Introduction

• 
  Preface.
• 
  Committees.
• 
  Referees.

Keynote Address

• 
  Russ B. Altman: Challenges in Creating an Infrastructure for Physics-Based Simulation of Biological Structures. 3

Invited Talks

• 
  Michael Ashburner: Ontologies for Biologists - A Community Model for the Annotation of Genomic Data. 7
• 
  Ron Kikinis: The National Alliance for Medical Imaging Computing (NA-MIC). 8
• 
  Arthur W. Toga: The Center for Computational Biology. 9

Genomics

• 
  Zheng Yun, Kwoh Chee Keong: Identifying Simple Discriminatory Gene Vectors with an Information Theory Approach. 13-24
• 
  Xutao Deng, Huimin Geng, Hesham H. Ali: Learning Yeast Gene Functions from Heterogeneous Sources of Data Using Hybrid Weighted Bayesian Networks. 25-34
• 
  Benjamin G. Jackson, Srinivas Aluru, Patrick S. Schnable: Consensus Genetic Maps: A Graph Theoretic Approach. 35-43
• 
  Sun Kim, Jeong-Hyeon Choi, Jiong Yang: Gene Teams with Relaxed Proximity Constraint. 44-55
• 
  Anantharaman Kalyanaraman, Srinivas Aluru: Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons. 56-64
• 
  Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail: Islands of Tractability for Parsimony Haplotyping. 65-72
• 
  Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu: Accurate Prediction of Orthologous Gene Groups in Microbes. 73-79
• 
  Vered Kunik, Zach Solan, Shimon Edelman, Eytan Ruppin, David Horn: Motif Extraction and Protein Classification. 80-85
• 
  Yuji Kawada, Yasubumi Sakakibara: Discriminative Discovery of Transcription Factor Binding Sites from Location Data. 86-89

Phylogeny and Evolution

• 
  Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey: Reconstructing Phylogenetic Networks Using Maximum Parsimony. 93-102
• 
  Ravi Vijaya Satya, Amar Mukherjee: An Efficient Algorithm for Perfect Phylogeny Haplotyping. 103-110
• 
  Aswath Manohar, Serafim Batzoglou: TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree. 111-119

Transcriptomes

• 
  Sun-Yuan Kung, Man-Wai Mak, Ilias Tagkopoulos: Multi-Metric and Multi-Substructure Biclustering Analysis for Gene Expression Data. 123-134
• 
  Anya Tsalenko, Roded Sharan, Hege Edvardsen, Vessela N. Kristensen, Anne-Lise Børresen-Dale, Amir Ben-Dor, Zohar Yakhini: Analysis of SNP-Expression Association Matrices. 135-143
• 
  Will Sheffler, Eli Upfal, John Sedivy, William Stafford Noble: A Learned Comparative Expression Measure for Affymetrix GeneChip DNA Microarrays. 144-154

Proteomics

• 
  Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner: Identification of Post-Translational Modifications via Blind Search of Mass-Spectra. 157-166
• 
  Changyu Shen, Lang Li, Jake Yue Chen: Discover True Association Rates in Multi-protein Complex Proteomics Data Sets. 167-174
• 
  Aaron A. Klammer, Christine C. Wu, Michael J. MacCoss, William Stafford Noble: Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra. 175-185

Structural Bioinformatics

• 
  Lincong Wang, Bruce Randall Donald: An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings. 189-202
• 
  Zhong Chen, Ying Xu: Multi-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins. 203-207
• 
  Peter M. Kasson, Mark M. Davis, Axel T. Brünger: Deformable Modeling for Improved Calculation of Molecular Velocities from Single-Particle Tracking. 208-211
• 
  Feng Gao, Mohammed Javeed Zaki: PSIST: Indexing Protein Structures Using Suffix Trees. 212-222
• 
  Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fangfang Pan, Liming Cai: Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes. 223-234
• 
  Lincong Wang, Ramgopal R. Mettu, Bruce Randall Donald: An Algebraic Geometry Approach to Protein Structure Determination from NMR Data. 235-246
• 
  Jinbo Xu, Feng Jiao, Bonnie Berger: A Tree-Decomposition Approach to Protein Structure Prediction. 247-256

Pathways and Networks

• 
  R. Nigam, S. Liang: A Pivoting Algorithm for Metabolic Networks in the Presence of Thermodynamic Constraints. 259-267
• 
  Pengjun Pei, Aidong Zhang: A Topological Measurement for Weighted Protein Interaction Network. 268-278
• 
  Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, G. Wesley Hatfield, Eric Mjolsness: Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes. 279-288
• 
  Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi: Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching. 289-298

Applied Bioinformatic

• 
  Tu Minh Phuong, Zhen Lin, Russ B. Altman: Choosing SNPs Using Feature Selection. 301-309
• 
  Haifeng Li, Keshu Zhang, Tao Jiang: Robust and Accurate Cancer Classification with Gene Expression Profiling. 310-321
• 
  Gabriela Alexe, Gyan Bhanot, Babu Venkataraghavan, Ramakrishna Ramaswamy, Jorge Lepre, Arnold J. Levine, Gustavo Stolovitzky: A Robust Meta-classification Strategy for Cancer Diagnosis from Gene Expression Data. 322-325

Data Mining and Ontology

• 
  Chengyong Yang, Erliang Zeng, Tao Li, Giri Narasimhan: Clustering Genes Using Gene Expression and Text Literature Data. 329-340
• 
  Susan L. Havre, Bobbie-Jo M. Webb-Robertson, Anuj R. Shah, Christian Posse, Banu Gopalan, Fred J. Brockman: Bioinformatic Insights from Metagenomics through Visualization. 341-350
• 
  Rui Mao, Weijia Xu, Smriti R. Ramakrishnan, Glen Nuckolls, Daniel P. Miranker: On Optimizing Distance-Based Similarity Search for Biological Databases. 351-361
• 
  Mohammed I. Rafiq, Martin J. O'Connor, Amar K. Das: Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases. 362-365
• 
  Nalini Polavarapu, Shamkant B. Navathe, Ramprasad Ramnarayanan, Abrar ul Haque, Saurav Sahay, Ying Liu: Investigation into Biomedical Literature Classification Using Support Vector Machines. 366-374

Miscellaneous

• 
  Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble: Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves. 377-385

Workshop Abstracts

• 
  Controlling Complexity.
• 
  BioImage Data Mining and Informatics.
• 
  BioSPICE and Use Cases.

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