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Actin Polymerization in Apicomplexan : A Structural, Functional and Evolutionary Analysis / / edited by Avinash Kale
| Actin Polymerization in Apicomplexan : A Structural, Functional and Evolutionary Analysis / / edited by Avinash Kale |
| Edizione | [1st ed. 2019.] |
| Pubbl/distr/stampa | Singapore : , : Springer Singapore : , : Imprint : Springer, , 2019 |
| Descrizione fisica | 1 online resource (XI, 101 p. 11 illus. in color.) |
| Disciplina | 616.96 |
| Soggetto topico |
Enginyeria de proteïnes
Parasitology Biomechanics Proteins Bioinformatics Protein Science Protein Structure |
| Soggetto genere / forma | Llibres electrònics |
| ISBN | 981-13-7450-3 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Chapter 1. Synthesis and Characterization of nano Apicomplexan motility: A cellular perspective particles -- Chapter 2. Introduction: Gliding Motility- The model and the mechanism -- Chapter 3. Actin: The central ubiquitous player in the phenomenon -- Chapter 4. Formin: The multidomain elongator of polymer -- Chapter 5. Profilin: The associates of Formin -- Chapter 6. ADF (Actin Depolymerizing Factor): The breaker of the polymer in homeostasis -- Chapter 7. Cyclase associated protein (CAP): The silent worker -- Chapter 8. Capping Protein (CP): The formin competitor -- Chapter 9. Coronin: An Overview -- Chapter 10. Mathematical Model: A revelation of synergistic cross talks between the actin regulators -- Chapter 11. Evolution: The hallmarks of Gliding motility in apicomplexan. |
| Record Nr. | UNINA-9910373917803321 |
| Singapore : , : Springer Singapore : , : Imprint : Springer, , 2019 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Advanced Technologies for Protein Complex Production and Characterization / / edited by M. Cristina Vega
| Advanced Technologies for Protein Complex Production and Characterization / / edited by M. Cristina Vega |
| Edizione | [1st ed. 2016.] |
| Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2016 |
| Descrizione fisica | 1 online resource (XIII, 382 p. 87 illus., 71 illus. in color.) |
| Disciplina | 660.63 |
| Collana | Advances in Experimental Medicine and Biology |
| Soggetto topico |
Proteins
Systems biology Protein Science Protein Structure Systems Biology |
| ISBN | 3-319-27216-0 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Protein complex production from the drug discovery standpoint -- Choose a suitable expression host: a survey of available protein production platforms -- ACEMBL Tool-Kits for High-Throughput Multigene Delivery and Expression in Prokaryotic and Eukaryotic Hosts -- Complex reconstitution and characterization by combining co-expression techniques in Escherichia coli with high-throughput -- Membrane protein production in E. coli for applications in drug discovery -- Cell-free Synthesis of Macromolecular Complexes -- A Bacillus megaterium system for the production of recombinant proteins and protein complexes -- Protein complex production in alternative prokaryotic hosts -- Production of Protein Complexes in Non-methylotrophic and Methylotrophic Yeasts -- Leishmania tarentolae for the Production of Multi-Subunit Complexes -- Alternative Eukaryotic Expression Systems for the Production of Proteins and Protein Complexes -- Fundamentals of baculovirus expression and applications -- The MultiBac Baculovirus / Insect Cell Expression Vector System for Producing Complex Protein Biologics -- Fundamentals of expression in mammalian cells -- Assembling multi-subunit complexes using mammalian expression -- Microalgae as solar-powered protein factories -- Strategies and methodologies for the co-expression of multiple proteins in plants -- Transient expression systems in plants—potentialities and constraints -- Complex reconstitution from individual protein modules -- Structural reconstruction of protein-protein complexes involved in intracellular signaling -- The use of small-angle scattering for the characterization of multi subunit complexes -- Application of nuclear magnetic resonance and hybrid methods to structure determination of complex systems. . |
| Record Nr. | UNINA-9910253889603321 |
| Cham : , : Springer International Publishing : , : Imprint : Springer, , 2016 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Advances in Bioengineering / / edited by Renu Vyas
| Advances in Bioengineering / / edited by Renu Vyas |
| Edizione | [1st ed. 2020.] |
| Pubbl/distr/stampa | Singapore : , : Springer Singapore : , : Imprint : Springer, , 2020 |
| Descrizione fisica | 1 online resource (229 p.) |
| Disciplina | 660.6 |
| Soggetto topico |
Biomedical engineering
Molecular biology Proteins Bioinformatics Human physiology Biomedical Engineering/Biotechnology Molecular Medicine Protein Structure Human Physiology Bioenginyeria Bioinformàtica Materials nanoestructurats Nanopartícules |
| Soggetto genere / forma | Llibres electrònics |
| ISBN | 981-15-2063-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Chapter 1. Modeling of protein complexes involved in signaling pathway for Non-Small Cell Lung Cancer -- Chapter 2. Role of BioJava in the Department of Bioinformatics Tools -- Chapter 3. Overview of machine learning methods in ADHD prediction -- Chapter 4. Simplified Protein Structure Prediction Using Parallel Genetic Algorithms -- Chapter 5. Applications of deep learning in drug discovery -- Chapter 6. Big Data Analytics for Handling NGS Data & its Applications in Identifying Cancer Mutations -- Chapter 7. Medicinal Properties of Fruit waste -- Chapter 8. Epigenetic toxicity of nanoparticles -- Chapter 9. Protein Misfolding and Aggregation in Neurodegenerative diseases -- Chapter 10. Enzyme technology prospectus & their Biomedical Applications -- Chapter 11. Polyunsaturated fatty acids enhance the recovery of bone marrow impairment caused after radiation -- Chapter 12. Nanomaterial Enabled Rapid Electrochemical Biosensors For Bacterial Pathogens -- Chapter 13. Heart Rate Variability Analysis in lung cancer patients to study the effect of treatment -- Chapter 14. Co-Relation of Physiological Signals And Therapy for Diagnostics Purpose of Periodic Limb Movement Disorder (Plmd) -- Chapter 15. Analysis of Forward Head Posture -- Chapter 16. Biopolymeric Smart Nano-Carriers for Drug Delivery Applications. |
| Record Nr. | UNINA-9910409691903321 |
| Singapore : , : Springer Singapore : , : Imprint : Springer, , 2020 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Advances in Membrane Proteins : Building, Signaling and Malfunction / / edited by Yu Cao
| Advances in Membrane Proteins : Building, Signaling and Malfunction / / edited by Yu Cao |
| Edizione | [1st ed. 2019.] |
| Pubbl/distr/stampa | Singapore : , : Springer Singapore : , : Imprint : Springer, , 2019 |
| Descrizione fisica | 1 online resource (132 pages) |
| Disciplina | QP552.M44 |
| Soggetto topico |
Proteins
Pharmaceutical technology Protein Science Pharmaceutical Sciences/Technology Protein Structure |
| ISBN | 981-13-9077-0 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | 1. Cell adhesion molecules and development -- 2. Receptors and signal transduction -- 3. Single-transmembrane proteins and antibody drugs -- 4. Viral membrane proteins -- 5. Biosynthesis and folding of oily peptide chains -- 6. Quality control in producing membrane proteins. |
| Record Nr. | UNINA-9910350349503321 |
| Singapore : , : Springer Singapore : , : Imprint : Springer, , 2019 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Advances in Membrane Proteins : Part I: Mass Processing and Transportation / / edited by Yu Cao
| Advances in Membrane Proteins : Part I: Mass Processing and Transportation / / edited by Yu Cao |
| Edizione | [1st ed. 2018.] |
| Pubbl/distr/stampa | Singapore : , : Springer Singapore : , : Imprint : Springer, , 2018 |
| Descrizione fisica | 1 online resource (183 pages) |
| Disciplina | 572.696 |
| Soggetto topico |
Proteins
Pharmaceutical technology Protein Science Pharmaceutical Sciences/Technology Protein Structure |
| ISBN |
978-981-13-0532-0
981-13-0532-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Chapter 1: Membrane Proteins as Critical Molecules -- Chapter 2: Channels -- Chapter 3: Solute Transporters. Chapter 4. Cytoplasmic Membrane Proteins -- Chapter 5: Nuclear Membrane Proteins: the transportation of genetic materials -- Chapter 6. Membrane Embedded Enzymes and Hydrophobic bio-catalysis. |
| Record Nr. | UNINA-9910298421903321 |
| Singapore : , : Springer Singapore : , : Imprint : Springer, , 2018 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Algorithms in Bioinformatics [[electronic resource] ] : 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings / / edited by Mihai Pop, Hélène Touzet
| Algorithms in Bioinformatics [[electronic resource] ] : 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings / / edited by Mihai Pop, Hélène Touzet |
| Edizione | [1st ed. 2015.] |
| Pubbl/distr/stampa | Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2015 |
| Descrizione fisica | 1 online resource (XX, 328 p. 85 illus.) |
| Disciplina | 572.80285 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Bioinformatics
Algorithms Computer science—Mathematics Data mining Proteins Computational Biology/Bioinformatics Algorithm Analysis and Problem Complexity Discrete Mathematics in Computer Science Data Mining and Knowledge Discovery Protein Structure |
| ISBN | 3-662-48221-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Preface -- Organization -- Abstracts -- Reference-free Compression of High Throughput Sequencing Data with a Probabilistic de Bruijn Graph -- Genome Scaffolding with PE-Contaminated Mate-Pair Libraries -- Network Properties of the Ensemble of RNA Structures -- Contents -- BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules -- 1 Introduction -- 2 Background -- 3 Solution -- 3.1 Network Modules with Flexible Coherency -- 3.2 BicNET: Efficient Biclustering of Biological Networks -- 4 Results and Discussion -- 4.1 Results on Synthetic Data -- 4.2 Results on Real Data -- 5 Conclusions and Future Work -- References -- Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via WAVE -- 1 Introduction -- 1.1 Motivation -- 1.2 Related Work -- 1.3 Our Contributions and Significance -- 2 Methods -- 2.1 Data -- 2.2 Combining Topological and Sequence Information Within NCF -- 2.3 Evaluation of Alignment Quality -- 2.4 Our Methodology -- 3 Results and Discussion -- 3.1 Comparison of Edge-Weighted and Edge-Unweighted Versions of WAVE -- 3.2 Comparison of Different Parameter Values Within WAVE -- 3.3 Comparison of Five NCF-AS Methods -- 3.4 Comparison of WAVE with Very Recent Methods -- 4 Concluding Remarks -- A Appendix -- A.1 Appendix Figures -- References -- The Topological Profile of a Model of Protein Network Evolution Can Direct Model Improvement -- 1 Introduction -- 2 Methods -- 2.1 The Evolutionary Model -- 2.2 The Empirical Network -- 2.3 Topological Measures Assessed -- 3 Results -- 3.1 Success of Driving Properties Towards the Empirical Topology -- 3.2 Non-Optimized Topological Properties that Trend Towards Empirical Values -- 3.3 Variability of Topological Measures -- 3.4 Correlation Among Topological Characteristics -- 3.5 Improving the Evolutionary Model -- 4 Conclusion.
References -- Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns -- 1 Introduction -- 2 Regular Tree Grammars and Curry-Encoding -- 3 The RTG Network Parse-and-Search Problem -- 4 Algorithms for Solving Problem 2 -- 4.1 Stage 1: Hypergraph Construction and Its Optimal Derivation -- 4.2 Stage 2: Computing K-Best Scoring Trees -- 5 Results -- 6 Discussion -- References -- Orthology Relation and Gene Tree Correction: Complexity Results -- 1 Introduction -- 2 Trees and Orthology Relations -- 2.1 Evolution of a Gene Family -- 2.2 Relation Graph -- 3 Relation Correction Problems -- 3.1 The Minimum Edge-Removal Consistency Problem -- 3.2 The Minimum Node-Removal Consistency Problem -- 4 Gene Tree Correction Problems -- 4.1 The Maximum Homology Correction Problem -- 4.2 The Maximum Clade Correction Problem -- 5 Algorithmic Avenues -- 6 Conclusion -- References -- Finding a Perfect Phylogeny from Mixed Tumor Samples -- 1 Introduction -- 2 Problem Formulation -- 3 A Characterization of Row-Conflict Graphs -- 4 Complexity Results -- 5 An Algorithm for the Case When No Column Is Contained in both Columns of a Pair of Conflicting Columns -- 6 Discussion -- References -- A Sub-quadratic Time and Space Complexity Solution for the Dated Tree Reconciliation Problem for Select Tree Topologies -- 1 Background -- 2 Methodology -- 2.1 The Number of Mapping Sites Required for Each Parasite Node -- 2.2 Space Complexity Reduction -- 2.3 Time Complexity Reduction -- 3 Results and Discussion -- 3.1 Analysis of Space Complexity Improvements (Synthetic Data) -- 3.2 Analysis of Time Complexity Improvements (Synthetic Data) -- 3.3 Time and Space Complexity Improvements for Biological Data -- References -- Maximum Parsimony Analysis of Gene Copy Number Changes -- 1 Introduction -- 2 Methods. 2.1 The Rectilinear Steiner Minimum Tree (RSMT) Problem -- 2.2 The Maximum Parsimony Tree (MPT) Problem -- 2.3 From MPT to RSMT -- 3 Experimental Results -- 3.1 Real Cancer Datasets -- 3.2 Simulated Cancer Data -- 4 Discussion -- References -- Multiple-Ancestor Localization for Recently Admixed Individuals -- 1 Introduction -- 2 Materials and Methods -- 2.1 Estimation of Spatial Parameters from Training Data -- 2.2 Localization of Individuals of 1-Generation Admixture -- 2.3 A Spatial Model for Individuals of g-generations Admixture -- 2.4 Simulation Setup -- 2.5 Method Comparison -- 3 Results -- 3.1 Localization of Simulated 1-Generation Admixed Individuals -- 3.2 Localization of Real Europeans from the POPRES Dataset -- 3.3 Localization of Simulated g-generation Admixed Individuals -- 4 Discussion -- References -- Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming -- 1 Biological Background and CH-Model -- 1.1 A Formal Model of a CH-trait at a Single Gene -- 2 The Phenotypic Distance Problem -- 2.1 An ILP Formulation for the Phenotypic Distance Problem -- 3 Simulated Data -- 4 The Most Striking and Positive Empirical Results -- 4.1 Speeding Up the Computations for Non-causal Genes and Permuted Data -- References -- Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data -- 1 Introduction -- 1.1 Additional Related Work -- 2 The nTDP Model -- 2.1 The Likelihood Function -- 2.2 Nonparametric Form of the Effect Functions -- 3 Optimal Algorithms for Training and Inference -- 3.1 Training -- 3.2 Training Extensions -- 3.3 Inferring Domains Using the Trained Model -- 4 Results -- 4.1 Experimental Setup -- 4.2 nTDP Finds a Small Subset of Modifications Predictive of TADs -- 4.3 Predicting TADs from Histone Marks in Human -- 4.4 Multiscale Analysis of the Predicted TADs. 5 Conclusion -- References -- Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads -- 1 Introduction -- 2 Preliminaries -- 2.1 Pooling Design -- 2.2 Read Decoding -- 3 Methods -- 3.1 Indexing k-mers -- 3.2 Identification and Correction of Sequencing Errors -- 4 Experimental Results -- 4.1 Results on Synthetic Reads for the Rice Genome -- 4.2 Results on Real Reads from the Barley Genome -- References -- Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches -- 1 Introduction -- 1.1 Related Work -- 2 Methods -- 2.1 Overview -- 2.2 Correction of the de Bruijn Graph -- 2.3 Aligning Reads to a de Bruijn Graph -- 3 Results Concerning Maximal Exact Matches -- 3.1 Coverage by Exact Regions -- 3.2 Occurrence of Exact Regions -- 3.3 Applications -- 4 Results -- 4.1 Data -- 4.2 Parameters -- 4.3 Evaluation Metrics -- 4.4 Evaluation -- References -- Optimizing Read Reversals for Sequence Compression -- 1 Introduction -- 2 Problem Taxonomy -- 3 Hardness Results -- 4 Approximation Algorithms -- 4.1 Approximations Based on TSP -- 4.2 Ordering with Reversals for Palindromic Value Functions -- 5 Experimental Results -- References -- Circular Sequence Comparison with q-grams -- 1 Introduction -- 2 Definitions and Properties -- 3 Algorithms -- 3.1 Algorithm hCSC: a Heuristic Algorithm -- 3.2 Algorithm saCSC: an Exact Suffix-Array-based Algorithm -- 4 Experimental Results -- 4.1 Accuracy -- 4.2 Time Performance -- 4.3 Application to Real Data -- 5 Final Remarks -- References -- Bloom Filter Trie -- A Data Structure for Pan-Genome Storage -- 1 Introduction -- 2 Existing Approaches -- 2.1 Data Structures -- 2.2 Software for Pan-Genome Storage -- 3 The Bloom Filter Trie -- 3.1 Uncompressed Container -- 3.2 Compressed Container -- 4 Operations Supported by the Bloom Filter Trie -- 4.1 Look-Up -- 4.2 Insertion. 4.3 Color Compression -- 5 Traversing Successors and Predecessors -- 6 Evaluation -- 7 Conclusion -- References -- A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches -- 1 Introduction -- 2 Preliminaries -- 2.1 Related Work -- 3 The MissMax Algorithm -- 3.1 Initial Set Up: MaxCork(1) -- 3.2 Minimum MaxCork from the Previous Step -- 3.3 Potential Candidates from the Previous Step -- 3.4 Theoretical and Practical Considerations -- 4 Preliminary Experimental Analysis -- 5 Concluding Remarks -- References -- Models and Algorithms for Genome Rearrangement with Positional Constraints -- 1 Introduction -- 1.1 Genomes as Sets of Signed Integers -- 1.2 DCJ and Sorting DCJs -- 1.3 The Minimum Weighted Rearrangements Problem -- 1.4 Positional Constraints as Colored Adjacencies -- 1.5 Locality and the Adjacency Graph -- 1.6 A Positional Weight Function -- 2 Minimum Local Parsimonious Scenario -- 2.1 Colored Partitions -- 2.2 Even-length Paths -- 3 Conclusion -- References -- Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction -- 1 Introduction -- 2 Time and Space Efficient Computation of the MFE -- 2.1 Time and Space Efficient Bp-Based Folding -- 2.2 Time and Space Efficient Calculation of the MFE -- 2.3 The Difficulty of MFE Fold Reconstruction Compared to Bp-Based Folding -- 3 MFE Folding with Fold Reconstruction -- 3.1 Adding Trace Arrows -- 3.2 Avoiding Trace Arrows -- 3.3 Garbage Collecting Trace Arrows -- 3.4 Algorithm Summary -- 3.5 Complexity -- 4 Empirical Results -- 5 Conclusion and Future Work -- References -- A Sparsified Four-Russian Algorithm for RNA Folding -- 1 Introduction -- 2 Problem Definition and Basic Algorithm -- 2.1 Extending the Notation and Moving Towards a Vector by Vector Computation of -- 3 Sparsification of the SSF Algorithm -- 3.1 OCT and STEP Sub-instances of Sequence. 4 On-demand Four Russians Speedup. |
| Record Nr. | UNISA-996200356903316 |
| Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Algorithms in Bioinformatics : 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings / / edited by Mihai Pop, Hélène Touzet
| Algorithms in Bioinformatics : 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings / / edited by Mihai Pop, Hélène Touzet |
| Edizione | [1st ed. 2015.] |
| Pubbl/distr/stampa | Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2015 |
| Descrizione fisica | 1 online resource (XX, 328 p. 85 illus.) |
| Disciplina | 572.80285 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Bioinformatics
Algorithms Computer science—Mathematics Data mining Proteins Computational Biology/Bioinformatics Algorithm Analysis and Problem Complexity Discrete Mathematics in Computer Science Data Mining and Knowledge Discovery Protein Structure |
| ISBN | 3-662-48221-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Preface -- Organization -- Abstracts -- Reference-free Compression of High Throughput Sequencing Data with a Probabilistic de Bruijn Graph -- Genome Scaffolding with PE-Contaminated Mate-Pair Libraries -- Network Properties of the Ensemble of RNA Structures -- Contents -- BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules -- 1 Introduction -- 2 Background -- 3 Solution -- 3.1 Network Modules with Flexible Coherency -- 3.2 BicNET: Efficient Biclustering of Biological Networks -- 4 Results and Discussion -- 4.1 Results on Synthetic Data -- 4.2 Results on Real Data -- 5 Conclusions and Future Work -- References -- Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via WAVE -- 1 Introduction -- 1.1 Motivation -- 1.2 Related Work -- 1.3 Our Contributions and Significance -- 2 Methods -- 2.1 Data -- 2.2 Combining Topological and Sequence Information Within NCF -- 2.3 Evaluation of Alignment Quality -- 2.4 Our Methodology -- 3 Results and Discussion -- 3.1 Comparison of Edge-Weighted and Edge-Unweighted Versions of WAVE -- 3.2 Comparison of Different Parameter Values Within WAVE -- 3.3 Comparison of Five NCF-AS Methods -- 3.4 Comparison of WAVE with Very Recent Methods -- 4 Concluding Remarks -- A Appendix -- A.1 Appendix Figures -- References -- The Topological Profile of a Model of Protein Network Evolution Can Direct Model Improvement -- 1 Introduction -- 2 Methods -- 2.1 The Evolutionary Model -- 2.2 The Empirical Network -- 2.3 Topological Measures Assessed -- 3 Results -- 3.1 Success of Driving Properties Towards the Empirical Topology -- 3.2 Non-Optimized Topological Properties that Trend Towards Empirical Values -- 3.3 Variability of Topological Measures -- 3.4 Correlation Among Topological Characteristics -- 3.5 Improving the Evolutionary Model -- 4 Conclusion.
References -- Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns -- 1 Introduction -- 2 Regular Tree Grammars and Curry-Encoding -- 3 The RTG Network Parse-and-Search Problem -- 4 Algorithms for Solving Problem 2 -- 4.1 Stage 1: Hypergraph Construction and Its Optimal Derivation -- 4.2 Stage 2: Computing K-Best Scoring Trees -- 5 Results -- 6 Discussion -- References -- Orthology Relation and Gene Tree Correction: Complexity Results -- 1 Introduction -- 2 Trees and Orthology Relations -- 2.1 Evolution of a Gene Family -- 2.2 Relation Graph -- 3 Relation Correction Problems -- 3.1 The Minimum Edge-Removal Consistency Problem -- 3.2 The Minimum Node-Removal Consistency Problem -- 4 Gene Tree Correction Problems -- 4.1 The Maximum Homology Correction Problem -- 4.2 The Maximum Clade Correction Problem -- 5 Algorithmic Avenues -- 6 Conclusion -- References -- Finding a Perfect Phylogeny from Mixed Tumor Samples -- 1 Introduction -- 2 Problem Formulation -- 3 A Characterization of Row-Conflict Graphs -- 4 Complexity Results -- 5 An Algorithm for the Case When No Column Is Contained in both Columns of a Pair of Conflicting Columns -- 6 Discussion -- References -- A Sub-quadratic Time and Space Complexity Solution for the Dated Tree Reconciliation Problem for Select Tree Topologies -- 1 Background -- 2 Methodology -- 2.1 The Number of Mapping Sites Required for Each Parasite Node -- 2.2 Space Complexity Reduction -- 2.3 Time Complexity Reduction -- 3 Results and Discussion -- 3.1 Analysis of Space Complexity Improvements (Synthetic Data) -- 3.2 Analysis of Time Complexity Improvements (Synthetic Data) -- 3.3 Time and Space Complexity Improvements for Biological Data -- References -- Maximum Parsimony Analysis of Gene Copy Number Changes -- 1 Introduction -- 2 Methods. 2.1 The Rectilinear Steiner Minimum Tree (RSMT) Problem -- 2.2 The Maximum Parsimony Tree (MPT) Problem -- 2.3 From MPT to RSMT -- 3 Experimental Results -- 3.1 Real Cancer Datasets -- 3.2 Simulated Cancer Data -- 4 Discussion -- References -- Multiple-Ancestor Localization for Recently Admixed Individuals -- 1 Introduction -- 2 Materials and Methods -- 2.1 Estimation of Spatial Parameters from Training Data -- 2.2 Localization of Individuals of 1-Generation Admixture -- 2.3 A Spatial Model for Individuals of g-generations Admixture -- 2.4 Simulation Setup -- 2.5 Method Comparison -- 3 Results -- 3.1 Localization of Simulated 1-Generation Admixed Individuals -- 3.2 Localization of Real Europeans from the POPRES Dataset -- 3.3 Localization of Simulated g-generation Admixed Individuals -- 4 Discussion -- References -- Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming -- 1 Biological Background and CH-Model -- 1.1 A Formal Model of a CH-trait at a Single Gene -- 2 The Phenotypic Distance Problem -- 2.1 An ILP Formulation for the Phenotypic Distance Problem -- 3 Simulated Data -- 4 The Most Striking and Positive Empirical Results -- 4.1 Speeding Up the Computations for Non-causal Genes and Permuted Data -- References -- Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data -- 1 Introduction -- 1.1 Additional Related Work -- 2 The nTDP Model -- 2.1 The Likelihood Function -- 2.2 Nonparametric Form of the Effect Functions -- 3 Optimal Algorithms for Training and Inference -- 3.1 Training -- 3.2 Training Extensions -- 3.3 Inferring Domains Using the Trained Model -- 4 Results -- 4.1 Experimental Setup -- 4.2 nTDP Finds a Small Subset of Modifications Predictive of TADs -- 4.3 Predicting TADs from Histone Marks in Human -- 4.4 Multiscale Analysis of the Predicted TADs. 5 Conclusion -- References -- Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads -- 1 Introduction -- 2 Preliminaries -- 2.1 Pooling Design -- 2.2 Read Decoding -- 3 Methods -- 3.1 Indexing k-mers -- 3.2 Identification and Correction of Sequencing Errors -- 4 Experimental Results -- 4.1 Results on Synthetic Reads for the Rice Genome -- 4.2 Results on Real Reads from the Barley Genome -- References -- Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches -- 1 Introduction -- 1.1 Related Work -- 2 Methods -- 2.1 Overview -- 2.2 Correction of the de Bruijn Graph -- 2.3 Aligning Reads to a de Bruijn Graph -- 3 Results Concerning Maximal Exact Matches -- 3.1 Coverage by Exact Regions -- 3.2 Occurrence of Exact Regions -- 3.3 Applications -- 4 Results -- 4.1 Data -- 4.2 Parameters -- 4.3 Evaluation Metrics -- 4.4 Evaluation -- References -- Optimizing Read Reversals for Sequence Compression -- 1 Introduction -- 2 Problem Taxonomy -- 3 Hardness Results -- 4 Approximation Algorithms -- 4.1 Approximations Based on TSP -- 4.2 Ordering with Reversals for Palindromic Value Functions -- 5 Experimental Results -- References -- Circular Sequence Comparison with q-grams -- 1 Introduction -- 2 Definitions and Properties -- 3 Algorithms -- 3.1 Algorithm hCSC: a Heuristic Algorithm -- 3.2 Algorithm saCSC: an Exact Suffix-Array-based Algorithm -- 4 Experimental Results -- 4.1 Accuracy -- 4.2 Time Performance -- 4.3 Application to Real Data -- 5 Final Remarks -- References -- Bloom Filter Trie -- A Data Structure for Pan-Genome Storage -- 1 Introduction -- 2 Existing Approaches -- 2.1 Data Structures -- 2.2 Software for Pan-Genome Storage -- 3 The Bloom Filter Trie -- 3.1 Uncompressed Container -- 3.2 Compressed Container -- 4 Operations Supported by the Bloom Filter Trie -- 4.1 Look-Up -- 4.2 Insertion. 4.3 Color Compression -- 5 Traversing Successors and Predecessors -- 6 Evaluation -- 7 Conclusion -- References -- A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches -- 1 Introduction -- 2 Preliminaries -- 2.1 Related Work -- 3 The MissMax Algorithm -- 3.1 Initial Set Up: MaxCork(1) -- 3.2 Minimum MaxCork from the Previous Step -- 3.3 Potential Candidates from the Previous Step -- 3.4 Theoretical and Practical Considerations -- 4 Preliminary Experimental Analysis -- 5 Concluding Remarks -- References -- Models and Algorithms for Genome Rearrangement with Positional Constraints -- 1 Introduction -- 1.1 Genomes as Sets of Signed Integers -- 1.2 DCJ and Sorting DCJs -- 1.3 The Minimum Weighted Rearrangements Problem -- 1.4 Positional Constraints as Colored Adjacencies -- 1.5 Locality and the Adjacency Graph -- 1.6 A Positional Weight Function -- 2 Minimum Local Parsimonious Scenario -- 2.1 Colored Partitions -- 2.2 Even-length Paths -- 3 Conclusion -- References -- Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction -- 1 Introduction -- 2 Time and Space Efficient Computation of the MFE -- 2.1 Time and Space Efficient Bp-Based Folding -- 2.2 Time and Space Efficient Calculation of the MFE -- 2.3 The Difficulty of MFE Fold Reconstruction Compared to Bp-Based Folding -- 3 MFE Folding with Fold Reconstruction -- 3.1 Adding Trace Arrows -- 3.2 Avoiding Trace Arrows -- 3.3 Garbage Collecting Trace Arrows -- 3.4 Algorithm Summary -- 3.5 Complexity -- 4 Empirical Results -- 5 Conclusion and Future Work -- References -- A Sparsified Four-Russian Algorithm for RNA Folding -- 1 Introduction -- 2 Problem Definition and Basic Algorithm -- 2.1 Extending the Notation and Moving Towards a Vector by Vector Computation of -- 3 Sparsification of the SSF Algorithm -- 3.1 OCT and STEP Sub-instances of Sequence. 4 On-demand Four Russians Speedup. |
| Record Nr. | UNINA-9910484594803321 |
| Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Application of Computational Intelligence to Biology / / edited by Ravi Bhramaramba, Akula Chandra Sekhar
| Application of Computational Intelligence to Biology / / edited by Ravi Bhramaramba, Akula Chandra Sekhar |
| Edizione | [1st ed. 2016.] |
| Pubbl/distr/stampa | Singapore : , : Springer Singapore : , : Imprint : Springer, , 2016 |
| Descrizione fisica | 1 online resource (107 p.) |
| Disciplina | 570.28563 |
| Collana | SpringerBriefs in Forensic and Medical Bioinformatics |
| Soggetto topico |
Computational intelligence
Bioinformatics Diabetes Proteins Biomedical engineering Health informatics Computational Intelligence Computational Biology/Bioinformatics Protein Structure Biomedical Engineering and Bioengineering Health Informatics |
| ISBN | 981-10-0391-2 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Enhancing the performance of Multi-parameter Patient Monitors by Homogeneous Kernel Maps -- Augmenting the performance of Multi-patient Parameter Monitoring system -- An Efficient Classification Model based on Ensemble of Fuzzy-Rough Classifier for Analysis of Medical Data -- A Comparative Study of Various Minutiae Extraction Methods for Fingerprint Recognition Based on Score Level Fusion -- Hybrid Model for Analysis of Abnormalities in Diabetic Cardiomyopathy -- Computational Screening of DrugBank DataBase for Novel Cell Cycle Inhibitors -- Pathway analysis of highly conserved Mitogen Activated Protein Kinases (MAPKs) -- Identification of drug targets from integrated database of diabetes mellitus Genes using Protein-Protein Interactions -- Distributed Data Mining for modeling and prediction of skin condiction in Cosmetic Industry - A Rough Set Theory Approach. |
| Record Nr. | UNINA-9910254239703321 |
| Singapore : , : Springer Singapore : , : Imprint : Springer, , 2016 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Arrestins - Pharmacology and Therapeutic Potential / / edited by Vsevolod V. Gurevich
| Arrestins - Pharmacology and Therapeutic Potential / / edited by Vsevolod V. Gurevich |
| Edizione | [1st ed. 2014.] |
| Pubbl/distr/stampa | Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2014 |
| Descrizione fisica | 1 online resource (441 p.) |
| Disciplina | 572.696 |
| Collana | Handbook of Experimental Pharmacology |
| Soggetto topico |
Pharmacology
Biochemistry Proteins Gene therapy Cell physiology Pharmacology/Toxicology Biochemistry, general Protein Structure Gene Therapy Cell Physiology Receptors |
| ISBN | 3-642-41199-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Therapeutic Potential of Small Molecules and Engineered Proteins.-Arrestin Interactions with G Protein-coupled Receptors -- Arrestin-biased GPCR Agonists -- Arrestin-1 Expression Levels, Rod Function and Health -- Protective Functions of Arrestin-1 in Photoreceptors -- Arrestin-4 and Cone Function -- Enhanced Phosphorylation-independent Arrestins and Gene Therapy -- Targeting Particular Receptors with Redesigned Non-visual Arrestins.- Arrestins binding to clathrin, AP2 and Role in GPCR trafficking -- Arrestins in Ubiquitination and Deubiquitination -- Arrestin Self-association -- Arrestin-dependent Activation of ERK and Src -- Arrestin-dependent Activation of JNK Family Kinases -- Arrestin-Mediated P38 Activation.- Arrestin-dependent PDE Localization -- Arrestins in Cell Migration -- Arrestins in Host-pathogen Interactions -- Arrestin Regulation of Small GTPases -- GPCRs and Arrestins in Airways: Implications for Asthma -- Arrestins as Regulatory Signaling Hubs in Cancer Pathways -- Arrestins in Pain and Anesthesia. |
| Record Nr. | UNINA-9910298309403321 |
| Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2014 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Bioinformatics: Sequences, Structures, Phylogeny / / edited by Asheesh Shanker
| Bioinformatics: Sequences, Structures, Phylogeny / / edited by Asheesh Shanker |
| Edizione | [1st ed. 2018.] |
| Pubbl/distr/stampa | Singapore : , : Springer Singapore : , : Imprint : Springer, , 2018 |
| Descrizione fisica | 1 online resource (402 pages) : illustrations |
| Disciplina | 570.285 |
| Soggetto topico |
Bioinformatics
Bioinformatics Computational biology Proteins Computer simulation Computational Biology/Bioinformatics Computer Appl. in Life Sciences Protein Structure Simulation and Modeling |
| ISBN | 981-13-1562-0 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Chapter 1 Bioinformatics and Intellectual Property Rights: An Introduction -- Chapter 2 Next Generation Sequencing: Technology, Advancements and Applications -- Chapter 3 Sequence Analysis -- Chapter 4 Understanding Genomic Variations in the Context of Health and Disease -- Chapter 5 Metagenomics: A Long Way to Go -- Chapter 6 Computational Epigenomics and Its Application in Regulatory Genomics -- Chapter 7 Data Mining to Detect Common, Unique and Polymorphic Simple Sequence Repeats -- Chapter 8 R-programming for Genome-wide Data Analysis -- Chapter 9 Phylogenetic Analysis -- Chapter 10 Structural Bioinformatics: Life Through the 3D Glasses -- Chapter 11 An Introduction to the Protein Folding Process and Survey of the Structural Parameters of Proteins Used for Computational Predictions -- Chapter 12 Quality Assessment of Protein Tertiary Structures: Past, Present and Future -- Chapter 13 Predicting Protein Function Using Homology Based Methods -- Chapter 14 Drug Discovery: An In Silico Approach -- Chapter 15 Advanced In-silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Corona Virus -- Chapter 16 Machine Learning: What, Why & How? -- Chapter 17 Command Line Tools in Linux for Handling Large Data Files. |
| Record Nr. | UNINA-9910298423803321 |
| Singapore : , : Springer Singapore : , : Imprint : Springer, , 2018 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Soggetto topico
-
Protein Structure
(75)
- Proteins (60)
- Protein Science (26)
- Bioinformatics (16)
- Proteins (14)