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Biological Data Integration : Computer and Statistical Approaches / / coordinated by Christine Froidevaux, Marie-Laure Martin-Magniette, and Guillem Rigaill
| Biological Data Integration : Computer and Statistical Approaches / / coordinated by Christine Froidevaux, Marie-Laure Martin-Magniette, and Guillem Rigaill |
| Edizione | [First edition.] |
| Pubbl/distr/stampa | London, England : , : ISTE Ltd, , [2023] |
| Descrizione fisica | 1 online resource (276 pages) |
| Disciplina | 570.113 |
| Soggetto topico | Systems biology |
| ISBN |
1-394-25731-7
1-394-25729-5 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover -- Title Page -- Copyright Page -- Contents -- Preface -- Part 1. Knowledge Integration -- Chapter 1. Clinical Data Warehouses -- 1.1. Introduction to clinical information systems and biomedical warehousing: data warehouses for what purposes? -- 1.1.1. Warehouse history -- 1.1.2. Using data warehouses today -- 1.2. Challenge: widely scattered data -- 1.3. Data warehouses and clinical data -- 1.3.1. Warehouse structures -- 1.3.2. Warehouse construction and supply -- 1.3.3. Uses -- 1.4. Warehouses and omics data: challenges -- 1.4.1. Challenges of data volumetry and structuring omic data -- 1.4.2. Attempted solutions -- 1.5. Challenges and prospects -- 1.5.1. Toward general-purpose warehouses -- 1.5.2. Ethical dimension of the implementation and the use of warehouses -- 1.5.3. Origin and reproducibility -- 1.5.4. Data quality -- 1.5.5. Data warehousing federation and data sharing -- 1.6. References -- Chapter 2. Semantic Web Methods for Data Integration in Life Sciences -- 2.1. Data-related requirements in life sciences -- 2.1.1. Databases for the life sciences -- 2.1.2. Requirements -- 2.1.3. Common approaches: InterMine and BioMart -- 2.2. Semantic Web -- 2.2.1. Techniques -- 2.2.2. Implementation -- 2.3. Perspectives -- 2.3.1. Facilitating appropriation to users -- 2.3.2. Facilitating the appropriation by software programs: FAIR data -- 2.3.3. Federated queries -- 2.4. Conclusion -- 2.5. References -- Chapter 3. Workflows for Bioinformatics Data Integration -- 3.1. Introduction -- 3.2. Bioinformatics data processing chains: difficulties -- 3.2.1. Designing a data processing chain -- 3.2.2. Analysis execution and reproducibility -- 3.2.3. Maintenance, sharing and reuse -- 3.3. Solutions provided by scientific workflow systems -- 3.3.1. Fundamentals of workflow systems -- 3.3.2. Workflow systems -- 3.4. Use case: RNA-seq data analysis.
3.4.1. Study description -- 3.4.2. From data processing chain to workflows -- 3.4.3. Data processing chains implemented as workflows: conclusion -- 3.5. Challenges, open problems and research opportunities -- 3.5.1. Formalizing workflow development -- 3.5.2. Workflow testing -- 3.5.3. Discovering and sharing workflows -- 3.6. Conclusion -- 3.7. References -- Part 2. Integration and Statistics -- Chapter 4. Variable Selection in the General Linear Model: Application to Multiomic Approaches for the Study of Seed Quality -- 4.1. Introduction -- 4.2. Methodology -- 4.2.1. Estimation of the covariance matrix ƒ°q -- 4.2.2. Estimation of B -- 4.3. Numerical experiments -- 4.3.1. Statistical performance -- 4.3.2. Numerical performance -- 4.4. Application to the study of seed quality -- 4.4.1. Metabolomics data -- 4.4.2. Proteomics data -- 4.5. Conclusion -- 4.6. Appendices -- 4.6.1. Example of using the package MultiVarSel for metabolomic data analysis -- 4.6.2. Example of using the package MultiVarSel for proteomic data analysis -- 4.7. Acknowledgments -- 4.8. References -- Chapter 5. Structured Compression of Genetic Information and Genome-Wide Association Study by Additive Models -- 5.1. Genome-wide association studies -- 5.1.1. Introduction to genetic mapping and linkage analysis -- 5.1.2. Principles of genome-wide association studies -- 5.1.3. Single nucleotide polymorphism -- 5.1.4. Disease penetrance and odds ratio -- 5.1.5. Single marker analysis -- 5.1.6. Multi-marker analysis -- 5.2. Structured compression and association study -- 5.2.1. Context -- 5.2.2. New structured compression approach -- 5.3. Application to ankylosing spondylitis (AS) -- 5.3.1. Data -- 5.3.2. Predictive power evaluation -- 5.3.3. Manhattan diagram -- 5.3.4. Estimation for the most significant SNP aggregates -- 5.4. Conclusion -- 5.5. References -- Chapter 6. Kernels for Omics. 6.1. Introduction -- 6.2. Relational data -- 6.2.1. Data described by the kernel -- 6.2.2. Data described by a general (dis)similarity measure -- 6.3. Exploratory analysis for relational data -- 6.3.1. Kernel clustering -- 6.3.2. Kernel principal component analysis -- 6.3.3. Kernel self-organizing maps -- 6.3.4. Limitations of relational methods -- 6.4. Combining relational data -- 6.4.1. Data integration in systems biology -- 6.4.2. Kernel approaches in data integration -- 6.4.3. A consensual kernel -- 6.4.4. A parsimonious kernel that preserves the topology of the initial data -- 6.4.5. A complete kernel preserving the topology of the initial data -- 6.5. Application -- 6.5.1. Loading Tara Ocean data -- 6.5.2. Data integration by kernel approaches -- 6.5.3. Exploratory analysis: kernel PCA -- 6.6. Session information for the results of the example -- 6.7. References -- Chapter 7. Multivariate Models for Data Integration and Biomarker Selection in 'Omics Data -- 7.1. Introduction -- 7.2. Background -- 7.2.1. Mathematical notations -- 7.2.2. Terminology -- 7.2.3. Multivariate projection-based approaches -- 7.2.4. A criterion to maximize specific to each methodology -- 7.2.5. A linear combination of variables to reduce the dimension of the data -- 7.2.6. Identifying a subset of relevant molecular features -- 7.2.7. Summary -- 7.3. From the biological question to the statistical analysis -- 7.3.1. Exploration of one dataset: PCA -- 7.3.2. Classify samples: projection to latent structure discriminant analysis -- 7.3.3. Integration of two datasets: projection to latent structure and related methods -- 7.3.4. Integration of several datasets: multi-block approaches -- 7.4. Graphical outputs -- 7.4.1. Individual plots -- 7.4.2. Variable plots -- 7.5. Overall summary -- 7.6. Liver toxicity study -- 7.6.1. The datasets. 7.6.2. Biological questions and statistical methods -- 7.6.3. Single dataset analysis -- 7.6.4. Integrative analysis -- 7.7. Conclusion -- 7.8. Acknowledgments -- 7.9. Appendix: reproducible R code -- 7.9.1. Toy examples -- 7.9.2. Liver toxicity -- 7.10. References -- List of Authors -- Index -- EULA. |
| Record Nr. | UNINA-9910830623303321 |
| London, England : , : ISTE Ltd, , [2023] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Biological Networks in Human Health and Disease [[electronic resource] /] / edited by Romana Ishrat
| Biological Networks in Human Health and Disease [[electronic resource] /] / edited by Romana Ishrat |
| Autore | Ishrat Romana |
| Edizione | [1st ed. 2023.] |
| Pubbl/distr/stampa | Singapore : , : Springer Nature Singapore : , : Imprint : Springer, , 2023 |
| Descrizione fisica | 1 online resource (132 pages) |
| Disciplina |
570.285
570.113 |
| Soggetto topico |
Bioinformatics
Diseases Computational and Systems Biology |
| ISBN |
9789819942428
9789819942411 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Chapter 1. Graph Theory in the Biological Networks -- Chapter 2. Biological Networks Analysis -- Chapter 3. Network Analysis based software packages, tools, and web servers to accelerate bioinformatics research -- Chapter 4. Networks Analytics of Heterogeneous Big Data -- Chapter 5. Network Medicine: Methods and Applications -- Chapter 6. Role of R in Biological Network Analysis -- Chapter 7. Machine Learning in Biological Networks. |
| Record Nr. | UNINA-9910751392603321 |
Ishrat Romana
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| Singapore : , : Springer Nature Singapore : , : Imprint : Springer, , 2023 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Case studies in systems biology / / Pavel Kraikivski, editor
| Case studies in systems biology / / Pavel Kraikivski, editor |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (310 pages) |
| Disciplina | 570.113 |
| Soggetto topico | Systems biology |
| ISBN | 3-030-67742-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910502992903321 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Case studies in systems biology / / Pavel Kraikivski, editor
| Case studies in systems biology / / Pavel Kraikivski, editor |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (310 pages) |
| Disciplina | 570.113 |
| Soggetto topico | Systems biology |
| ISBN | 3-030-67742-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNISA-996464418003316 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Computational methods in systems biology : 21st International Conference, CMSB 2023, Luxembourg City, Luxembourg, September 13-15, 2023, Proceedings / / edited by Jun Pang, Joachim Niehren
| Computational methods in systems biology : 21st International Conference, CMSB 2023, Luxembourg City, Luxembourg, September 13-15, 2023, Proceedings / / edited by Jun Pang, Joachim Niehren |
| Edizione | [1st ed. 2023.] |
| Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
| Descrizione fisica | 1 online resource (xviii, 270 pages) : illustrations (some color) |
| Disciplina |
570.285
570.113 |
| Altri autori (Persone) |
PangJun (Computer scientist)
NiehrenJoachim |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Computational biology
Systems biology |
| ISBN | 3-031-42697-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | A Formal Approach for Tuning Stochastic Oscillators -- Phenotype Control of Partially Specified Boolean Networks -- A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI -- Intuitive Modelling and Formal Analysis of Collective Behaviour in Foraging Ants -- Cell-Level Pathway Scoring Comparison with a Bconstrained Variational Autoencoder -- On Estimating Derivatives of Input Signals in Biochemistry -- Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting -- Approximate Constrained Lumping of Polynomial Differential Equations -- Core SBML and its Formal Semantics -- Average Sensitivity of Canalizing Multivalued Functions -- Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks -- SAF: SAT-Based Attractor Finder in Asynchronous Automata Networks -- Condition for Periodic Attractor in 4-Dimensional Repressilators -- Attractor Identification in Asynchronous Boolean Dynamics with Network Reduction -- 3D Hybrid Cellular Automata for Cardiac Electrophysiology: a Concept Study -- Fridge Compiler: Optimal Circuits from Molecular Inventories -- Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution. |
| Record Nr. | UNISA-996550559903316 |
| Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Computational methods in systems biology : 21st International Conference, CMSB 2023, Luxembourg City, Luxembourg, September 13-15, 2023, Proceedings / / edited by Jun Pang, Joachim Niehren
| Computational methods in systems biology : 21st International Conference, CMSB 2023, Luxembourg City, Luxembourg, September 13-15, 2023, Proceedings / / edited by Jun Pang, Joachim Niehren |
| Edizione | [1st ed. 2023.] |
| Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
| Descrizione fisica | 1 online resource (xviii, 270 pages) : illustrations (some color) |
| Disciplina |
570.285
570.113 |
| Altri autori (Persone) |
PangJun (Computer scientist)
NiehrenJoachim |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Computational biology
Systems biology |
| ISBN | 3-031-42697-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | A Formal Approach for Tuning Stochastic Oscillators -- Phenotype Control of Partially Specified Boolean Networks -- A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI -- Intuitive Modelling and Formal Analysis of Collective Behaviour in Foraging Ants -- Cell-Level Pathway Scoring Comparison with a Bconstrained Variational Autoencoder -- On Estimating Derivatives of Input Signals in Biochemistry -- Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting -- Approximate Constrained Lumping of Polynomial Differential Equations -- Core SBML and its Formal Semantics -- Average Sensitivity of Canalizing Multivalued Functions -- Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks -- SAF: SAT-Based Attractor Finder in Asynchronous Automata Networks -- Condition for Periodic Attractor in 4-Dimensional Repressilators -- Attractor Identification in Asynchronous Boolean Dynamics with Network Reduction -- 3D Hybrid Cellular Automata for Cardiac Electrophysiology: a Concept Study -- Fridge Compiler: Optimal Circuits from Molecular Inventories -- Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution. |
| Record Nr. | UNINA-9910746092303321 |
| Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Evolutionary systems biology : advances, questions, and opportunities / / Anton Crombach, editor
| Evolutionary systems biology : advances, questions, and opportunities / / Anton Crombach, editor |
| Edizione | [Second edition.] |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (X, 294 p. 49 illus., 31 illus. in color.) |
| Disciplina | 570.113 |
| Soggetto topico |
Systems biology
Evolution (Biology) |
| ISBN | 3-030-71737-2 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Part 1. Theory and philosophy -- Biology as a process and the consequences for studying it -- Capturing the genotype—phenotype map with the adaptive multiscape -- Evolution plays a high-dimensional game -- What is next for evolutionary systems biology? -- Part 2. Single celled organisms -- Experimental evolution of microbial host-parasite relations -- Engineering microbial communities that evolve in a spatial setting -- Sharing is caring: differential gene flow in microbial communities.-Synthetic biology to study the evolution of gene regulatory networks -- Evolution of stem cell differentiation -- The evolution of epigenetic switches and cellular clocks -- Part 3. Multicellular organisms -- Measuring the genotype—phenotype map in eukaryotes -- Pigment evolution in Drosophila fly species: time for theory? -- Birds of a feather: using experiment and theory to understand the evolution of feather patterning -- A regulatory network that explains both fish fins and mouse limbs -- Quantitative system drift of the fly body plan -- Part 4. Immunity and disease -- Of mice, men, and immunity -- Immunity as an evolving adaptive system -- Cancer is a microevolutionary systemic disease -- A systems approach to cancer. |
| Record Nr. | UNINA-9910494556603321 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Evolutionary systems biology : advances, questions, and opportunities / / Anton Crombach, editor
| Evolutionary systems biology : advances, questions, and opportunities / / Anton Crombach, editor |
| Edizione | [Second edition.] |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (X, 294 p. 49 illus., 31 illus. in color.) |
| Disciplina | 570.113 |
| Soggetto topico |
Systems biology
Evolution (Biology) |
| ISBN | 3-030-71737-2 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Part 1. Theory and philosophy -- Biology as a process and the consequences for studying it -- Capturing the genotype—phenotype map with the adaptive multiscape -- Evolution plays a high-dimensional game -- What is next for evolutionary systems biology? -- Part 2. Single celled organisms -- Experimental evolution of microbial host-parasite relations -- Engineering microbial communities that evolve in a spatial setting -- Sharing is caring: differential gene flow in microbial communities.-Synthetic biology to study the evolution of gene regulatory networks -- Evolution of stem cell differentiation -- The evolution of epigenetic switches and cellular clocks -- Part 3. Multicellular organisms -- Measuring the genotype—phenotype map in eukaryotes -- Pigment evolution in Drosophila fly species: time for theory? -- Birds of a feather: using experiment and theory to understand the evolution of feather patterning -- A regulatory network that explains both fish fins and mouse limbs -- Quantitative system drift of the fly body plan -- Part 4. Immunity and disease -- Of mice, men, and immunity -- Immunity as an evolving adaptive system -- Cancer is a microevolutionary systemic disease -- A systems approach to cancer. |
| Record Nr. | UNISA-996464380103316 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
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Guide to Simulation and Modeling for Biosciences [[electronic resource] /] / by David J. Barnes, Dominique Chu
| Guide to Simulation and Modeling for Biosciences [[electronic resource] /] / by David J. Barnes, Dominique Chu |
| Autore | Barnes David J |
| Edizione | [2nd ed. 2015.] |
| Pubbl/distr/stampa | London : , : Springer London : , : Imprint : Springer, , 2015 |
| Descrizione fisica | 1 online resource (XII, 339 p. 80 illus.) |
| Disciplina | 570.113 |
| Collana | Simulation Foundations, Methods and Applications |
| Soggetto topico |
Computer simulation
Mathematical models Bioinformatics Bioinformatics Computational biology Simulation and Modeling Mathematical Modeling and Industrial Mathematics Computational Biology/Bioinformatics Computer Appl. in Life Sciences |
| ISBN | 1-4471-6762-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Foundations of Modeling -- Agent-based Modeling -- ABMs using Repast Simphony -- Differential Equations -- Mathematical Tools -- Other Stochastic Methods and Prism -- Simulating Biochemical Systems -- Biochemical Models Beyond the Perfect Mixing Assumption -- Reference Material. |
| Record Nr. | UNINA-9910299204103321 |
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Barnes David J
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| London : , : Springer London : , : Imprint : Springer, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Modeling Dynamic Biological Systems [[electronic resource] /] / by Bruce Hannon, Matthias Ruth
| Modeling Dynamic Biological Systems [[electronic resource] /] / by Bruce Hannon, Matthias Ruth |
| Autore | Hannon Bruce |
| Edizione | [2nd ed. 2014.] |
| Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2014 |
| Descrizione fisica | 1 online resource (XVI, 434 p. 298 illus., 280 illus. in color.) |
| Disciplina | 570.113 |
| Collana | Modeling Dynamic Systems |
| Soggetto topico |
Ecology
Biomathematics Population Biochemistry Computers Ecology Mathematical and Computational Biology Population Economics Biochemistry, general Models and Principles |
| ISBN | 3-319-05615-8 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | I. INTRODUCTION -- 1. Modeling Dynamic Biological Systems -- 2. Exploring Dynamic Biological Systems -- 3. Risky Population -- 4. Steady State, Oscillation and Chaos in Population Dynamics -- 5. Spatial Dynamics.- II. PHYSICAL AND BIOCHEMICAL MODELS.- 6. Law of Mass Action -- 7. Catalyzed Product -- 8. Two-Stage Nutrient Uptake -- 9. Iodine Compartment -- 10. The Brusselator -- 11. Signal Transmission -- III. Genetic Models -- 12. Mating and Mutation of Alleles -- 13. Artificial Worms -- 14. Langur Infanticide and Long-term Matriline Fitness -- IV. MODELS OF ORGANISM -- 15. Odor Sensing -- 16. Stochastic Resonance -- 17. Heart Beat -- 18. Bat Thermo-Regulation -- 19. The Optimum Plant -- 20. Soybean Plant Growth -- 21. Infectious Diseases -- VI. SINGLE POPULATION MODELS -- 22. Adaptive Population Control -- 23. Roan Herds -- 24. Population Dynamics of Voles -- 25. Lemming Population Dynamics -- 26. Multi-Stage Insect Models -- 27. Two Age-Class Parasites -- 28. Monkey Travels -- 29. Biosynchronicity -- VII. MULTIPLE POPULATION MODELS -- 30. Plant Microbe Interaction -- 31. Wildebeest -- 32. Nicholson-Bailey Host-Parasite Interaction -- 33. Diseased and Healthy Immigrating Insects -- 34. Two-Species Colonization Model -- 35. Herbivore-Algae Predator-Prey Dynamics -- 36. The Grass Carp -- 37. Recruitment and Trophic Dynamics of Gizzard Shad -- 38. Salamander Dispersal. 39. Quail Movement -- 40. Modeling Spatial Dynamics of Spatial Predator-Prey Interactions in a Changing -- VII. CATASTROPHE AND SELF-ORGANIZATION -- 41. Catastrophe -- 42. Spruce Budworm Dynamics -- 43. Game of Life -- 44. Daisyworld -- VIII. CONCLUSION -- 45. Building a Modeling Community. . |
| Record Nr. | UNINA-9910298327603321 |
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Hannon Bruce
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| Cham : , : Springer International Publishing : , : Imprint : Springer, , 2014 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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