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ORCID4. CSB 2005: Stanford, CA, USA
- Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2005, Stanford, CA, USA, August 8-11, 2005. IEEE Computer Society 2005, ISBN 0-7695-2344-7
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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