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Bioinformatics algorithms [[electronic resource] ] : techniques and applications / / edited by Ion I. Măndoiu and Alexander Zelikovsky
| Bioinformatics algorithms [[electronic resource] ] : techniques and applications / / edited by Ion I. Măndoiu and Alexander Zelikovsky |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Interscience, c2008 |
| Descrizione fisica | 1 online resource (517 p.) |
| Disciplina | 572.80285 |
| Altri autori (Persone) |
MăndoiuIon
ZelikovskyAlexander |
| Collana | Wiley series on bioinformatics |
| Soggetto topico |
Bioinformatics
Algorithms |
| ISBN |
1-281-23744-2
9786611237448 0-470-25344-4 0-470-25342-8 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
BIOINFORMATICS ALGORITHMS; CONTENTS; Preface; Contributors; 1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians; PART I TECHNIQUES; 2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison; 3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes; 4 Advances in Hidden Markov Models for Sequence Annotation; 5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns; 6 A Survey of Seeding for Sequence Alignment; 7 The Comparison of Phylogenetic Networks: Algorithms and Complexity
PART II GENOME AND SEQUENCE ANALYSIS8 Formal Models of Gene Clusters; 9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters; 10 Efficient Combinatorial Algorithms for DNA Sequence Processing; 11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints; 12 Recent Developments in Alignment and Motif Finding for Sequences and Networks; PART III MICROARRAY DESIGN AND DATA ANALYSIS; 13 Algorithms for Oligonucleotide Microarray Layout; 14 Classification Accuracy Based Microarray Missing Value Imputation; 15 Meta-Analysis of Microarray Data PART IV GENETIC VARIATION ANALYSIS16 Phasing Genotypes Using a Hidden Markov Model; 17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us?; 18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies; PART V STRUCTURAL AND SYSTEMS BIOLOGY; 19 Topological Indices in Combinatorial Chemistry; 20 Efficient Algorithms for Structural Recall in Databases; 21 Computational Approaches to Predict Protein-Protein and Domain-Domain Interactions; Index |
| Record Nr. | UNINA-9910145416003321 |
| Hoboken, N.J., : Wiley-Interscience, c2008 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Bioinformatics algorithms [[electronic resource] ] : techniques and applications / / edited by Ion I. Măndoiu and Alexander Zelikovsky
| Bioinformatics algorithms [[electronic resource] ] : techniques and applications / / edited by Ion I. Măndoiu and Alexander Zelikovsky |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Interscience, c2008 |
| Descrizione fisica | 1 online resource (517 p.) |
| Disciplina | 572.80285 |
| Altri autori (Persone) |
MăndoiuIon
ZelikovskyAlexander |
| Collana | Wiley series on bioinformatics |
| Soggetto topico |
Bioinformatics
Algorithms |
| ISBN |
1-281-23744-2
9786611237448 0-470-25344-4 0-470-25342-8 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
BIOINFORMATICS ALGORITHMS; CONTENTS; Preface; Contributors; 1 Educating Biologists in the 21st Century: Bioinformatics Scientists versus Bioinformatics Technicians; PART I TECHNIQUES; 2 Dynamic Programming Algorithms for Biological Sequence and Structure Comparison; 3 Graph Theoretical Approaches to Delineate Dynamics of Biological Processes; 4 Advances in Hidden Markov Models for Sequence Annotation; 5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns; 6 A Survey of Seeding for Sequence Alignment; 7 The Comparison of Phylogenetic Networks: Algorithms and Complexity
PART II GENOME AND SEQUENCE ANALYSIS8 Formal Models of Gene Clusters; 9 Integer Linear Programming Techniques for Discovering Approximate Gene Clusters; 10 Efficient Combinatorial Algorithms for DNA Sequence Processing; 11 Algorithms for Multiplex PCR Primer Set Selection with Amplification Length Constraints; 12 Recent Developments in Alignment and Motif Finding for Sequences and Networks; PART III MICROARRAY DESIGN AND DATA ANALYSIS; 13 Algorithms for Oligonucleotide Microarray Layout; 14 Classification Accuracy Based Microarray Missing Value Imputation; 15 Meta-Analysis of Microarray Data PART IV GENETIC VARIATION ANALYSIS16 Phasing Genotypes Using a Hidden Markov Model; 17 Analytical and Algorithmic Methods for Haplotype Frequency Inference: What Do They Tell Us?; 18 Optimization Methods for Genotype Data Analysis in Epidemiological Studies; PART V STRUCTURAL AND SYSTEMS BIOLOGY; 19 Topological Indices in Combinatorial Chemistry; 20 Efficient Algorithms for Structural Recall in Databases; 21 Computational Approaches to Predict Protein-Protein and Domain-Domain Interactions; Index |
| Record Nr. | UNINA-9910823387503321 |
| Hoboken, N.J., : Wiley-Interscience, c2008 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Bioinformatics research and applications : third international symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007 : proceedings / / Ion Măndoiu, Alexander Zelikovsky (Eds.)
| Bioinformatics research and applications : third international symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007 : proceedings / / Ion Măndoiu, Alexander Zelikovsky (Eds.) |
| Edizione | [1st ed. 2007.] |
| Pubbl/distr/stampa | Berlin, Germany ; ; New York, New York State : , : Springer, , [2007] |
| Descrizione fisica | 1 online resource (665 p.) |
| Disciplina | 570.285 |
| Collana | Lecture notes in bioinformatics |
| Soggetto topico |
Computational biology
Bioinformatics |
| ISBN | 3-540-72031-6 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | GFBA: A Biclustering Algorithm for Discovering Value-Coherent Biclusters -- Significance Analysis of Time-Course Gene Expression Profiles -- Data-Driven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in 0-Time Normalized Time-Course Microarray Data -- Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming -- A Multi-Stack Based Phylogenetic Tree Building Method -- A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance -- A Bootstrap Correspondence Analysis for Factorial Microarray Experiments with Replications -- Clustering Algorithms Optimizer: A Framework for Large Datasets -- Ranking Function Based on Higher Order Statistics (RF-HOS) for Two-Sample Microarray Experiments -- Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples -- Algorithm for Haplotype Inferring Via Galled-Tree Networks with Simple Galls -- Estimating Bacterial Diversity from Environmental DNA: A Maximum Likelihood Approach -- Invited Talk: Modern Homology Search -- Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data -- Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods -- An Empirical Comparison of Dimensionality Reduction Methods for Classifying Gene and Protein Expression Datasets -- NEURONgrid: A Toolkit for Generating Parameter-Space Maps Using NEURON in a Grid Environment -- An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets -- Wavelet Image Interpolation (WII): A Wavelet-Based Approach to Enhancement of Digital Mammography Images -- High Level Programming Environment System for Protein Structure Data -- Finding Minimal Sets of Informative Genes in Microarray Data -- Noise-Based Feature Perturbation as a Selection Method for Microarray Data -- Efficient Generation of Biologically Relevant Enriched Gene Sets -- Space and Time Efficient Algorithms to Discover Endogenous RNAi Patterns in Complete Genome Data -- A Fast Approximate Covariance-Model-Based Database Search Method for Non-coding RNA -- Extensions of Naive Bayes and Their Applications to Bioinformatics -- The Solution Space of Sorting by Reversals -- A Fast and Exact Algorithm for the Perfect Reversal Median Problem -- Genomic Signatures from DNA Word Graphs -- Enhancing Motif Refinement by Incorporating Comparative Genomics Data -- Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions -- Enhanced Prediction of Cleavage in Bovine Precursor Sequences -- Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome -- The Identification of Antisense Gene Pairs Through Available Software -- Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices -- Markov Model Variants for Appraisal of Coding Potential in Plant DNA -- Predicting Palmitoylation Sites Using a Regularised Bio-basis Function Neural Network -- A Novel Kernel-Based Approach for Predicting Binding Peptides for HLA Class II Molecules -- A Database for Prediction of Unique Peptide Motifs as Linear Epitopes -- A Novel Greedy Algorithm for the Minimum Common String Partition Problem -- An Efficient Algorithm for Finding Gene-Specific Probes for DNA Microarrays -- Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm -- Cancer Class Discovery Using Non-negative Matrix Factorization Based on Alternating Non-negativity-Constrained Least Squares -- A Support Vector Machine Ensemble for Cancer Classification Using Gene Expression Data -- Combining SVM Classifiers Using Genetic Fuzzy Systems Based on AUC for Gene Expression Data Analysis -- A BP-SCFG Based Approach for RNA Secondary Structure Prediction with Consecutive Bases Dependency and Their Relative Positions Information -- Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice -- Statistical Estimate for the Size of the Protein Structural Vocabulary -- Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI -- An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes -- Using Multi Level Nearest Neighbor Classifiers for G-Protein Coupled Receptor Sub-families Prediction -- Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood -- Reconstruction of 3D Structures from Protein Contact Maps -- A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction -- DNA Sites Buried in Nucleosome Become Accessible at Room Temperature: A Discrete-Event-Simulation Based Modeling Approach -- Comparative Analysis of Gene-Coexpression Networks Across Species -- Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information -- Extending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level. |
| Record Nr. | UNINA-9910483120303321 |
| Berlin, Germany ; ; New York, New York State : , : Springer, , [2007] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Bioinformatics research and applications : third international symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007 : proceedings / / Ion Măndoiu, Alexander Zelikovsky (Eds.)
| Bioinformatics research and applications : third international symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007 : proceedings / / Ion Măndoiu, Alexander Zelikovsky (Eds.) |
| Edizione | [1st ed. 2007.] |
| Pubbl/distr/stampa | Berlin, Germany ; ; New York, New York State : , : Springer, , [2007] |
| Descrizione fisica | 1 online resource (665 p.) |
| Disciplina | 570.285 |
| Collana | Lecture notes in bioinformatics |
| Soggetto topico |
Computational biology
Bioinformatics |
| ISBN | 3-540-72031-6 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | GFBA: A Biclustering Algorithm for Discovering Value-Coherent Biclusters -- Significance Analysis of Time-Course Gene Expression Profiles -- Data-Driven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in 0-Time Normalized Time-Course Microarray Data -- Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming -- A Multi-Stack Based Phylogenetic Tree Building Method -- A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance -- A Bootstrap Correspondence Analysis for Factorial Microarray Experiments with Replications -- Clustering Algorithms Optimizer: A Framework for Large Datasets -- Ranking Function Based on Higher Order Statistics (RF-HOS) for Two-Sample Microarray Experiments -- Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples -- Algorithm for Haplotype Inferring Via Galled-Tree Networks with Simple Galls -- Estimating Bacterial Diversity from Environmental DNA: A Maximum Likelihood Approach -- Invited Talk: Modern Homology Search -- Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data -- Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods -- An Empirical Comparison of Dimensionality Reduction Methods for Classifying Gene and Protein Expression Datasets -- NEURONgrid: A Toolkit for Generating Parameter-Space Maps Using NEURON in a Grid Environment -- An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets -- Wavelet Image Interpolation (WII): A Wavelet-Based Approach to Enhancement of Digital Mammography Images -- High Level Programming Environment System for Protein Structure Data -- Finding Minimal Sets of Informative Genes in Microarray Data -- Noise-Based Feature Perturbation as a Selection Method for Microarray Data -- Efficient Generation of Biologically Relevant Enriched Gene Sets -- Space and Time Efficient Algorithms to Discover Endogenous RNAi Patterns in Complete Genome Data -- A Fast Approximate Covariance-Model-Based Database Search Method for Non-coding RNA -- Extensions of Naive Bayes and Their Applications to Bioinformatics -- The Solution Space of Sorting by Reversals -- A Fast and Exact Algorithm for the Perfect Reversal Median Problem -- Genomic Signatures from DNA Word Graphs -- Enhancing Motif Refinement by Incorporating Comparative Genomics Data -- Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions -- Enhanced Prediction of Cleavage in Bovine Precursor Sequences -- Invited Talk: A Computational Study of Bidirectional Promoters in the Human Genome -- The Identification of Antisense Gene Pairs Through Available Software -- Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices -- Markov Model Variants for Appraisal of Coding Potential in Plant DNA -- Predicting Palmitoylation Sites Using a Regularised Bio-basis Function Neural Network -- A Novel Kernel-Based Approach for Predicting Binding Peptides for HLA Class II Molecules -- A Database for Prediction of Unique Peptide Motifs as Linear Epitopes -- A Novel Greedy Algorithm for the Minimum Common String Partition Problem -- An Efficient Algorithm for Finding Gene-Specific Probes for DNA Microarrays -- Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm -- Cancer Class Discovery Using Non-negative Matrix Factorization Based on Alternating Non-negativity-Constrained Least Squares -- A Support Vector Machine Ensemble for Cancer Classification Using Gene Expression Data -- Combining SVM Classifiers Using Genetic Fuzzy Systems Based on AUC for Gene Expression Data Analysis -- A BP-SCFG Based Approach for RNA Secondary Structure Prediction with Consecutive Bases Dependency and Their Relative Positions Information -- Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice -- Statistical Estimate for the Size of the Protein Structural Vocabulary -- Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI -- An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes -- Using Multi Level Nearest Neighbor Classifiers for G-Protein Coupled Receptor Sub-families Prediction -- Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood -- Reconstruction of 3D Structures from Protein Contact Maps -- A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction -- DNA Sites Buried in Nucleosome Become Accessible at Room Temperature: A Discrete-Event-Simulation Based Modeling Approach -- Comparative Analysis of Gene-Coexpression Networks Across Species -- Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information -- Extending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level. |
| Record Nr. | UNISA-996465879003316 |
| Berlin, Germany ; ; New York, New York State : , : Springer, , [2007] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky
| Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, , [2016] |
| Descrizione fisica | 1 online resource (461 p.) |
| Disciplina | 611/.0181663 |
| Collana | Wiley series on bioinformatics : computational techniques and engineering |
| Soggetto topico |
Nucleotide sequence - Methodology
Nucleotide sequence - Data processing |
| ISBN |
1-119-27217-3
1-119-27216-5 1-119-27218-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Copyright; Contents; Contributors; Preface; About the Companion Website; Part I Computing and Experimental Infrastructure for NGS; Chapter 1 Cloud Computing for Next-Generation Sequencing Data Analysis; 1.1 Introduction; 1.2 Challenges for NGS Data Analysis; 1.3 Background For Cloud Computing and its Programming Models; 1.4 Cloud Computing Services for NGS Data Analysis; 1.5 Conclusions and Future Directions; References; Chapter 2 Introduction to the Analysis of Environmental Sequence Information Using Metapathways; 2.1 Introduction & Overview; 2.2 Background
2.3 Metapathways Processes2.4 Big Data Processing; 2.5 Downstream Analyses; 2.6 Conclusions; References; Chapter 3 Pooling Strategy for Massive Viral Sequencing; 3.1 Introduction; 3.2 Design of Pools for Big Viral Data; 3.3 Deconvolution of Viral Samples From Pools; 3.4 Performance of Pooling Methods on Simulated Data; 3.5 Experimental Validation of Pooling Strategy; 3.6 Conclusion; References; Chapter 4 Applications of High-Fidelity Sequencing Protocol to RNA Viruses; 4.1 Introduction; 4.2 High-Fidelity Sequencing Protocol; 4.3 Assembly of High-Fidelity Sequencing Data 4.4 Performance of VGA on Simulated Data4.5 Performance of Existing Viral Assemblers on Simulated Consensus Error-Corrected Reads; 4.6 Performance of VGA on Real Hiv Data; 4.7 Comparison of Alignment on Error-Corrected Reads; 4.8 Evaluating of Error Correction Tools Based on High-Fidelity Sequencing Reads; Acknowledgment; References; Part II Genomics and Epigenomics; Chapter 5 Scaffolding Algorithms; 5.1 Scaffolding; 5.2 State-of-The-Art Scaffolding Tools; 5.3 Recent Scaffolding Tools; 5.4 Scaffolding Software Evaluation; References; Chapter 6 Genomic Variants Detection and Genotyping 6.1 Introduction6.2 Methods for Detection and Genotyping OF SNPs and Small Indels; 6.3 Methods for Detection and Genotyping of CNVs; 6.4 Putting Everything Together; References; Chapter 7 Discovering and Genotyping Twilight Zone Deletions; 7.1 Introduction; 7.2 Notation; 7.3 Non-Twilight-Zone Deletion Discovery; 7.4 Discovering ""Twilight Zone"" Deletions: New Solutions; 7.5 Genotyping ""Twilight Zone"" Deletions; 7.6 Results; 7.7 Discussion; 7.8 Availability; Acknowledgments; References; Chapter 8 Computational Approaches for Finding Long Insertions and Deletions with NGS Data 8.1 Background8.2 Methods; 8.3 Applications; 8.4 Conclusions and Future Directions; Acknowledgment; References; Chapter 9 Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies; 9.1 Introduction; 9.2 Enrichment-Based Approaches; 9.3 Bisulfite Treatment-Based Approaches; 9.4 Conclusion; References; Chapter 10 Bisulfite-Conversion-Based Methods for DNA Methylation Sequencing Data Analysis; 10.1 Introduction; 10.2 The Problem of Mapping BS-Treated Reads; 10.3 Algorithmic Approaches to the Problem Of Mapping BS-Treated Reads 10.4 Methylation Estimation |
| Record Nr. | UNINA-9910135021603321 |
| Hoboken, New Jersey : , : John Wiley & Sons, , [2016] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky
| Computational methods for next generation sequencing data analysis / / edited by Ion Măndoiu, Alexander Zelikovsky |
| Pubbl/distr/stampa | Hoboken, New Jersey : , : John Wiley & Sons, , [2016] |
| Descrizione fisica | 1 online resource (461 p.) |
| Disciplina | 611/.0181663 |
| Collana | Wiley series on bioinformatics : computational techniques and engineering |
| Soggetto topico |
Nucleotide sequence - Methodology
Nucleotide sequence - Data processing |
| ISBN |
1-119-27217-3
1-119-27216-5 1-119-27218-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Title Page; Copyright; Contents; Contributors; Preface; About the Companion Website; Part I Computing and Experimental Infrastructure for NGS; Chapter 1 Cloud Computing for Next-Generation Sequencing Data Analysis; 1.1 Introduction; 1.2 Challenges for NGS Data Analysis; 1.3 Background For Cloud Computing and its Programming Models; 1.4 Cloud Computing Services for NGS Data Analysis; 1.5 Conclusions and Future Directions; References; Chapter 2 Introduction to the Analysis of Environmental Sequence Information Using Metapathways; 2.1 Introduction & Overview; 2.2 Background
2.3 Metapathways Processes2.4 Big Data Processing; 2.5 Downstream Analyses; 2.6 Conclusions; References; Chapter 3 Pooling Strategy for Massive Viral Sequencing; 3.1 Introduction; 3.2 Design of Pools for Big Viral Data; 3.3 Deconvolution of Viral Samples From Pools; 3.4 Performance of Pooling Methods on Simulated Data; 3.5 Experimental Validation of Pooling Strategy; 3.6 Conclusion; References; Chapter 4 Applications of High-Fidelity Sequencing Protocol to RNA Viruses; 4.1 Introduction; 4.2 High-Fidelity Sequencing Protocol; 4.3 Assembly of High-Fidelity Sequencing Data 4.4 Performance of VGA on Simulated Data4.5 Performance of Existing Viral Assemblers on Simulated Consensus Error-Corrected Reads; 4.6 Performance of VGA on Real Hiv Data; 4.7 Comparison of Alignment on Error-Corrected Reads; 4.8 Evaluating of Error Correction Tools Based on High-Fidelity Sequencing Reads; Acknowledgment; References; Part II Genomics and Epigenomics; Chapter 5 Scaffolding Algorithms; 5.1 Scaffolding; 5.2 State-of-The-Art Scaffolding Tools; 5.3 Recent Scaffolding Tools; 5.4 Scaffolding Software Evaluation; References; Chapter 6 Genomic Variants Detection and Genotyping 6.1 Introduction6.2 Methods for Detection and Genotyping OF SNPs and Small Indels; 6.3 Methods for Detection and Genotyping of CNVs; 6.4 Putting Everything Together; References; Chapter 7 Discovering and Genotyping Twilight Zone Deletions; 7.1 Introduction; 7.2 Notation; 7.3 Non-Twilight-Zone Deletion Discovery; 7.4 Discovering ""Twilight Zone"" Deletions: New Solutions; 7.5 Genotyping ""Twilight Zone"" Deletions; 7.6 Results; 7.7 Discussion; 7.8 Availability; Acknowledgments; References; Chapter 8 Computational Approaches for Finding Long Insertions and Deletions with NGS Data 8.1 Background8.2 Methods; 8.3 Applications; 8.4 Conclusions and Future Directions; Acknowledgment; References; Chapter 9 Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies; 9.1 Introduction; 9.2 Enrichment-Based Approaches; 9.3 Bisulfite Treatment-Based Approaches; 9.4 Conclusion; References; Chapter 10 Bisulfite-Conversion-Based Methods for DNA Methylation Sequencing Data Analysis; 10.1 Introduction; 10.2 The Problem of Mapping BS-Treated Reads; 10.3 Algorithmic Approaches to the Problem Of Mapping BS-Treated Reads 10.4 Methylation Estimation |
| Record Nr. | UNINA-9910812209403321 |
| Hoboken, New Jersey : , : John Wiley & Sons, , [2016] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
