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Comparative Gene Finding : Models, Algorithms and Implementation / / by Marina Axelson-Fisk
| Comparative Gene Finding : Models, Algorithms and Implementation / / by Marina Axelson-Fisk |
| Autore | Axelson-Fisk Marina |
| Edizione | [2nd ed. 2015.] |
| Pubbl/distr/stampa | London : , : Springer London : , : Imprint : Springer, , 2015 |
| Descrizione fisica | 1 online resource (396 p.) |
| Disciplina | 572.860285 |
| Collana | Computational Biology |
| Soggetto topico |
Bioinformatics
Computational Biology/Bioinformatics |
| ISBN | 1-4471-6693-0 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Introduction -- Single Species Gene Finding -- Sequence Alignment -- Comparative Gene Finding -- Gene Structure Submodels -- Parameter Training -- Implementation of a Comparative Gene Finder -- Annotation Pipelines for Next Generation Sequencing Projects. |
| Record Nr. | UNINA-9910299247603321 |
Axelson-Fisk Marina
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| London : , : Springer London : , : Imprint : Springer, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Computational biology and genome informatics [[electronic resource] /] / editors, Jason T.L. Wang, Cathy H. Wu, Paul P. Wang
| Computational biology and genome informatics [[electronic resource] /] / editors, Jason T.L. Wang, Cathy H. Wu, Paul P. Wang |
| Pubbl/distr/stampa | New Jersey, : World Scientific, c2003 |
| Descrizione fisica | 1 online resource (266 p.) |
| Disciplina | 572.860285 |
| Altri autori (Persone) |
WangJason T. L
WuCathy H WangPaul P |
| Soggetto topico |
Computational biology
Genetics - Mathematical models Genomics |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-281-34773-6
9786611347734 981-256-449-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Preface; Contents; Chapter 1 Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm; Chapter 2 Introduction to Self-Assembling DNA Nanostructures for Computation and Nanofabrication; Chapter 3 Mapping Sequence to Rice FPC; Chapter 4 Graph Theoretic Sequence Clustering Algorithms and Their Applications to Genome Comparison; Chapter 5 The Protein Information Resource for Functional Genomics and Proteomics; Chapter 6 High-Grade Ore for Data Mining in 3D Structures; Chapter 7 Protein Classification: A Geometric Hashing Approach
Chapter 8 Interrelated Clustering: An Approach for Gene Expression Data AnalysisChapter 9 Creating Metabolic Network Models using Text Mining and Expert Knowledge; Chapter 10 Phyloinformatics and Tree Networks; Index |
| Record Nr. | UNINA-9910450109703321 |
| New Jersey, : World Scientific, c2003 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Computational biology and genome informatics [[electronic resource] /] / editors, Jason T.L. Wang, Cathy H. Wu, Paul P. Wang
| Computational biology and genome informatics [[electronic resource] /] / editors, Jason T.L. Wang, Cathy H. Wu, Paul P. Wang |
| Pubbl/distr/stampa | New Jersey, : World Scientific, c2003 |
| Descrizione fisica | 1 online resource (266 p.) |
| Disciplina | 572.860285 |
| Altri autori (Persone) |
WangJason T. L
WuCathy H WangPaul P |
| Soggetto topico |
Computational biology
Genetics - Mathematical models Genomics |
| ISBN |
1-281-34773-6
9786611347734 981-256-449-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Preface; Contents; Chapter 1 Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm; Chapter 2 Introduction to Self-Assembling DNA Nanostructures for Computation and Nanofabrication; Chapter 3 Mapping Sequence to Rice FPC; Chapter 4 Graph Theoretic Sequence Clustering Algorithms and Their Applications to Genome Comparison; Chapter 5 The Protein Information Resource for Functional Genomics and Proteomics; Chapter 6 High-Grade Ore for Data Mining in 3D Structures; Chapter 7 Protein Classification: A Geometric Hashing Approach
Chapter 8 Interrelated Clustering: An Approach for Gene Expression Data AnalysisChapter 9 Creating Metabolic Network Models using Text Mining and Expert Knowledge; Chapter 10 Phyloinformatics and Tree Networks; Index |
| Record Nr. | UNINA-9910783223903321 |
| New Jersey, : World Scientific, c2003 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Genome informatics 2009 : proceedings of the 20th international conference : Pacifico Yokohama, Japan, 14-16 December 2009. / / editors: Shinichi Morishita, Sang Yup Lee, Yasubumi Sakakibara
| Genome informatics 2009 : proceedings of the 20th international conference : Pacifico Yokohama, Japan, 14-16 December 2009. / / editors: Shinichi Morishita, Sang Yup Lee, Yasubumi Sakakibara |
| Autore | Shinichi Morishita |
| Pubbl/distr/stampa | London, : Imperial College Press, 2009 |
| Descrizione fisica | xv, 224 p. : ill |
| Disciplina | 572.860285 |
| Altri autori (Persone) |
MorishitaShinichi <1960->
YiSang-yŏp <1964-> SakakibaraYasubumi |
| Collana | Genome informatics series |
| Soggetto topico |
Genomics - Data processing
Bioinformatics |
| Soggetto non controllato |
Computational Systems Biology
Genomics Computational Biology Proteomics Genome Informatics Bioinformatics |
| ISBN |
1-282-76016-5
9786612760167 1-84816-563-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Predicting protein-protein relationships from literature using latent topics / T. Aso & K. Eguchi -- Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast / M. Fernandez ... [et al.] -- Quality control and reproducibility in DNA microarray experiments / A. Fujita ... [et al.] -- Comparative analysis of topological patterns in different mammalian networks / B. Goemann ... [et al.] -- Tools for investigating mechanisms of antigenic variation : new extensions to varDB / C. N. Hayes ... [et al.] -- Localized suffix array and its application to genome mapping problems for paired-end short reads / K. Kimura & A. Koike -- Comparative analysis of aerobic and anaerobic prokaryotes to identify correlation between oxygen requirement and gene-gene functional association patterns / Y. Lin & H. Wu -- Calculation of protein-ligand binding free energy using Smooth Reaction Path Generation (SRPG) method : a comparison of the explicit water model, GB/SA model and docking score function / D. Mitomo ... [et al.] -- Structural insights into the enzyme mechanism of a new family of D-2-hydroxyacid dehydrogenases, a close homolog of 2-Ketopantoate reductase / S. Mondal & K. Mizuguchi -- Comprehensive analysis of sequence-structure relationships in the loop regions of proteins / S. Nakamura & K. Shimizu -- The prediction of local modular structures in a co-expression network based on gene expression datasets / Y. Ogata ... [et al.] -- Gradient-based optimization of hyperparameters for base-pairing profile local alignment kernels / K. Sato, Y. Saito & Y. Sakakibara -- A method for efficient execution of bioinformatics workfiows / J. Seo ... [et al.] -- Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression / M. Shirota, T. Ishida & K. Kinoshita -- Refining Markov clustering for protein complex prediction by incorporating core-attachment structure / S. Srihari, K. Ning & H. W. Leong -- An assessment of prediction algorithms for nucleosome positioning / Y. Tanaka & K. Nakai -- Cancer classification using single genes / X. Wang & O. Gotoh -- RECOUNT : expectation maximization based error correction tool for next generation sequencing data / E. Wijaya ... [et al.] -- A new generation of homology search tools based on probabilistic inference / S. R. Eddy -- Representation and analysis of molecular networks involving diseases and drugs / M. Kanehisa -- Systems biotechnology / S. Y. Lee -- Strategies toward CNS-regeneration using induced pluripotent stem cells / H. Okano -- Thinking laterally about genomes / M. A. Ragan. |
| Record Nr. | UNINA-9910346696103321 |
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Shinichi Morishita
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| London, : Imperial College Press, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi
| Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi |
| Autore | Bernasconi Anna |
| Edizione | [1st ed. 2023.] |
| Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
| Descrizione fisica | 1 online resource (277 pages) |
| Disciplina | 572.860285 |
| Collana | Lecture Notes in Business Information Processing |
| Soggetto topico |
Application software
Bioinformatics Quantitative research Artificial intelligence - Data processing Computer and Information Systems Applications Data Analysis and Big Data Data Science |
| ISBN | 3-031-44907-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Foreword -- Preface -- Acknowledgements -- Contents -- Acronyms -- Introduction -- Genomic Data Integration -- Thesis Contribution within the GeCo Project -- The Recent COVID-19 Pandemic -- Thesis Structure -- Part I Human Genomic Data Integration -- Genomic Data Players and Processes -- Technological Pipeline of Genomic Data -- Production -- Integration -- Services and Access -- Taxonomy of Players Involved in Data Production and Integration -- Main Genomic Data Players -- Contributors -- Repository Hosts -- Consortia -- Integrators -- Modeling Genomic Data -- The Genomic Data Model -- The Genomic Conceptual Model -- Analysis of Metadata Attributes -- Model Design -- Validation: Source-Specific Views of GCM -- Related Works -- Integrating Genomic Data -- Theoretical Rationale -- Approach Overview -- Data Download -- Data Transformation -- Data Cleaning -- Data Mapping -- Data Normalization and Enrichment -- Search Service and Ontology Selection -- Enrichment Process -- Data Constraint Checking -- Architecture Implementation -- Data Persistence -- Architecture Validation -- Lossless Integration -- Semantic Enrichment -- User Evaluation -- Related Works -- Snapshot of the Data Repository -- Included Data Sources -- OpenGDC: Integrating Cancer Genomic Data and Metadata -- Towards Automated Integration of Unstructured Metadata -- Experiments -- Related Works -- Searching Genomic Data -- Issues in Exploiting Semantic Knowledge in Genomics -- Inference Explanation -- GeKnowGraph: Exploration-Based Interface -- Exploration Interaction -- GenoSurf: a Web-Based Search Server for Genomic Datasets -- Data Search -- Key-Value Search -- Query Sessions -- Result Visualization -- Additional Functionalities -- Use Cases -- Validation of GenoSurf -- Related Works -- Future Directions of the Data Repository -- Including New Data Sources.
Improving Genomic Data Quality Dimensions -- Towards Better Interoperability -- Simplifying Data and Tools for End Users -- Monitoring Integration and Search Value -- Part II Viral Sequence Data Integration -- Viral Sequences Data Management Resources -- Landscape of Data Resources for Viral Sequences -- Fully Open-Source Resources -- GISAID and its Resources -- Integration of Sources of Viral Sequences -- Metadata Integration -- Value Harmonization and Ontological Efforts -- Replicated Sequences in Multiple Sources -- SARS-CoV-2 Search Systems -- Portals to NCBI and GISAID Resources -- Integrative Search Systems -- Comparison -- Discussion -- GISAID Restrictions -- Metadata Quality -- (Un)Willingness to Share Sequence Data -- Modeling Viral Sequence Data -- Conceptual Modeling for Viral Genomics -- Answering Complex Biological Queries -- Related Works -- Integrating Viral Sequence Data -- Database Content -- Relational Schema -- Data Import -- Annotation and Variant Calling -- Data Curation -- Searching Viral Sequence Data -- Requirements Analysis -- Lessons Learnt -- Web Interface -- Example Queries -- Discussion -- Related Works -- Future Directions of the Viral Sequence Repository -- Research Agenda -- ViruSurf Extensions -- Visualization Support: VirusViz -- Active Monitoring of SARS-CoV-2 Variations -- Integrating Host-Pathogen Information -- The Virus Genotype - Host Phenotype Connection -- The Host Genotype - Host Phenotype Connection -- Part III Epilogue -- Conclusions and Vision -- Summary of Thesis Contributions -- Achievements within GeCo Project -- Outlook -- META-BASE tool configuration -- User Manual -- Process Configuration -- Mapper Configuration -- Experimental setup GEO metadata extraction -- Mappings of viral sources attributes into ViruSurf -- References. |
| Record Nr. | UNINA-9910770265603321 |
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Bernasconi Anna
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| Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi
| Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi |
| Autore | Bernasconi Anna |
| Edizione | [1st ed. 2023.] |
| Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
| Descrizione fisica | 1 online resource (277 pages) |
| Disciplina | 572.860285 |
| Collana | Lecture Notes in Business Information Processing |
| Soggetto topico |
Application software
Bioinformatics Quantitative research Artificial intelligence - Data processing Computer and Information Systems Applications Data Analysis and Big Data Data Science |
| ISBN | 3-031-44907-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Foreword -- Preface -- Acknowledgements -- Contents -- Acronyms -- Introduction -- Genomic Data Integration -- Thesis Contribution within the GeCo Project -- The Recent COVID-19 Pandemic -- Thesis Structure -- Part I Human Genomic Data Integration -- Genomic Data Players and Processes -- Technological Pipeline of Genomic Data -- Production -- Integration -- Services and Access -- Taxonomy of Players Involved in Data Production and Integration -- Main Genomic Data Players -- Contributors -- Repository Hosts -- Consortia -- Integrators -- Modeling Genomic Data -- The Genomic Data Model -- The Genomic Conceptual Model -- Analysis of Metadata Attributes -- Model Design -- Validation: Source-Specific Views of GCM -- Related Works -- Integrating Genomic Data -- Theoretical Rationale -- Approach Overview -- Data Download -- Data Transformation -- Data Cleaning -- Data Mapping -- Data Normalization and Enrichment -- Search Service and Ontology Selection -- Enrichment Process -- Data Constraint Checking -- Architecture Implementation -- Data Persistence -- Architecture Validation -- Lossless Integration -- Semantic Enrichment -- User Evaluation -- Related Works -- Snapshot of the Data Repository -- Included Data Sources -- OpenGDC: Integrating Cancer Genomic Data and Metadata -- Towards Automated Integration of Unstructured Metadata -- Experiments -- Related Works -- Searching Genomic Data -- Issues in Exploiting Semantic Knowledge in Genomics -- Inference Explanation -- GeKnowGraph: Exploration-Based Interface -- Exploration Interaction -- GenoSurf: a Web-Based Search Server for Genomic Datasets -- Data Search -- Key-Value Search -- Query Sessions -- Result Visualization -- Additional Functionalities -- Use Cases -- Validation of GenoSurf -- Related Works -- Future Directions of the Data Repository -- Including New Data Sources.
Improving Genomic Data Quality Dimensions -- Towards Better Interoperability -- Simplifying Data and Tools for End Users -- Monitoring Integration and Search Value -- Part II Viral Sequence Data Integration -- Viral Sequences Data Management Resources -- Landscape of Data Resources for Viral Sequences -- Fully Open-Source Resources -- GISAID and its Resources -- Integration of Sources of Viral Sequences -- Metadata Integration -- Value Harmonization and Ontological Efforts -- Replicated Sequences in Multiple Sources -- SARS-CoV-2 Search Systems -- Portals to NCBI and GISAID Resources -- Integrative Search Systems -- Comparison -- Discussion -- GISAID Restrictions -- Metadata Quality -- (Un)Willingness to Share Sequence Data -- Modeling Viral Sequence Data -- Conceptual Modeling for Viral Genomics -- Answering Complex Biological Queries -- Related Works -- Integrating Viral Sequence Data -- Database Content -- Relational Schema -- Data Import -- Annotation and Variant Calling -- Data Curation -- Searching Viral Sequence Data -- Requirements Analysis -- Lessons Learnt -- Web Interface -- Example Queries -- Discussion -- Related Works -- Future Directions of the Viral Sequence Repository -- Research Agenda -- ViruSurf Extensions -- Visualization Support: VirusViz -- Active Monitoring of SARS-CoV-2 Variations -- Integrating Host-Pathogen Information -- The Virus Genotype - Host Phenotype Connection -- The Host Genotype - Host Phenotype Connection -- Part III Epilogue -- Conclusions and Vision -- Summary of Thesis Contributions -- Achievements within GeCo Project -- Outlook -- META-BASE tool configuration -- User Manual -- Process Configuration -- Mapper Configuration -- Experimental setup GEO metadata extraction -- Mappings of viral sources attributes into ViruSurf -- References. |
| Record Nr. | UNISA-996574259503316 |
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Bernasconi Anna
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| Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
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