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Evolutionary computation in gene regulatory network research / / edited by Hitoshi Iba, Nasimul Noman ; contributors, Tatsuya Akutsu [and thirty others]
| Evolutionary computation in gene regulatory network research / / edited by Hitoshi Iba, Nasimul Noman ; contributors, Tatsuya Akutsu [and thirty others] |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : Wiley, , 2016 |
| Descrizione fisica | 1 online resource (462 pages) |
| Disciplina | 572.8650113 |
| Collana |
Wiley Series in Bioinformatics: Computational Techniques and Engineering
THEi Wiley ebooks. |
| Soggetto topico |
Genetic regulation - Mathematical models
Gene regulatory networks - Computer simulation Genetic algorithms Evolutionary computation |
| ISBN |
1-119-07978-0
1-119-07977-2 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910137485303321 |
| Hoboken, New Jersey : , : Wiley, , 2016 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Evolutionary computation in gene regulatory network research / / edited by Hitoshi Iba, Nasimul Noman ; contributors, Tatsuya Akutsu [and thirty others]
| Evolutionary computation in gene regulatory network research / / edited by Hitoshi Iba, Nasimul Noman ; contributors, Tatsuya Akutsu [and thirty others] |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : Wiley, , 2016 |
| Descrizione fisica | 1 online resource (462 pages) |
| Disciplina | 572.8650113 |
| Collana |
Wiley Series in Bioinformatics: Computational Techniques and Engineering
THEi Wiley ebooks. |
| Soggetto topico |
Genetic regulation - Mathematical models
Gene regulatory networks - Computer simulation Genetic algorithms Evolutionary computation |
| ISBN |
1-119-07978-0
1-119-07977-2 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910818177103321 |
| Hoboken, New Jersey : , : Wiley, , 2016 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Genome informatics 2010 [[electronic resource] ] : the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) : Kyoto University, Japan, 26-28 July 2010 / / editors, Tatsuya Akutsu ... [et al.]
| Genome informatics 2010 [[electronic resource] ] : the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) : Kyoto University, Japan, 26-28 July 2010 / / editors, Tatsuya Akutsu ... [et al.] |
| Pubbl/distr/stampa | London, : Imperial College Press, c2010 |
| Descrizione fisica | 1 online resource (280 p.) |
| Disciplina |
572.80285
572.86 |
| Altri autori (Persone) | AkutsuTatsuya <1962-> |
| Collana | Genome informatics series |
| Soggetto topico |
Genomics - Data processing
Genomics Bioinformatics Biological systems |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-283-14348-8
9786613143488 1-84816-658-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
CONTENTS; PREFACE; PROGRAM COMMITTEE; KINETIC MODELLING OF DNA REPLICATION INITIATION IN BUDDING YEAST; 1. Introduction; 2. ODE Model of the DNA Replication Initiation; 2.1. Model Construction; 2.2. Deriving Parameters from Experimental Data; 2.3. Fitting Parameters to Experimental Data; 3. Results; 3.1. Simulation Results and Network Properties; 3.2. DNA Replication Mutants; 4. Discussion; 5. Conclusion; Acknowledgments; Appendix A.; Appendix A.1. Detailed Description of the Replisome Activation; Appendix A.1.1. Assembly of the Pre-RC
Appendix A.1.2. Assembly of the Pre-IC and Replisome Activation References; PREDICTING PROTEIN COMPLEX GEOMETRIES WITH LINEAR SCORING FUNCTIONS; 1. Introduction; 2. Methods; 2.1. Database of protein complexes and decoys; 2.2. Linear scoring function; 3. Results and Discussion; 3.1. Performance comparison; 4. Conclusions; Acknowledgments; References; CHARACTERIZING COMMON SUBSTRUCTURES OF LIGANDS FOR GPCR PROTEIN SUBFAMILIES; 1. Introduction; 2. Methods; 2.1. Dataset; 2.2. Chemical structure comparison; 2.3. Extracting common substructures; 3. Results; 4. Discussion; Acknowledgments; References A SYSTEMS BIOLOGY APPROACH: MODELLING OF AQUAPORIN-2 TRAFFICKING 1. Introduction; 1.1. Biological background; 1.2. Existing models; 1.3. Aims; 2. Methods; 2.1. Time course simulation, parameter estimation and time-dependent sensitivity analysis; 2.2. Cell surface biotinylation; 3. Results; 3.1. The model; 3.2. Time course simulation and parameter estimation; 3.3. Model variations and ranking; 3.4. Time-dependent sensitivity analysis; 3.5. Experiment: AQP2 transloeation after dDAVP stimulation; 3.6. Model predictions, analysis, and comparison with recent data; 4. Discussion; Acknowledgements References COMPARISON OF GENE EXPRESSION PROFILES PRODUCED BY CAGE, ILLUMINA MICRO-ARRAY AND REAL TIME RT-PCR; 1. Introduction; 2. Materials and Methods; 2.1. CAGE data summary; 2.2. Qualitative comparison between CAGE, illumina microarray and qRT-PCR; 2.3. Correlation analysis; 3. Results and Discussions; 3.1. Qualitative analysis; 3.2. Quantitative analysis; 4. Conclusions; Acknowledgements; References; ON THE PERFORMANCE OF METHODS FOR FINDING A SWITCHING MECHANISM IN GENE EXPRESSION; 1. Introduction; 2. Method; 2.1. Notations and preliminaries 2.2. Fast finding three-way gene interaction (FTGI)2.2.1. Logistic regression; 2.2.2. Log-likelihood test; 2.2.3. Mean-Co-variance (MC) test; 2.2.4. Procedure of FTGI; 2.3. The difference of correlation coefficients; 2.3.1. Pearson correlation coefficient; 2.3.2. Spearman correlation coefficient; 2.3.3. Biweight midcorrelation; 3. Experimental Result; 3.1. Data; 3.2. Computation time; 3.3. Top ranked gene combinations; 4. Discussion; Acknowledgements; References; GENE REGULATORY NETWORK CLUSTERING FOR GRAPH LAYOUT BASED ON MICROARRAY GENE EXPRESSION DATA; 1. Introduction; 2. Methods 2.1. Model setting |
| Record Nr. | UNINA-9910464062703321 |
| London, : Imperial College Press, c2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Genome informatics 2010 [[electronic resource] ] : the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) : Kyoto University, Japan, 26-28 July 2010 / / editors, Tatsuya Akutsu ... [et al.]
| Genome informatics 2010 [[electronic resource] ] : the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) : Kyoto University, Japan, 26-28 July 2010 / / editors, Tatsuya Akutsu ... [et al.] |
| Pubbl/distr/stampa | London, : Imperial College Press, c2010 |
| Descrizione fisica | 1 online resource (280 p.) |
| Disciplina |
572.80285
572.86 |
| Altri autori (Persone) | AkutsuTatsuya <1962-> |
| Collana | Genome informatics series |
| Soggetto topico |
Genomics - Data processing
Genomics Bioinformatics Biological systems |
| ISBN |
1-283-14348-8
9786613143488 1-84816-658-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
CONTENTS; PREFACE; PROGRAM COMMITTEE; KINETIC MODELLING OF DNA REPLICATION INITIATION IN BUDDING YEAST; 1. Introduction; 2. ODE Model of the DNA Replication Initiation; 2.1. Model Construction; 2.2. Deriving Parameters from Experimental Data; 2.3. Fitting Parameters to Experimental Data; 3. Results; 3.1. Simulation Results and Network Properties; 3.2. DNA Replication Mutants; 4. Discussion; 5. Conclusion; Acknowledgments; Appendix A.; Appendix A.1. Detailed Description of the Replisome Activation; Appendix A.1.1. Assembly of the Pre-RC
Appendix A.1.2. Assembly of the Pre-IC and Replisome Activation References; PREDICTING PROTEIN COMPLEX GEOMETRIES WITH LINEAR SCORING FUNCTIONS; 1. Introduction; 2. Methods; 2.1. Database of protein complexes and decoys; 2.2. Linear scoring function; 3. Results and Discussion; 3.1. Performance comparison; 4. Conclusions; Acknowledgments; References; CHARACTERIZING COMMON SUBSTRUCTURES OF LIGANDS FOR GPCR PROTEIN SUBFAMILIES; 1. Introduction; 2. Methods; 2.1. Dataset; 2.2. Chemical structure comparison; 2.3. Extracting common substructures; 3. Results; 4. Discussion; Acknowledgments; References A SYSTEMS BIOLOGY APPROACH: MODELLING OF AQUAPORIN-2 TRAFFICKING 1. Introduction; 1.1. Biological background; 1.2. Existing models; 1.3. Aims; 2. Methods; 2.1. Time course simulation, parameter estimation and time-dependent sensitivity analysis; 2.2. Cell surface biotinylation; 3. Results; 3.1. The model; 3.2. Time course simulation and parameter estimation; 3.3. Model variations and ranking; 3.4. Time-dependent sensitivity analysis; 3.5. Experiment: AQP2 transloeation after dDAVP stimulation; 3.6. Model predictions, analysis, and comparison with recent data; 4. Discussion; Acknowledgements References COMPARISON OF GENE EXPRESSION PROFILES PRODUCED BY CAGE, ILLUMINA MICRO-ARRAY AND REAL TIME RT-PCR; 1. Introduction; 2. Materials and Methods; 2.1. CAGE data summary; 2.2. Qualitative comparison between CAGE, illumina microarray and qRT-PCR; 2.3. Correlation analysis; 3. Results and Discussions; 3.1. Qualitative analysis; 3.2. Quantitative analysis; 4. Conclusions; Acknowledgements; References; ON THE PERFORMANCE OF METHODS FOR FINDING A SWITCHING MECHANISM IN GENE EXPRESSION; 1. Introduction; 2. Method; 2.1. Notations and preliminaries 2.2. Fast finding three-way gene interaction (FTGI)2.2.1. Logistic regression; 2.2.2. Log-likelihood test; 2.2.3. Mean-Co-variance (MC) test; 2.2.4. Procedure of FTGI; 2.3. The difference of correlation coefficients; 2.3.1. Pearson correlation coefficient; 2.3.2. Spearman correlation coefficient; 2.3.3. Biweight midcorrelation; 3. Experimental Result; 3.1. Data; 3.2. Computation time; 3.3. Top ranked gene combinations; 4. Discussion; Acknowledgements; References; GENE REGULATORY NETWORK CLUSTERING FOR GRAPH LAYOUT BASED ON MICROARRAY GENE EXPRESSION DATA; 1. Introduction; 2. Methods 2.1. Model setting |
| Record Nr. | UNINA-9910788467003321 |
| London, : Imperial College Press, c2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Genome informatics 2010 : the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) : Kyoto University, Japan, 26-28 July 2010 / / editors, Tatsuya Akutsu ... [et al.]
| Genome informatics 2010 : the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) : Kyoto University, Japan, 26-28 July 2010 / / editors, Tatsuya Akutsu ... [et al.] |
| Edizione | [1st ed.] |
| Pubbl/distr/stampa | London, : Imperial College Press, c2010 |
| Descrizione fisica | 1 online resource (280 p.) |
| Disciplina |
572.80285
572.86 |
| Altri autori (Persone) | AkutsuTatsuya <1962-> |
| Collana | Genome informatics series |
| Soggetto topico |
Genomics - Data processing
Genomics Bioinformatics Biological systems |
| ISBN |
1-283-14348-8
9786613143488 1-84816-658-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
CONTENTS; PREFACE; PROGRAM COMMITTEE; KINETIC MODELLING OF DNA REPLICATION INITIATION IN BUDDING YEAST; 1. Introduction; 2. ODE Model of the DNA Replication Initiation; 2.1. Model Construction; 2.2. Deriving Parameters from Experimental Data; 2.3. Fitting Parameters to Experimental Data; 3. Results; 3.1. Simulation Results and Network Properties; 3.2. DNA Replication Mutants; 4. Discussion; 5. Conclusion; Acknowledgments; Appendix A.; Appendix A.1. Detailed Description of the Replisome Activation; Appendix A.1.1. Assembly of the Pre-RC
Appendix A.1.2. Assembly of the Pre-IC and Replisome Activation References; PREDICTING PROTEIN COMPLEX GEOMETRIES WITH LINEAR SCORING FUNCTIONS; 1. Introduction; 2. Methods; 2.1. Database of protein complexes and decoys; 2.2. Linear scoring function; 3. Results and Discussion; 3.1. Performance comparison; 4. Conclusions; Acknowledgments; References; CHARACTERIZING COMMON SUBSTRUCTURES OF LIGANDS FOR GPCR PROTEIN SUBFAMILIES; 1. Introduction; 2. Methods; 2.1. Dataset; 2.2. Chemical structure comparison; 2.3. Extracting common substructures; 3. Results; 4. Discussion; Acknowledgments; References A SYSTEMS BIOLOGY APPROACH: MODELLING OF AQUAPORIN-2 TRAFFICKING 1. Introduction; 1.1. Biological background; 1.2. Existing models; 1.3. Aims; 2. Methods; 2.1. Time course simulation, parameter estimation and time-dependent sensitivity analysis; 2.2. Cell surface biotinylation; 3. Results; 3.1. The model; 3.2. Time course simulation and parameter estimation; 3.3. Model variations and ranking; 3.4. Time-dependent sensitivity analysis; 3.5. Experiment: AQP2 transloeation after dDAVP stimulation; 3.6. Model predictions, analysis, and comparison with recent data; 4. Discussion; Acknowledgements References COMPARISON OF GENE EXPRESSION PROFILES PRODUCED BY CAGE, ILLUMINA MICRO-ARRAY AND REAL TIME RT-PCR; 1. Introduction; 2. Materials and Methods; 2.1. CAGE data summary; 2.2. Qualitative comparison between CAGE, illumina microarray and qRT-PCR; 2.3. Correlation analysis; 3. Results and Discussions; 3.1. Qualitative analysis; 3.2. Quantitative analysis; 4. Conclusions; Acknowledgements; References; ON THE PERFORMANCE OF METHODS FOR FINDING A SWITCHING MECHANISM IN GENE EXPRESSION; 1. Introduction; 2. Method; 2.1. Notations and preliminaries 2.2. Fast finding three-way gene interaction (FTGI)2.2.1. Logistic regression; 2.2.2. Log-likelihood test; 2.2.3. Mean-Co-variance (MC) test; 2.2.4. Procedure of FTGI; 2.3. The difference of correlation coefficients; 2.3.1. Pearson correlation coefficient; 2.3.2. Spearman correlation coefficient; 2.3.3. Biweight midcorrelation; 3. Experimental Result; 3.1. Data; 3.2. Computation time; 3.3. Top ranked gene combinations; 4. Discussion; Acknowledgements; References; GENE REGULATORY NETWORK CLUSTERING FOR GRAPH LAYOUT BASED ON MICROARRAY GENE EXPRESSION DATA; 1. Introduction; 2. Methods 2.1. Model setting |
| Record Nr. | UNINA-9910810161203321 |
| London, : Imperial College Press, c2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Proceedings of the 6th Asia-Pacific Bioinformatics Conference [[electronic resource] ] : Kyoto, Japan, 14-17 January 2008 / / editors, Alvis Brazma, Satoru Miyano, Tatsuya Akutsu
| Proceedings of the 6th Asia-Pacific Bioinformatics Conference [[electronic resource] ] : Kyoto, Japan, 14-17 January 2008 / / editors, Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| Pubbl/distr/stampa | London, : Imperial College Press |
| Descrizione fisica | 1 online resource (413 p.) |
| Disciplina | 572.8633 |
| Altri autori (Persone) |
AkutsuTatsuya <1962->
BrazmaAlvis MiyanoSatoru |
| Collana | Series on advances in bioinformatics and computational biology |
| Soggetto topico |
Bioinformatics
Biology - Data processing |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-281-86579-6
9786611865795 1-84816-109-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
CONTENTS; Preface; APBC 2008 Organization; Program Committee; Additional Reviewers; Keynote Papers; Recent Progress in Phylogenetic Combinatorics Andreas Dress; 1. Background; 2. Discussion; References; KEGG for Medical and Pharmaceutical Applications Minoru Kanehisa; Protein Interactions Extracted from Genomes and Papers Alfonso Valencia; Contributed Papers; String Kernels with Feature Selection for SVM Protein Classification Wen-Yun Yang and Bao-Liang Lu; 1. Introduction; 2. A string kernel framework; 2.1. Notations; 2.2. Pramework definition; 2.3. Relations with existing string kernels
3. Efficient computation3.1. Tree data structure with leaf links; 3.2. Leaf traversal algorithm; 4. Selecting feature groups and weights; 4.1. Reduction of spectrum string kernel; 4.2. Statistically selecting feature groups; 5. Experiment; 6. Discussion and future work; Acknowledgments; References; Predicting Nucleolar Proteins Using Support-Vector Machines Mikael Bod&.; 1. Introduction; 2. Background; 3. Methods; 3.1. Data set; 3.2. Model; 4. Results; 5 . Conclusion; Acknowledgments; References Supervised Ensembles of Prediction Methods for Subcellular Localization Johannes Apfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei and Arthur Zimek1. Introduction; 2. Survey on Prominent Prediction Methods for Subcellular Localization; 2.1. Amino Acid Composition; 2.2. Sorting Signals; 2.3. Homology; 2.4. Hybrid Methods; 3. Ensemble Methods; 3.1. Theory; 3.2. Selection of Base Methods for Ensembles; 3.3. Ensemble Method Based on a Voting Schema; 3.4. Ensemble Method Based on Decision Trees; 4. Evaluation; 5. Conclusions; References Chemical Compound Classification with Automatically Mined Structure Patterns Aaron M. Smalter, J. Huan and Gerald H. Lushington1. Introduction; 2. Related Work; 2.1. Marginalized and Optimal Assignment Graph Kernels; 2.2. Frequent Subgraph Mining; 3. Background; 3.1. Chemical Structure; 4. Algorithm Design; 4.1. Structure Pattern Mining; 4.2. Optimal Assignment Kernel; 4.3. Reduced Graph Representation; 4.4. Pattern-based Descriptors; 5. Experimental Study; 5.1. Data Sets; 5.2. Methods; 5.3. Results; 6. Conclusions; Acknowledgments; References Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers Alireza Hadj Khodabakhshi, Jdn Mariuch, Arash Rafiey and Arvind Gupta1. Introduction; 2. Definitions; 2.1. Hydropho bic-polar- c ysteine (HP C) model; 2.2. Snake structures; 2.3. The strong HPC model; 3. Proof techniques; 3.1. Saturated folds; 3.2. 2DHPSolver: a semi-automatic prover; 4. Stability of the snake structures; 5. Conclusions; References; Discrimination of Native Folds Using Network Properties of Protein Structures Alper Kiiciikural, 0. Ug'ur Sezerman and Aytiil Ercal; 1 Introduction 2 Methods |
| Record Nr. | UNINA-9910458498403321 |
| London, : Imperial College Press | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Proceedings of the 6th Asia-Pacific Bioinformatics Conference [[electronic resource] ] : Kyoto, Japan, 14-17 January 2008 / / editors, Alvis Brazma, Satoru Miyano, Tatsuya Akutsu
| Proceedings of the 6th Asia-Pacific Bioinformatics Conference [[electronic resource] ] : Kyoto, Japan, 14-17 January 2008 / / editors, Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| Pubbl/distr/stampa | London, : Imperial College Press |
| Descrizione fisica | 1 online resource (413 p.) |
| Disciplina | 572.8633 |
| Altri autori (Persone) |
AkutsuTatsuya <1962->
BrazmaAlvis MiyanoSatoru |
| Collana | Series on advances in bioinformatics and computational biology |
| Soggetto topico |
Bioinformatics
Biology - Data processing |
| ISBN |
1-281-86579-6
9786611865795 1-84816-109-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
CONTENTS; Preface; APBC 2008 Organization; Program Committee; Additional Reviewers; Keynote Papers; Recent Progress in Phylogenetic Combinatorics Andreas Dress; 1. Background; 2. Discussion; References; KEGG for Medical and Pharmaceutical Applications Minoru Kanehisa; Protein Interactions Extracted from Genomes and Papers Alfonso Valencia; Contributed Papers; String Kernels with Feature Selection for SVM Protein Classification Wen-Yun Yang and Bao-Liang Lu; 1. Introduction; 2. A string kernel framework; 2.1. Notations; 2.2. Pramework definition; 2.3. Relations with existing string kernels
3. Efficient computation3.1. Tree data structure with leaf links; 3.2. Leaf traversal algorithm; 4. Selecting feature groups and weights; 4.1. Reduction of spectrum string kernel; 4.2. Statistically selecting feature groups; 5. Experiment; 6. Discussion and future work; Acknowledgments; References; Predicting Nucleolar Proteins Using Support-Vector Machines Mikael Bod&.; 1. Introduction; 2. Background; 3. Methods; 3.1. Data set; 3.2. Model; 4. Results; 5 . Conclusion; Acknowledgments; References Supervised Ensembles of Prediction Methods for Subcellular Localization Johannes Apfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei and Arthur Zimek1. Introduction; 2. Survey on Prominent Prediction Methods for Subcellular Localization; 2.1. Amino Acid Composition; 2.2. Sorting Signals; 2.3. Homology; 2.4. Hybrid Methods; 3. Ensemble Methods; 3.1. Theory; 3.2. Selection of Base Methods for Ensembles; 3.3. Ensemble Method Based on a Voting Schema; 3.4. Ensemble Method Based on Decision Trees; 4. Evaluation; 5. Conclusions; References Chemical Compound Classification with Automatically Mined Structure Patterns Aaron M. Smalter, J. Huan and Gerald H. Lushington1. Introduction; 2. Related Work; 2.1. Marginalized and Optimal Assignment Graph Kernels; 2.2. Frequent Subgraph Mining; 3. Background; 3.1. Chemical Structure; 4. Algorithm Design; 4.1. Structure Pattern Mining; 4.2. Optimal Assignment Kernel; 4.3. Reduced Graph Representation; 4.4. Pattern-based Descriptors; 5. Experimental Study; 5.1. Data Sets; 5.2. Methods; 5.3. Results; 6. Conclusions; Acknowledgments; References Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers Alireza Hadj Khodabakhshi, Jdn Mariuch, Arash Rafiey and Arvind Gupta1. Introduction; 2. Definitions; 2.1. Hydropho bic-polar- c ysteine (HP C) model; 2.2. Snake structures; 2.3. The strong HPC model; 3. Proof techniques; 3.1. Saturated folds; 3.2. 2DHPSolver: a semi-automatic prover; 4. Stability of the snake structures; 5. Conclusions; References; Discrimination of Native Folds Using Network Properties of Protein Structures Alper Kiiciikural, 0. Ug'ur Sezerman and Aytiil Ercal; 1 Introduction 2 Methods |
| Record Nr. | UNINA-9910784519503321 |
| London, : Imperial College Press | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Proceedings of the 6th Asia-Pacific Bioinformatics Conference : Kyoto, Japan, 14-17 January 2008 / / editors, Alvis Brazma, Satoru Miyano, Tatsuya Akutsu
| Proceedings of the 6th Asia-Pacific Bioinformatics Conference : Kyoto, Japan, 14-17 January 2008 / / editors, Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| Edizione | [1st ed.] |
| Pubbl/distr/stampa | London, : Imperial College Press |
| Descrizione fisica | 1 online resource (413 p.) |
| Disciplina | 572.8633 |
| Altri autori (Persone) |
AkutsuTatsuya <1962->
BrazmaAlvis MiyanoSatoru |
| Collana | Series on advances in bioinformatics and computational biology |
| Soggetto topico |
Bioinformatics
Biology - Data processing |
| ISBN |
1-281-86579-6
9786611865795 1-84816-109-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
CONTENTS; Preface; APBC 2008 Organization; Program Committee; Additional Reviewers; Keynote Papers; Recent Progress in Phylogenetic Combinatorics Andreas Dress; 1. Background; 2. Discussion; References; KEGG for Medical and Pharmaceutical Applications Minoru Kanehisa; Protein Interactions Extracted from Genomes and Papers Alfonso Valencia; Contributed Papers; String Kernels with Feature Selection for SVM Protein Classification Wen-Yun Yang and Bao-Liang Lu; 1. Introduction; 2. A string kernel framework; 2.1. Notations; 2.2. Pramework definition; 2.3. Relations with existing string kernels
3. Efficient computation3.1. Tree data structure with leaf links; 3.2. Leaf traversal algorithm; 4. Selecting feature groups and weights; 4.1. Reduction of spectrum string kernel; 4.2. Statistically selecting feature groups; 5. Experiment; 6. Discussion and future work; Acknowledgments; References; Predicting Nucleolar Proteins Using Support-Vector Machines Mikael Bod&.; 1. Introduction; 2. Background; 3. Methods; 3.1. Data set; 3.2. Model; 4. Results; 5 . Conclusion; Acknowledgments; References Supervised Ensembles of Prediction Methods for Subcellular Localization Johannes Apfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei and Arthur Zimek1. Introduction; 2. Survey on Prominent Prediction Methods for Subcellular Localization; 2.1. Amino Acid Composition; 2.2. Sorting Signals; 2.3. Homology; 2.4. Hybrid Methods; 3. Ensemble Methods; 3.1. Theory; 3.2. Selection of Base Methods for Ensembles; 3.3. Ensemble Method Based on a Voting Schema; 3.4. Ensemble Method Based on Decision Trees; 4. Evaluation; 5. Conclusions; References Chemical Compound Classification with Automatically Mined Structure Patterns Aaron M. Smalter, J. Huan and Gerald H. Lushington1. Introduction; 2. Related Work; 2.1. Marginalized and Optimal Assignment Graph Kernels; 2.2. Frequent Subgraph Mining; 3. Background; 3.1. Chemical Structure; 4. Algorithm Design; 4.1. Structure Pattern Mining; 4.2. Optimal Assignment Kernel; 4.3. Reduced Graph Representation; 4.4. Pattern-based Descriptors; 5. Experimental Study; 5.1. Data Sets; 5.2. Methods; 5.3. Results; 6. Conclusions; Acknowledgments; References Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers Alireza Hadj Khodabakhshi, Jdn Mariuch, Arash Rafiey and Arvind Gupta1. Introduction; 2. Definitions; 2.1. Hydropho bic-polar- c ysteine (HP C) model; 2.2. Snake structures; 2.3. The strong HPC model; 3. Proof techniques; 3.1. Saturated folds; 3.2. 2DHPSolver: a semi-automatic prover; 4. Stability of the snake structures; 5. Conclusions; References; Discrimination of Native Folds Using Network Properties of Protein Structures Alper Kiiciikural, 0. Ug'ur Sezerman and Aytiil Ercal; 1 Introduction 2 Methods |
| Altri titoli varianti | Proceedings of the Sixth Asia-Pacific Bioinformatics Conference |
| Record Nr. | UNINA-9910822764803321 |
| London, : Imperial College Press | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||