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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
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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
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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
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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
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Lo trovi qui: Univ. Federico II
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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
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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
Opac: Controlla la disponibilità qui
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
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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
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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
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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
Opac: Controlla la disponibilità qui