Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 /
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| Meeting name: | Computational Systems Bioinformatics Conference (6th : 2007 : San Diego, Calif.) |
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| Imprint: | London : Imperial College Press ; Singapore ; Hackensack, NJ : Distributed by World Scientific, 2007. |
| Description: | 1 online resource (xvi, 454 pages) : illustrations |
| Language: | English |
| Series: | Series on advances in bioinformatics and computational biology Series on Advances in Bioinformatics and Computational Biology ; v.6 Series on advances in bioinformatics and computational biology. |
| Subject: | |
| Format: | E-Resource Book |
| URL for this record: | http://pi.lib.uchicago.edu/1001/cat/bib/11217773 |
Table of Contents:
- Preface; Committees; Referees; Keynote Address; Quantitative Aspects of Gene Regulation in Bacteria: Amplification. Threshold, and Combinatorial Control Terry Hwa; Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo Julia ZeitlingeK Rob Zinzen, Dmitri Papatsenko et al.; Invited Talks; Learning Predictive Models of Gene Regulation Christina Leslie; The Phylofacts Phylogenomic Encyclopedias: Structural Phylogenomic Analysis Across the Tree of Life Kimmen Golander; Mapping and Analysis of the Human Interactome Network Kavitha Venkatesan; 1. INTRODUCTION
- Gene-Centered Protein-DNA lnteractome Mapping A.J. Marian WalhoutProteomics; Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-S ymmetric Computational Model Kang Ning and Hon Wai Leong; 1. INTRODUCTION; Preprocessing to remove noisy peaks; The anti-symmetric problem; 2. ANALYSIS OF PROBLEMS AND CURRENT ALGORITHMS; 2.1. General Terminologies; 2.2. Datasets; 2.3. Problems Analysis; 3. NEW COMPUTATIONAL MODELS AND ALGORITHM; 3.1. Preprocessing to remove noisy peaks and introduce pseudo peaks; 3.2. The Anti-symmetric Problem
- 3.3. Novel Peptide Sequencing Algorithm4. EXPERIMENTS; 4.1. Experiment Settings; 4.2. Results; 5. CONCLUSIONS; References; Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination Wei Zheng, Xiaoduan Ye, Alan A4 Friedman and Chris Bailey-Kellogg; 1. INTRODUCTION; 2. METHODS; 2.1. Library Diversity; 2.2. Metrics for Breakpoint Selection; 2.3. Dynamic Programming for Breakpoint Selection; 3. RESULTS A N D DISCUSSION; 4. CONCLUSION; ACKNOWLEDGMENTS; References
- An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry Timothy Lee, Rahul Singh, Ten-Yang Yen and Bruce Macher1. INTRODUCTION; 1.1. Comparison of the Proposed Approach with Related Works; 2. THE PROPOSED METHOD; 2.1. Problem Formulation; 2.2. Algorithmic Framework; 2.2.1. Finding the MS spectrum match; 2.2.2. Finding the MS/MS spectrum match; 2.2.3. Finding a perfect matching of maximum weight for a fully connected graph; 2.2.4. Consideration of missed proteolytic cleavages and intra-molecular bonded cysteines
- 2.2.5. Peak finding in the presence of noise2.2.6. Addressing isotopic variation and neutral loss; 2.2.7. Interpretation of peaks given charge state uncertainty; 2.2.8. Overall complexity; 3. EXPERIMENTAL RESULTS; 3.1. Description of the Data and Experimental Procedures; 3.2. Summary of Results; 3.2.1. Analysis of the effect of varying threshold t on results; 3.2.2. Comparison with MS2Assign program; 4. CONCLUSIONS AND DISCUSSION; Acknowledgments; References; Biomedical Application; Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification Xiaoxu Hun; 1. INTRODUCTION