4. CSB 2005: Stanford, CA, USA

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 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.