Biocomputing 2012 - Proceedings Of The Pacific Symposium.
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Place / Publishing House: | Singapore : : World Scientific Publishing Company,, 2011. ©2012. |
Year of Publication: | 2011 |
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Language: | English |
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Physical Description: | 1 online resource (455 pages) |
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Klein, Teri E. Biocomputing 2012 - Proceedings Of The Pacific Symposium. 1st ed. Singapore : World Scientific Publishing Company, 2011. ©2012. 1 online resource (455 pages) text txt rdacontent computer c rdamedia online resource cr rdacarrier Intro -- Contents -- Preface -- IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA -- Session Introduction Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, and Joel S. Bader -- Introduction -- Genetic interaction networks in model organisms -- Human data and local subnetworks -- Converging problems and challenges -- References -- SSLPred : Predicting Synthetic Sickness Lethality Nirmalya Bandyopadhyayy, Sanjay Ranka, and Tamer Kahveci -- 1. Introduction -- 2. Background -- 3. Methods -- 3.1. Problem Formulation and Notation -- 3.2. Between Pathway Conjectures -- 3.3. Regression based solution -- 4. Experiments -- 4.1. Datasets -- 4.2. Comparison with Hescott's Method -- 5. Conclusion -- References -- Predicting the Effects of Copy-Number Variation in Double and Triple Mutant Combinations Gregory W. Carter, Michelle Hays, Song Li, and Timothy Galitski -- 1. Introduction -- 2. Network Model Inference -- 2.1.1. Yeast Gene Expression Profiling -- 2.1.2. Singular Value Decomposition Analysis -- 2.1.3. Genetic Influences Decomposition -- 2.2. Predictions and Validation for a Multicopy Perturbation -- 2.2.1. Prediction for Multi-Copy Strains -- 2.2.2. Experimental Test of Predictions -- 3. Discussion and Conclusions -- 4. Supplementary Material -- 5. Acknowledgments -- References -- Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer Li Chen, Jianhua Xuan, Jinghua Gu, Yue Wang, Li Chen, Zhen Zhang, Tian-Li Wang, and Ie-Ming Shih -- 1. Introduction -- 2. Materials and method -- 2.1. Integrative framework -- 2.2. Data description -- 2.3. DNA copy number consensus region detection -- 2.4. Network identification by bootstrapping MRF (BMRF) -- 2.5. Network constrained support vector machines (NetSVM) -- 2.6. Classification performance merits and survival analysis -- 3. Results and discussion. 4. Conclusion -- 5. Acknowledgments -- References -- Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways Shahin Mohammadi, Giorgos Kollias, and Ananth Grama -- 1. Introduction -- 2. Methods -- 2.1. Notations -- 2.2. Performance of local methods for predicting functional similarity of gene pairs -- 2.3. Constructing the neighborhood overlap graph (NOG) -- 2.4. Identifying interaction ports and inferring cross-pathway dependencies -- 3. Results -- 3.1. Datasets -- 3.1.1. Genetic interaction network -- 3.1.2. Functional annotations -- 3.1.3. Availability -- 3.2. Similarity of genetic neighborhood as a predictor of functional similarity -- 3.3. Constructing KEGG crosstalk map -- 4. Discussion -- 5. Acknowledgments -- References -- Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer Fabio Vandin, Patrick Clay, Eli Upfal, and Benjamin J. Raphael -- 1. Introduction -- 2. Methods -- 2.1. Generalized HotNet -- 2.2. Adaptation to Clinical Data -- 2.2.1. Gene Scores -- 2.2.2. Selection of parameters t and -- 2.2.3. The Null Hypothesis Distribution -- 3. Results -- 3.1. Simulated data -- 3.2. Ovarian TCGA data -- 4. Discussion -- 5. Acknowledgements -- References -- INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION, SIMULATION, AND BIOLOGY -- Session Introduction Jianhan Chen, Jianlin Cheng, and A. Keith Dunker -- 1. Introduction -- 2. Papers in this Session -- Analysis of IDPs' function and evolution -- Simulation of IDPs' conformation -- Prediction of IDPs -- Acknowledgements -- Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanly, Pratul K. Agarwal, and Chakra S. Chennubhotla -- 1. Introduction -- 2. Approach -- 3. Molecular Simulations for NCBD. 4. dQAA: Quasi-anharmonic analysis in the dihedral angle space -- 5. Hierarchical clustering in the dQAA-space to identify meta-stable states -- 6. Intermediate states of ligand-free NCBD access ligand-bound conformations -- 7. Conclusions and Future Work -- References -- Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations Charles K. Fisher, Orly Ullman, and Collin M. Stultz -- 1. Introduction -- 2. Theory -- 2.1. Optimal Structure Selection -- 2.2. Variational Bayesian Weighting -- 2.3. Variational Bayes with Structure Selection -- 2.3. Approximate Confidence Intervals -- 3. Results and Discussion -- 3.1. Validation with Reference Ensembles -- 3.2. α-Synuclein Ensemble -- 4. Conclusions -- 5. Acknowledgements -- References -- Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein Jianjiong Gao and Dong Xu -- 1. Background -- 2. Results -- 2.1. Correlation of PTM sites and their predicted disorder scores -- 2.2. Correlation of PTM sites and their spatial fluctuations in NMR 3-D structures -- 2.3. Spatial fluctuation changes in 3-D structure due to PTM -- 3. Discussion -- Acknowledgments -- References -- Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors Xin Guo, Martha L. Bulyk, and Alexander J. Hartemink -- 1. Introduction -- 2. Materials and Methods -- 2.1. Constructing the TF and non-TF control sets of proteins -- 2.2. Comparing the TF and non-TF control sets of proteins -- 2.3. Identifying DNA-binding domains (DBDs) and their locations within proteins -- 2.4. Predicting intrinsically disordered regions (IDRs) and their locations within proteins using multiple existing methods -- 2.5. Defining disorder features: spatial relationships of IDRs relative to DBDs within TFs. 2.6. Calculating statistical significance of disorder features -- 3. Results -- 3.1. Comparing the three methods for predicting IDRs within proteins -- 3.2. Assessing significance of order or disorder within and anking human TF DBDs -- 3.3. Investigating detailed spatial relationships of IDRs relative to DBDs within TFs -- 3.4. Analyzing spatial relationships for some DBD classes prevalent in human TFs -- 3.4.1. Zinc ngers -- 3.4.2. Homeobox -- 3.4.3. HLH -- 4. Discussion -- 5. Acknowledgments -- References -- Intrinsic Protein Disorder and Protein-Protein Interactions Wei-Lun Hsu, Christopher Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 Disordered hub dataset -- 2.2 Functional consequences of MoRF (or ELM) binding -- 2.3 Binding to multiple partners, conservation at structure-matching sites -- 3. Discussion -- 4. Methods -- 4.1 Disordered hub dataset -- 4.2 Sequence and Structure analysis -- References -- Subclassifying Disordered Proteins by the CH-CDF Plot Method Fei Huang, Christopher Oldfield, Jingwei Meng, Wei-lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 CH-CDF plot -- 2.2 PDB coverage -- 2.3 Sequence window CH-CDF analysis -- 2.4 Match PDB coverage to disorder prediction -- 2.5 Function analysis for each quadrant -- 3. Discussion -- 3.1 Overview -- 3.2 Structural Partitioning by the CH-CDF plot -- 3.2 The rare protein quadrant (Q1) -- 3.3 Disorder subtypes and IDP functions -- 4. Methods -- 4.1 Protein data -- 4.2 PDB Coverage -- 4.2 GO term analysis -- References -- Coevolved Residues and the Functional Association for Intrinsically Disordered Protein Chan-Seok Jeong and Dongsup Kim -- 1. Introduction -- 2. Materials and methods -- 2.1. Data set. 2.2. Multiple sequence alignment construction -- 2.3. Coevolution estimation -- 2.4. Sequence conservation estimation -- 2.5. Disorder conservation estimation -- 2.6. Functional categories -- 3. Results -- 3.1. Distribution of coevolved residues for disordered proteins -- 3.2. Relationship between coevolution and functions -- 4. Discussion -- Acknowledgments -- References -- Cryptic Disorder: An Order-Disorder Transformation Regulates the Function of Nucleophosmin Diana M. Mitrea and Richard W. Kriwacki -- 1. Biological Function and Structural Features of Npm -- 2. Alteration of the electrostatic features of Npm-N through phosphorylation -- 3. In Silico site-directed mutagenesis -- 4. Probing for structural strain in Npm-N -- 5. Mechanistic insights on Npm's order-disorder polymorphism -- 6. Materials and Methods -- References -- Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, and Daron M Standley -- 1. Introduction Intrinsically disordered domains -- 2. Methodology -- 2.1. Preparation of IDD dataset -- 2.2. Similarity scores -- 2.2.1. Similarity score based on Euclidean distance -- 2.2.2. BLAST score -- 2.3. Pfam domain and Gene Ontology term prediction -- 2.4. Evaluation of function prediction -- 2.5. Web server -- 3. Results and Discussion -- 3.1 IDD Navigator Function prediction -- 3.2 Comparing different methods in IDD Navigator -- 3.3 Function prediction for IDD clusters -- 3.4 Case Studies -- 3.4.1 GRA15 from T. gondii -- 3.4.2 Cyclon from M. musculus -- 3.4.3 STIM1 from M. musculus -- 3.4.4 ROP16 from T. gondii -- 4. Conclusions -- 5. Acknowledgements -- References -- On the Complementarity of the Consensus-Based Disorder Prediction Zhenling Peng and Lukasz Kurgan -- 1. Introduction -- 2. Methods. 2.1. Considered disorder predictors. Description based on publisher supplied metadata and other sources. Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries. Electronic books. Jung, Tiffany A. Hunter, Lawrence. Dunker, A Keith. Altman, Russ B. Print version: Klein, Teri E Biocomputing 2012 - Proceedings Of The Pacific Symposium Singapore : World Scientific Publishing Company,c2011 9789814596374 ProQuest (Firm) https://ebookcentral.proquest.com/lib/oeawat/detail.action?docID=6383184 Click to View |
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Klein, Teri E. |
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Klein, Teri E. Biocomputing 2012 - Proceedings Of The Pacific Symposium. Intro -- Contents -- Preface -- IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA -- Session Introduction Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, and Joel S. Bader -- Introduction -- Genetic interaction networks in model organisms -- Human data and local subnetworks -- Converging problems and challenges -- References -- SSLPred : Predicting Synthetic Sickness Lethality Nirmalya Bandyopadhyayy, Sanjay Ranka, and Tamer Kahveci -- 1. Introduction -- 2. Background -- 3. Methods -- 3.1. Problem Formulation and Notation -- 3.2. Between Pathway Conjectures -- 3.3. Regression based solution -- 4. Experiments -- 4.1. Datasets -- 4.2. Comparison with Hescott's Method -- 5. Conclusion -- References -- Predicting the Effects of Copy-Number Variation in Double and Triple Mutant Combinations Gregory W. Carter, Michelle Hays, Song Li, and Timothy Galitski -- 1. Introduction -- 2. Network Model Inference -- 2.1.1. Yeast Gene Expression Profiling -- 2.1.2. Singular Value Decomposition Analysis -- 2.1.3. Genetic Influences Decomposition -- 2.2. Predictions and Validation for a Multicopy Perturbation -- 2.2.1. Prediction for Multi-Copy Strains -- 2.2.2. Experimental Test of Predictions -- 3. Discussion and Conclusions -- 4. Supplementary Material -- 5. Acknowledgments -- References -- Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer Li Chen, Jianhua Xuan, Jinghua Gu, Yue Wang, Li Chen, Zhen Zhang, Tian-Li Wang, and Ie-Ming Shih -- 1. Introduction -- 2. Materials and method -- 2.1. Integrative framework -- 2.2. Data description -- 2.3. DNA copy number consensus region detection -- 2.4. Network identification by bootstrapping MRF (BMRF) -- 2.5. Network constrained support vector machines (NetSVM) -- 2.6. Classification performance merits and survival analysis -- 3. Results and discussion. 4. Conclusion -- 5. Acknowledgments -- References -- Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways Shahin Mohammadi, Giorgos Kollias, and Ananth Grama -- 1. Introduction -- 2. Methods -- 2.1. Notations -- 2.2. Performance of local methods for predicting functional similarity of gene pairs -- 2.3. Constructing the neighborhood overlap graph (NOG) -- 2.4. Identifying interaction ports and inferring cross-pathway dependencies -- 3. Results -- 3.1. Datasets -- 3.1.1. Genetic interaction network -- 3.1.2. Functional annotations -- 3.1.3. Availability -- 3.2. Similarity of genetic neighborhood as a predictor of functional similarity -- 3.3. Constructing KEGG crosstalk map -- 4. Discussion -- 5. Acknowledgments -- References -- Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer Fabio Vandin, Patrick Clay, Eli Upfal, and Benjamin J. Raphael -- 1. Introduction -- 2. Methods -- 2.1. Generalized HotNet -- 2.2. Adaptation to Clinical Data -- 2.2.1. Gene Scores -- 2.2.2. Selection of parameters t and -- 2.2.3. The Null Hypothesis Distribution -- 3. Results -- 3.1. Simulated data -- 3.2. Ovarian TCGA data -- 4. Discussion -- 5. Acknowledgements -- References -- INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION, SIMULATION, AND BIOLOGY -- Session Introduction Jianhan Chen, Jianlin Cheng, and A. Keith Dunker -- 1. Introduction -- 2. Papers in this Session -- Analysis of IDPs' function and evolution -- Simulation of IDPs' conformation -- Prediction of IDPs -- Acknowledgements -- Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanly, Pratul K. Agarwal, and Chakra S. Chennubhotla -- 1. Introduction -- 2. Approach -- 3. Molecular Simulations for NCBD. 4. dQAA: Quasi-anharmonic analysis in the dihedral angle space -- 5. Hierarchical clustering in the dQAA-space to identify meta-stable states -- 6. Intermediate states of ligand-free NCBD access ligand-bound conformations -- 7. Conclusions and Future Work -- References -- Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations Charles K. Fisher, Orly Ullman, and Collin M. Stultz -- 1. Introduction -- 2. Theory -- 2.1. Optimal Structure Selection -- 2.2. Variational Bayesian Weighting -- 2.3. Variational Bayes with Structure Selection -- 2.3. Approximate Confidence Intervals -- 3. Results and Discussion -- 3.1. Validation with Reference Ensembles -- 3.2. α-Synuclein Ensemble -- 4. Conclusions -- 5. Acknowledgements -- References -- Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein Jianjiong Gao and Dong Xu -- 1. Background -- 2. Results -- 2.1. Correlation of PTM sites and their predicted disorder scores -- 2.2. Correlation of PTM sites and their spatial fluctuations in NMR 3-D structures -- 2.3. Spatial fluctuation changes in 3-D structure due to PTM -- 3. Discussion -- Acknowledgments -- References -- Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors Xin Guo, Martha L. Bulyk, and Alexander J. Hartemink -- 1. Introduction -- 2. Materials and Methods -- 2.1. Constructing the TF and non-TF control sets of proteins -- 2.2. Comparing the TF and non-TF control sets of proteins -- 2.3. Identifying DNA-binding domains (DBDs) and their locations within proteins -- 2.4. Predicting intrinsically disordered regions (IDRs) and their locations within proteins using multiple existing methods -- 2.5. Defining disorder features: spatial relationships of IDRs relative to DBDs within TFs. 2.6. Calculating statistical significance of disorder features -- 3. Results -- 3.1. Comparing the three methods for predicting IDRs within proteins -- 3.2. Assessing significance of order or disorder within and anking human TF DBDs -- 3.3. Investigating detailed spatial relationships of IDRs relative to DBDs within TFs -- 3.4. Analyzing spatial relationships for some DBD classes prevalent in human TFs -- 3.4.1. Zinc ngers -- 3.4.2. Homeobox -- 3.4.3. HLH -- 4. Discussion -- 5. Acknowledgments -- References -- Intrinsic Protein Disorder and Protein-Protein Interactions Wei-Lun Hsu, Christopher Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 Disordered hub dataset -- 2.2 Functional consequences of MoRF (or ELM) binding -- 2.3 Binding to multiple partners, conservation at structure-matching sites -- 3. Discussion -- 4. Methods -- 4.1 Disordered hub dataset -- 4.2 Sequence and Structure analysis -- References -- Subclassifying Disordered Proteins by the CH-CDF Plot Method Fei Huang, Christopher Oldfield, Jingwei Meng, Wei-lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 CH-CDF plot -- 2.2 PDB coverage -- 2.3 Sequence window CH-CDF analysis -- 2.4 Match PDB coverage to disorder prediction -- 2.5 Function analysis for each quadrant -- 3. Discussion -- 3.1 Overview -- 3.2 Structural Partitioning by the CH-CDF plot -- 3.2 The rare protein quadrant (Q1) -- 3.3 Disorder subtypes and IDP functions -- 4. Methods -- 4.1 Protein data -- 4.2 PDB Coverage -- 4.2 GO term analysis -- References -- Coevolved Residues and the Functional Association for Intrinsically Disordered Protein Chan-Seok Jeong and Dongsup Kim -- 1. Introduction -- 2. Materials and methods -- 2.1. Data set. 2.2. Multiple sequence alignment construction -- 2.3. Coevolution estimation -- 2.4. Sequence conservation estimation -- 2.5. Disorder conservation estimation -- 2.6. Functional categories -- 3. Results -- 3.1. Distribution of coevolved residues for disordered proteins -- 3.2. Relationship between coevolution and functions -- 4. Discussion -- Acknowledgments -- References -- Cryptic Disorder: An Order-Disorder Transformation Regulates the Function of Nucleophosmin Diana M. Mitrea and Richard W. Kriwacki -- 1. Biological Function and Structural Features of Npm -- 2. Alteration of the electrostatic features of Npm-N through phosphorylation -- 3. In Silico site-directed mutagenesis -- 4. Probing for structural strain in Npm-N -- 5. Mechanistic insights on Npm's order-disorder polymorphism -- 6. Materials and Methods -- References -- Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, and Daron M Standley -- 1. Introduction Intrinsically disordered domains -- 2. Methodology -- 2.1. Preparation of IDD dataset -- 2.2. Similarity scores -- 2.2.1. Similarity score based on Euclidean distance -- 2.2.2. BLAST score -- 2.3. Pfam domain and Gene Ontology term prediction -- 2.4. Evaluation of function prediction -- 2.5. Web server -- 3. Results and Discussion -- 3.1 IDD Navigator Function prediction -- 3.2 Comparing different methods in IDD Navigator -- 3.3 Function prediction for IDD clusters -- 3.4 Case Studies -- 3.4.1 GRA15 from T. gondii -- 3.4.2 Cyclon from M. musculus -- 3.4.3 STIM1 from M. musculus -- 3.4.4 ROP16 from T. gondii -- 4. Conclusions -- 5. Acknowledgements -- References -- On the Complementarity of the Consensus-Based Disorder Prediction Zhenling Peng and Lukasz Kurgan -- 1. Introduction -- 2. Methods. 2.1. Considered disorder predictors. |
author_facet |
Klein, Teri E. Jung, Tiffany A. Hunter, Lawrence. Dunker, A Keith. Altman, Russ B. |
author_variant |
t e k te tek |
author2 |
Jung, Tiffany A. Hunter, Lawrence. Dunker, A Keith. Altman, Russ B. |
author2_variant |
t a j ta taj l h lh a k d ak akd r b a rb rba |
author2_role |
TeilnehmendeR TeilnehmendeR TeilnehmendeR TeilnehmendeR |
author_sort |
Klein, Teri E. |
title |
Biocomputing 2012 - Proceedings Of The Pacific Symposium. |
title_full |
Biocomputing 2012 - Proceedings Of The Pacific Symposium. |
title_fullStr |
Biocomputing 2012 - Proceedings Of The Pacific Symposium. |
title_full_unstemmed |
Biocomputing 2012 - Proceedings Of The Pacific Symposium. |
title_auth |
Biocomputing 2012 - Proceedings Of The Pacific Symposium. |
title_new |
Biocomputing 2012 - Proceedings Of The Pacific Symposium. |
title_sort |
biocomputing 2012 - proceedings of the pacific symposium. |
publisher |
World Scientific Publishing Company, |
publishDate |
2011 |
physical |
1 online resource (455 pages) |
edition |
1st ed. |
contents |
Intro -- Contents -- Preface -- IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA -- Session Introduction Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, and Joel S. Bader -- Introduction -- Genetic interaction networks in model organisms -- Human data and local subnetworks -- Converging problems and challenges -- References -- SSLPred : Predicting Synthetic Sickness Lethality Nirmalya Bandyopadhyayy, Sanjay Ranka, and Tamer Kahveci -- 1. Introduction -- 2. Background -- 3. Methods -- 3.1. Problem Formulation and Notation -- 3.2. Between Pathway Conjectures -- 3.3. Regression based solution -- 4. Experiments -- 4.1. Datasets -- 4.2. Comparison with Hescott's Method -- 5. Conclusion -- References -- Predicting the Effects of Copy-Number Variation in Double and Triple Mutant Combinations Gregory W. Carter, Michelle Hays, Song Li, and Timothy Galitski -- 1. Introduction -- 2. Network Model Inference -- 2.1.1. Yeast Gene Expression Profiling -- 2.1.2. Singular Value Decomposition Analysis -- 2.1.3. Genetic Influences Decomposition -- 2.2. Predictions and Validation for a Multicopy Perturbation -- 2.2.1. Prediction for Multi-Copy Strains -- 2.2.2. Experimental Test of Predictions -- 3. Discussion and Conclusions -- 4. Supplementary Material -- 5. Acknowledgments -- References -- Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer Li Chen, Jianhua Xuan, Jinghua Gu, Yue Wang, Li Chen, Zhen Zhang, Tian-Li Wang, and Ie-Ming Shih -- 1. Introduction -- 2. Materials and method -- 2.1. Integrative framework -- 2.2. Data description -- 2.3. DNA copy number consensus region detection -- 2.4. Network identification by bootstrapping MRF (BMRF) -- 2.5. Network constrained support vector machines (NetSVM) -- 2.6. Classification performance merits and survival analysis -- 3. Results and discussion. 4. Conclusion -- 5. Acknowledgments -- References -- Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways Shahin Mohammadi, Giorgos Kollias, and Ananth Grama -- 1. Introduction -- 2. Methods -- 2.1. Notations -- 2.2. Performance of local methods for predicting functional similarity of gene pairs -- 2.3. Constructing the neighborhood overlap graph (NOG) -- 2.4. Identifying interaction ports and inferring cross-pathway dependencies -- 3. Results -- 3.1. Datasets -- 3.1.1. Genetic interaction network -- 3.1.2. Functional annotations -- 3.1.3. Availability -- 3.2. Similarity of genetic neighborhood as a predictor of functional similarity -- 3.3. Constructing KEGG crosstalk map -- 4. Discussion -- 5. Acknowledgments -- References -- Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer Fabio Vandin, Patrick Clay, Eli Upfal, and Benjamin J. Raphael -- 1. Introduction -- 2. Methods -- 2.1. Generalized HotNet -- 2.2. Adaptation to Clinical Data -- 2.2.1. Gene Scores -- 2.2.2. Selection of parameters t and -- 2.2.3. The Null Hypothesis Distribution -- 3. Results -- 3.1. Simulated data -- 3.2. Ovarian TCGA data -- 4. Discussion -- 5. Acknowledgements -- References -- INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION, SIMULATION, AND BIOLOGY -- Session Introduction Jianhan Chen, Jianlin Cheng, and A. Keith Dunker -- 1. Introduction -- 2. Papers in this Session -- Analysis of IDPs' function and evolution -- Simulation of IDPs' conformation -- Prediction of IDPs -- Acknowledgements -- Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanly, Pratul K. Agarwal, and Chakra S. Chennubhotla -- 1. Introduction -- 2. Approach -- 3. Molecular Simulations for NCBD. 4. dQAA: Quasi-anharmonic analysis in the dihedral angle space -- 5. Hierarchical clustering in the dQAA-space to identify meta-stable states -- 6. Intermediate states of ligand-free NCBD access ligand-bound conformations -- 7. Conclusions and Future Work -- References -- Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations Charles K. Fisher, Orly Ullman, and Collin M. Stultz -- 1. Introduction -- 2. Theory -- 2.1. Optimal Structure Selection -- 2.2. Variational Bayesian Weighting -- 2.3. Variational Bayes with Structure Selection -- 2.3. Approximate Confidence Intervals -- 3. Results and Discussion -- 3.1. Validation with Reference Ensembles -- 3.2. α-Synuclein Ensemble -- 4. Conclusions -- 5. Acknowledgements -- References -- Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein Jianjiong Gao and Dong Xu -- 1. Background -- 2. Results -- 2.1. Correlation of PTM sites and their predicted disorder scores -- 2.2. Correlation of PTM sites and their spatial fluctuations in NMR 3-D structures -- 2.3. Spatial fluctuation changes in 3-D structure due to PTM -- 3. Discussion -- Acknowledgments -- References -- Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors Xin Guo, Martha L. Bulyk, and Alexander J. Hartemink -- 1. Introduction -- 2. Materials and Methods -- 2.1. Constructing the TF and non-TF control sets of proteins -- 2.2. Comparing the TF and non-TF control sets of proteins -- 2.3. Identifying DNA-binding domains (DBDs) and their locations within proteins -- 2.4. Predicting intrinsically disordered regions (IDRs) and their locations within proteins using multiple existing methods -- 2.5. Defining disorder features: spatial relationships of IDRs relative to DBDs within TFs. 2.6. Calculating statistical significance of disorder features -- 3. Results -- 3.1. Comparing the three methods for predicting IDRs within proteins -- 3.2. Assessing significance of order or disorder within and anking human TF DBDs -- 3.3. Investigating detailed spatial relationships of IDRs relative to DBDs within TFs -- 3.4. Analyzing spatial relationships for some DBD classes prevalent in human TFs -- 3.4.1. Zinc ngers -- 3.4.2. Homeobox -- 3.4.3. HLH -- 4. Discussion -- 5. Acknowledgments -- References -- Intrinsic Protein Disorder and Protein-Protein Interactions Wei-Lun Hsu, Christopher Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 Disordered hub dataset -- 2.2 Functional consequences of MoRF (or ELM) binding -- 2.3 Binding to multiple partners, conservation at structure-matching sites -- 3. Discussion -- 4. Methods -- 4.1 Disordered hub dataset -- 4.2 Sequence and Structure analysis -- References -- Subclassifying Disordered Proteins by the CH-CDF Plot Method Fei Huang, Christopher Oldfield, Jingwei Meng, Wei-lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 CH-CDF plot -- 2.2 PDB coverage -- 2.3 Sequence window CH-CDF analysis -- 2.4 Match PDB coverage to disorder prediction -- 2.5 Function analysis for each quadrant -- 3. Discussion -- 3.1 Overview -- 3.2 Structural Partitioning by the CH-CDF plot -- 3.2 The rare protein quadrant (Q1) -- 3.3 Disorder subtypes and IDP functions -- 4. Methods -- 4.1 Protein data -- 4.2 PDB Coverage -- 4.2 GO term analysis -- References -- Coevolved Residues and the Functional Association for Intrinsically Disordered Protein Chan-Seok Jeong and Dongsup Kim -- 1. Introduction -- 2. Materials and methods -- 2.1. Data set. 2.2. Multiple sequence alignment construction -- 2.3. Coevolution estimation -- 2.4. Sequence conservation estimation -- 2.5. Disorder conservation estimation -- 2.6. Functional categories -- 3. Results -- 3.1. Distribution of coevolved residues for disordered proteins -- 3.2. Relationship between coevolution and functions -- 4. Discussion -- Acknowledgments -- References -- Cryptic Disorder: An Order-Disorder Transformation Regulates the Function of Nucleophosmin Diana M. Mitrea and Richard W. Kriwacki -- 1. Biological Function and Structural Features of Npm -- 2. Alteration of the electrostatic features of Npm-N through phosphorylation -- 3. In Silico site-directed mutagenesis -- 4. Probing for structural strain in Npm-N -- 5. Mechanistic insights on Npm's order-disorder polymorphism -- 6. Materials and Methods -- References -- Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, and Daron M Standley -- 1. Introduction Intrinsically disordered domains -- 2. Methodology -- 2.1. Preparation of IDD dataset -- 2.2. Similarity scores -- 2.2.1. Similarity score based on Euclidean distance -- 2.2.2. BLAST score -- 2.3. Pfam domain and Gene Ontology term prediction -- 2.4. Evaluation of function prediction -- 2.5. Web server -- 3. Results and Discussion -- 3.1 IDD Navigator Function prediction -- 3.2 Comparing different methods in IDD Navigator -- 3.3 Function prediction for IDD clusters -- 3.4 Case Studies -- 3.4.1 GRA15 from T. gondii -- 3.4.2 Cyclon from M. musculus -- 3.4.3 STIM1 from M. musculus -- 3.4.4 ROP16 from T. gondii -- 4. Conclusions -- 5. Acknowledgements -- References -- On the Complementarity of the Consensus-Based Disorder Prediction Zhenling Peng and Lukasz Kurgan -- 1. Introduction -- 2. Methods. 2.1. Considered disorder predictors. |
isbn |
9789814366496 9789814596374 |
genre |
Electronic books. |
genre_facet |
Electronic books. |
url |
https://ebookcentral.proquest.com/lib/oeawat/detail.action?docID=6383184 |
illustrated |
Not Illustrated |
oclc_num |
1117869453 |
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Biocomputing 2012 - Proceedings Of The Pacific Symposium. |
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<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>11025nam a22004693i 4500</leader><controlfield tag="001">5006383184</controlfield><controlfield tag="003">MiAaPQ</controlfield><controlfield tag="005">20240229073836.0</controlfield><controlfield tag="006">m o d | </controlfield><controlfield tag="007">cr cnu||||||||</controlfield><controlfield tag="008">240229s2011 xx o ||||0 eng d</controlfield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">9789814366496</subfield><subfield code="q">(electronic bk.)</subfield></datafield><datafield tag="020" ind1=" " ind2=" "><subfield code="z">9789814596374</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(MiAaPQ)5006383184</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(Au-PeEL)EBL6383184</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)1117869453</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">MiAaPQ</subfield><subfield code="b">eng</subfield><subfield code="e">rda</subfield><subfield code="e">pn</subfield><subfield code="c">MiAaPQ</subfield><subfield code="d">MiAaPQ</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Klein, Teri E.</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Biocomputing 2012 - Proceedings Of The Pacific Symposium.</subfield></datafield><datafield tag="250" ind1=" " ind2=" "><subfield code="a">1st ed.</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="a">Singapore :</subfield><subfield code="b">World Scientific Publishing Company,</subfield><subfield code="c">2011.</subfield></datafield><datafield tag="264" ind1=" " ind2="4"><subfield code="c">©2012.</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">1 online resource (455 pages)</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">computer</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">online resource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="505" ind1="0" ind2=" "><subfield code="a">Intro -- Contents -- Preface -- IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA -- Session Introduction Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, and Joel S. Bader -- Introduction -- Genetic interaction networks in model organisms -- Human data and local subnetworks -- Converging problems and challenges -- References -- SSLPred : Predicting Synthetic Sickness Lethality Nirmalya Bandyopadhyayy, Sanjay Ranka, and Tamer Kahveci -- 1. Introduction -- 2. Background -- 3. Methods -- 3.1. Problem Formulation and Notation -- 3.2. Between Pathway Conjectures -- 3.3. Regression based solution -- 4. Experiments -- 4.1. Datasets -- 4.2. Comparison with Hescott's Method -- 5. Conclusion -- References -- Predicting the Effects of Copy-Number Variation in Double and Triple Mutant Combinations Gregory W. Carter, Michelle Hays, Song Li, and Timothy Galitski -- 1. Introduction -- 2. Network Model Inference -- 2.1.1. Yeast Gene Expression Profiling -- 2.1.2. Singular Value Decomposition Analysis -- 2.1.3. Genetic Influences Decomposition -- 2.2. Predictions and Validation for a Multicopy Perturbation -- 2.2.1. Prediction for Multi-Copy Strains -- 2.2.2. Experimental Test of Predictions -- 3. Discussion and Conclusions -- 4. Supplementary Material -- 5. Acknowledgments -- References -- Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer Li Chen, Jianhua Xuan, Jinghua Gu, Yue Wang, Li Chen, Zhen Zhang, Tian-Li Wang, and Ie-Ming Shih -- 1. Introduction -- 2. Materials and method -- 2.1. Integrative framework -- 2.2. Data description -- 2.3. DNA copy number consensus region detection -- 2.4. Network identification by bootstrapping MRF (BMRF) -- 2.5. Network constrained support vector machines (NetSVM) -- 2.6. Classification performance merits and survival analysis -- 3. Results and discussion.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">4. Conclusion -- 5. Acknowledgments -- References -- Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways Shahin Mohammadi, Giorgos Kollias, and Ananth Grama -- 1. Introduction -- 2. Methods -- 2.1. Notations -- 2.2. Performance of local methods for predicting functional similarity of gene pairs -- 2.3. Constructing the neighborhood overlap graph (NOG) -- 2.4. Identifying interaction ports and inferring cross-pathway dependencies -- 3. Results -- 3.1. Datasets -- 3.1.1. Genetic interaction network -- 3.1.2. Functional annotations -- 3.1.3. Availability -- 3.2. Similarity of genetic neighborhood as a predictor of functional similarity -- 3.3. Constructing KEGG crosstalk map -- 4. Discussion -- 5. Acknowledgments -- References -- Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer Fabio Vandin, Patrick Clay, Eli Upfal, and Benjamin J. Raphael -- 1. Introduction -- 2. Methods -- 2.1. Generalized HotNet -- 2.2. Adaptation to Clinical Data -- 2.2.1. Gene Scores -- 2.2.2. Selection of parameters t and -- 2.2.3. The Null Hypothesis Distribution -- 3. Results -- 3.1. Simulated data -- 3.2. Ovarian TCGA data -- 4. Discussion -- 5. Acknowledgements -- References -- INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION, SIMULATION, AND BIOLOGY -- Session Introduction Jianhan Chen, Jianlin Cheng, and A. Keith Dunker -- 1. Introduction -- 2. Papers in this Session -- Analysis of IDPs' function and evolution -- Simulation of IDPs' conformation -- Prediction of IDPs -- Acknowledgements -- Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanly, Pratul K. Agarwal, and Chakra S. Chennubhotla -- 1. Introduction -- 2. Approach -- 3. Molecular Simulations for NCBD.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">4. dQAA: Quasi-anharmonic analysis in the dihedral angle space -- 5. Hierarchical clustering in the dQAA-space to identify meta-stable states -- 6. Intermediate states of ligand-free NCBD access ligand-bound conformations -- 7. Conclusions and Future Work -- References -- Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations Charles K. Fisher, Orly Ullman, and Collin M. Stultz -- 1. Introduction -- 2. Theory -- 2.1. Optimal Structure Selection -- 2.2. Variational Bayesian Weighting -- 2.3. Variational Bayes with Structure Selection -- 2.3. Approximate Confidence Intervals -- 3. Results and Discussion -- 3.1. Validation with Reference Ensembles -- 3.2. α-Synuclein Ensemble -- 4. Conclusions -- 5. Acknowledgements -- References -- Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein Jianjiong Gao and Dong Xu -- 1. Background -- 2. Results -- 2.1. Correlation of PTM sites and their predicted disorder scores -- 2.2. Correlation of PTM sites and their spatial fluctuations in NMR 3-D structures -- 2.3. Spatial fluctuation changes in 3-D structure due to PTM -- 3. Discussion -- Acknowledgments -- References -- Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors Xin Guo, Martha L. Bulyk, and Alexander J. Hartemink -- 1. Introduction -- 2. Materials and Methods -- 2.1. Constructing the TF and non-TF control sets of proteins -- 2.2. Comparing the TF and non-TF control sets of proteins -- 2.3. Identifying DNA-binding domains (DBDs) and their locations within proteins -- 2.4. Predicting intrinsically disordered regions (IDRs) and their locations within proteins using multiple existing methods -- 2.5. Defining disorder features: spatial relationships of IDRs relative to DBDs within TFs.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">2.6. Calculating statistical significance of disorder features -- 3. Results -- 3.1. Comparing the three methods for predicting IDRs within proteins -- 3.2. Assessing significance of order or disorder within and anking human TF DBDs -- 3.3. Investigating detailed spatial relationships of IDRs relative to DBDs within TFs -- 3.4. Analyzing spatial relationships for some DBD classes prevalent in human TFs -- 3.4.1. Zinc ngers -- 3.4.2. Homeobox -- 3.4.3. HLH -- 4. Discussion -- 5. Acknowledgments -- References -- Intrinsic Protein Disorder and Protein-Protein Interactions Wei-Lun Hsu, Christopher Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 Disordered hub dataset -- 2.2 Functional consequences of MoRF (or ELM) binding -- 2.3 Binding to multiple partners, conservation at structure-matching sites -- 3. Discussion -- 4. Methods -- 4.1 Disordered hub dataset -- 4.2 Sequence and Structure analysis -- References -- Subclassifying Disordered Proteins by the CH-CDF Plot Method Fei Huang, Christopher Oldfield, Jingwei Meng, Wei-lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A. Keith Dunker -- 1. Introduction -- 2. Results -- 2.1 CH-CDF plot -- 2.2 PDB coverage -- 2.3 Sequence window CH-CDF analysis -- 2.4 Match PDB coverage to disorder prediction -- 2.5 Function analysis for each quadrant -- 3. Discussion -- 3.1 Overview -- 3.2 Structural Partitioning by the CH-CDF plot -- 3.2 The rare protein quadrant (Q1) -- 3.3 Disorder subtypes and IDP functions -- 4. Methods -- 4.1 Protein data -- 4.2 PDB Coverage -- 4.2 GO term analysis -- References -- Coevolved Residues and the Functional Association for Intrinsically Disordered Protein Chan-Seok Jeong and Dongsup Kim -- 1. Introduction -- 2. Materials and methods -- 2.1. Data set.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">2.2. Multiple sequence alignment construction -- 2.3. Coevolution estimation -- 2.4. Sequence conservation estimation -- 2.5. Disorder conservation estimation -- 2.6. Functional categories -- 3. Results -- 3.1. Distribution of coevolved residues for disordered proteins -- 3.2. Relationship between coevolution and functions -- 4. Discussion -- Acknowledgments -- References -- Cryptic Disorder: An Order-Disorder Transformation Regulates the Function of Nucleophosmin Diana M. Mitrea and Richard W. Kriwacki -- 1. Biological Function and Structural Features of Npm -- 2. Alteration of the electrostatic features of Npm-N through phosphorylation -- 3. In Silico site-directed mutagenesis -- 4. Probing for structural strain in Npm-N -- 5. Mechanistic insights on Npm's order-disorder polymorphism -- 6. Materials and Methods -- References -- Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, and Daron M Standley -- 1. Introduction Intrinsically disordered domains -- 2. Methodology -- 2.1. Preparation of IDD dataset -- 2.2. Similarity scores -- 2.2.1. Similarity score based on Euclidean distance -- 2.2.2. BLAST score -- 2.3. Pfam domain and Gene Ontology term prediction -- 2.4. Evaluation of function prediction -- 2.5. Web server -- 3. Results and Discussion -- 3.1 IDD Navigator Function prediction -- 3.2 Comparing different methods in IDD Navigator -- 3.3 Function prediction for IDD clusters -- 3.4 Case Studies -- 3.4.1 GRA15 from T. gondii -- 3.4.2 Cyclon from M. musculus -- 3.4.3 STIM1 from M. musculus -- 3.4.4 ROP16 from T. gondii -- 4. Conclusions -- 5. Acknowledgements -- References -- On the Complementarity of the Consensus-Based Disorder Prediction Zhenling Peng and Lukasz Kurgan -- 1. Introduction -- 2. Methods.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">2.1. Considered disorder predictors.</subfield></datafield><datafield tag="588" ind1=" " ind2=" "><subfield code="a">Description based on publisher supplied metadata and other sources.</subfield></datafield><datafield tag="590" ind1=" " ind2=" "><subfield code="a">Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries. </subfield></datafield><datafield tag="655" ind1=" " ind2="4"><subfield code="a">Electronic books.</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Jung, Tiffany A.</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Hunter, Lawrence.</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Dunker, A Keith.</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Altman, Russ B.</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Print version:</subfield><subfield code="a">Klein, Teri E</subfield><subfield code="t">Biocomputing 2012 - Proceedings Of The Pacific Symposium</subfield><subfield code="d">Singapore : World Scientific Publishing Company,c2011</subfield><subfield code="z">9789814596374</subfield></datafield><datafield tag="797" ind1="2" ind2=" "><subfield code="a">ProQuest (Firm)</subfield></datafield><datafield tag="856" ind1="4" ind2="0"><subfield code="u">https://ebookcentral.proquest.com/lib/oeawat/detail.action?docID=6383184</subfield><subfield code="z">Click to View</subfield></datafield></record></collection> |