Genotype-Based Case-Control Analysis, Violation of Hardy-Weinberg Equilibrium, and Phase Diagrams
by Young Ju Suh, Wentian Li

Computing the Breakpoint Distance between Partially Ordered Genomes
by Zheng Fu, Tao Jiang

Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta
by Yonggang Lu, Jing He, Charlie Strauss

Semi-supervised Pattern Learning for Extracting Relations from Bioscience Texts
by Shilin Ding, Minlie Huang, Xiaoyan Zhu

Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions
by Masanori Arita, Kiyoshi Asai, Kinya Okada

Combining N-grams and Alignment in G-protein Coupling Specificity Prediction
by Betty Yee Man Cheng, Jaime Carbonell

Exploring Genome Rearrangements using Virtual Hybridization
by Mahdi Belcaid, Bergeron Anne, Chateau Annie, Cedric Chauve, Yannick Gingras, Poisson Guylaine, Marc Vendette

An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression Data
by Sara Madeira, Arlindo Oliveira

Two Plus Two Does not Equal Three: Statistical Tests for Multiple Genome Comparison
by Narayanan Raghupathy, Rose Hoberman, Dannie Durand

A Randomized Algorithm for Comparing Sets of Phylogenetic Trees
by Seung-Jin Sul, Tiffani Williams

Fitting Protein Chains to Cubic Lattice is NP-Complete
by Jan Manuch, Daya Gaur

A Global Maximum Likelihood Super-Quartet Phylogeny Method
by Penghao Wang, BingBing Zhou, Monther Tarawneh, Daniel Chu, Albert Zomaya