Bioinformatics Methods and Protocols

The book also includes a set of guidelines for designing and teaching an introductory bioinformatics course and numerous illustrative examples to teach the reader how to solve problems.

Author: Stephen Misener

Publisher: Springer Science & Business Media

ISBN: 9781592591923

Category: Computers

Page: 500

View: 564

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In Bioinformatics: Methods and Protocols, hands-on users and experts survey the key biological software packages, offering useful tips and an overview of current developments. Among the sequence analysis systems reviewed are GCG, Omiga, MacVector, DNASTAR, PepTool, GeneTool, and Staden. Molecular biology software includes Genotator and sequence-similarity searching using FASTA, CLUSTAL multiple sequence alignment, and phylogenic analysis. Web-based resources are examined for primary sequence databases, primary sequence analysis methods, and clinical databases useful in molecular medicine. The book also includes a set of guidelines for designing and teaching an introductory bioinformatics course and numerous illustrative examples to teach the reader how to solve problems. Bioinformatics: Methods and Protocols offers to experienced and novice biologists a broad overview of the computational tools that have reshaped modern biology. It constitutes a gold-standard reference for today's scientists who wish to develop and hone their bioinformatics skills towards the discovery of new biological relationships.
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Plant Bioinformatics

This book aims to assist research scientists in choosing the most applicable database or bioinformatics tools to aid and promote their research in plant biotechnology.

Author: David Edwards

Publisher: Springer Science & Business Media

ISBN: 9781588296535

Category: Science

Page: 552

View: 881

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This book aims to assist research scientists in choosing the most applicable database or bioinformatics tools to aid and promote their research in plant biotechnology. Chapters include practical examples and highlight common problems encountered in bioinformatics analysis. Further chapters are aimed at researchers developing bioinformatics databases and tools, detailing commonly applied database formats and biology-focused scripting languages.
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Bioinformatics for Omics Data

Divided into three convenient sections, this detailed volume covers central analysis strategies, standardization and data-management guidelines, and fundamental statistics for analyzing Omics profiles, followed by a section on ...

Author: Bernd Mayer

Publisher: Humana Press

ISBN: 1617790265

Category: Science

Page: 584

View: 758

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Presenting an area of research that intersects with and integrates diverse disciplines, including molecular biology, applied informatics, and statistics, among others, Bioinformatics for Omics Data: Methods and Protocols collects contributions from expert researchers in order to provide practical guidelines to this complex study. Divided into three convenient sections, this detailed volume covers central analysis strategies, standardization and data-management guidelines, and fundamental statistics for analyzing Omics profiles, followed by a section on bioinformatics approaches for specific Omics tracks, spanning genome, transcriptome, proteome, and metabolome levels, as well as an assortment of examples of integrated Omics bioinformatics applications, complemented by case studies on biomarker and target identification in the context of human disease. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Bioinformatics for Omics Data: Methods and Protocols serves as an ideal guide to scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this research field.
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Plant Bioinformatics

The second edition of this volume focuses on applied bioinformatics with specific applications to crops and model plants.

Author: David Edwards

Publisher:

ISBN: 1493931679

Category: Bioinformatics

Page: 365

View: 825

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The second edition of this volume focuses on applied bioinformatics with specific applications to crops and model plants. Plant Bioinformatics: Methods and Protocols is aimed at plant biologists who have an interest in, or requirement for, accessing and manipulating huge amounts of data being generated by high throughput technologies. This book would also be of interest to bioinformaticians and computer scientists who would benefit from an introduction to the different tools and systems available for plant research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and software, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Plant Bioinformatics: Methods and Protocols helps researchers with the increasing volume and diversity of data from different plants and also the integration of multiple diverse forms of data.
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Structural Bioinformatics

This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions.

Author: Zoltán Gáspári

Publisher: Humana

ISBN: 1071602721

Category: Science

Page: 256

View: 893

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This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions. The chapters in this book cover tools and servers such as LiteMol; Bio3D-Web; DALI; CATH; HoTMuSiC, a contact-base protein structure analysis tool known as CAD-Score; PyDockSaxs and HADDOCK; CombDock and DockStar; the BioMagResBank database; as well as BME and CoNSEnsX+. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Structural Bioinformatics: Methods and Protocols is a practical guide for researchers to learn more about the aforementioned tools to further enhance their studies in the growing field of structural bioinformatics. Chapter 13 is available open access under a CC-BY 4.0 license via link.springer.com.
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Next Generation Microarray Bioinformatics

Authoritative and practical, Next Generation Microarray Bioinformatics: Methods and Protocols seeks to aid scientists in the further study of this crucially important research into the human DNA.

Author: Junbai Wang

Publisher: Humana Press

ISBN: 161779399X

Category: Science

Page: 401

View: 866

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Recent improvements in the efficiency, quality, and cost of genome-wide sequencing have prompted biologists and biomedical researchers to move away from microarray-based technology to ultra high-throughput, massively parallel genomic sequencing (Next Generation Sequencing, NGS) technology. In Next Generation Microarray Bioinformatics: Methods and Protocols, expert researchers in the field provide techniques to bring together current computational and statistical methods to analyze and interpreting both microarray and NGS data. These methods and techniques include resources for microarray bioinformatics, microarray data analysis, microarray bioinformatics in systems biology, next generation sequencing data analysis, and emerging applications of microarray and next generation sequencing. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Authoritative and practical, Next Generation Microarray Bioinformatics: Methods and Protocols seeks to aid scientists in the further study of this crucially important research into the human DNA.
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Trichoderma reesei

This detailed book collects standard techniques and cutting-edge methods that are frequently used by the research community studying the fungus Trichoderma reesei.

Author: Astrid R. Mach-Aigner

Publisher: Humana

ISBN: 1071610473

Category: Science

Page: 364

View: 911

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This detailed book collects standard techniques and cutting-edge methods that are frequently used by the research community studying the fungus Trichoderma reesei. Beginning with overviews of its evolution, its use in the production of industrially-relevant enzymes, and synthetic biology applications, the volume continues with methods covering topics from transformation techniques and gene editing to downstream-analytical applications and -omics analyses and the corresponding bioinformatics approaches. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Trichoderma reesei: Methods and Protocols serves as an ideal guide for a wide range of audiences, from students who want to familiarize themselves with basic research protocols to experienced scientists who are planning to establish a new method in their laboratories, working with this dynamic fungus.
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Computational Cell Biology

This volume details computational techniques for analyses of a wide range of biological contexts, providing an overview of the most up-to-date techniques used in the field.

Author: Louise von Stechow

Publisher: Humana Press

ISBN: 1493986171

Category: Science

Page: 436

View: 519

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This volume details computational techniques for analyses of a wide range of biological contexts, providing an overview of the most up-to-date techniques used in the field. Chapters guide the reader through available data resources and analysis methods and easy-to-follow protocols that allow the researcher to apply various computational tools to an array of different data types. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory and computational protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Cell Biology: Method and Protocols aims to ensure successful results in the further study of this vital field.
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Therapeutic Proteins

Emphasizing the newest developments in the field, this second edition also includes additional emphasis on discovery, including new display and screening methods as well as the design and engineering of new types of therapeutic proteins.

Author: Vladimir Voynov

Publisher: Humana Press

ISBN: 1493959492

Category: Medical

Page: 516

View: 274

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Emphasizing the newest developments in the field, this volume presents detailed methodswith added emphasison therapeutic protein discovery. It features key tips and valuable implementation advice to ensure successful results."
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Notch Signaling

Notch Signaling: Methods and Protocols focuses on molecular, biochemical and bioinformatics aspects of Notch signaling.

Author: Hugo J. Bellen

Publisher: Humana Press

ISBN: 1493955101

Category: Science

Page: 351

View: 636

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Notch Signaling: Methods and Protocols focuses on molecular, biochemical and bioinformatics aspects of Notch signaling. Chapters analyze the Notch interactome, post-translational modifications of Notch, ligand binding assays, methods to assess proteolytic cleavage and transcriptional targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Notch Signaling: Methods and Protocols is a valuable contribution to hundreds of labs and thousands of scientists who pursue this research area with vigor.
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RNA Modifications

This detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications.

Author: Mary McMahon

Publisher: Humana

ISBN: 1071613731

Category: Science

Page: 427

View: 466

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This detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications. Importantly, the methodologies and tools described herein can be applied to a wide variety of organisms and can be used to address biological and clinical questions. Beginning with a section on bioinformatics tools, the collection continues with sections on detecting RNA modifications using Nanopore direct RNA sequencing, next-generation sequencing approaches, qPCR- and molecular biology-based methods, mass spectrometry- and NMR-based methods, as well as approaches to assess kinetics, determinants, and functions of RNA modifications. Written for the highly successful Methods in Molecular Biology series style, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Modifications: Methods and Protocols serves as an ideal guide for those working directly in the fields of epitranscriptomics and post-transcriptional gene regulation, as well as for scientists and clinicians interested in bioinformatic tools to study RNA modifications and techniques to dissect their roles in physiology and disease. /divChapter 20 is available open access under a CC BY 4.0 license.
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Multiple Sequence Alignment

Chapter “Alignment of Biological Sequences with Jalview” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Author: Kazutaka Katoh

Publisher: Humana

ISBN: 107161035X

Category: Science

Page: 323

View: 253

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This volume is a collection of protocols that discuss how to install and run tools for calculation and visualization of multiple sequence alignments (MSAs), and other analyses related to MSAs. Chapters cover basic MSA tools and specially designed tools to deal with new types of data resulting from recent developments in sequencing technologies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and data, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Multiple Sequence Alignments: Methods and Protocols is a valuable resource for experimental biologists who want to run MSA tools, and acquire basic and advanced information to further their understanding of the available technologies.
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Bioinformatics for Cancer Immunotherapy

This volume focuses on a variety of in silico protocols of the latest bioinformatics tools and computational pipelines developed for neo-antigen identification and immune cell analysis from high-throughput sequencing data for cancer ...

Author: Sebastian Boegel

Publisher: Humana

ISBN: 1071603264

Category: Medical

Page: 304

View: 335

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This volume focuses on a variety of in silico protocols of the latest bioinformatics tools and computational pipelines developed for neo-antigen identification and immune cell analysis from high-throughput sequencing data for cancer immunotherapy. The chapters in this book cover topics that discuss the two emerging concepts in recognition of tumor cells using endogenous T cells: cancer vaccines against neo-antigens presented on HLA class I and II alleles, and checkpoint inhibitors. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Bioinformatics for Cancer Immunotherapy: Methods and Protocols is a valuable research tool for any scientist and researcher interested in learning more about this exciting and developing field.
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Next Generation Microarray Bioinformatics

Authoritative and practical, Next Generation Microarray Bioinformatics: Methods and Protocols seeks to aid scientists in the further study of this crucially important research into the human DNA.

Author: Junbai Wang

Publisher: Humana Press

ISBN: 1493958577

Category: Science

Page: 401

View: 641

Download →

Recent improvements in the efficiency, quality, and cost of genome-wide sequencing have prompted biologists and biomedical researchers to move away from microarray-based technology to ultra high-throughput, massively parallel genomic sequencing (Next Generation Sequencing, NGS) technology. In Next Generation Microarray Bioinformatics: Methods and Protocols, expert researchers in the field provide techniques to bring together current computational and statistical methods to analyze and interpreting both microarray and NGS data. These methods and techniques include resources for microarray bioinformatics, microarray data analysis, microarray bioinformatics in systems biology, next generation sequencing data analysis, and emerging applications of microarray and next generation sequencing. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Authoritative and practical, Next Generation Microarray Bioinformatics: Methods and Protocols seeks to aid scientists in the further study of this crucially important research into the human DNA.
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DNA Modifications

This book provides an overview of methods and experimental protocols that are currently used to analyze the presence and abundance of non-canonical DNA nucleotides in different biological systems.

Author: Alexey Ruzov

Publisher: Humana

ISBN: 1071608754

Category: Science

Page: 495

View: 594

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This book provides an overview of methods and experimental protocols that are currently used to analyze the presence and abundance of non-canonical DNA nucleotides in different biological systems. Focusing particularly on the newly discovered and less studied DNA modifications that are enzymatically produced and are likely to play specific roles in various biological processes, the volume explores chromatography- and mass spectrometry-based techniques for the detection and quantification of DNA modifications, antibody-based approaches to study their spatial distribution in different cells and tissues, and methods to analyze their genomic distribution with the help of bioinformatics tools that interrogate the corresponding datasets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and comprehensive, DNA Modifications: Methods and Protocols serves as an ideal guide to research scientists and PhD students in this rapidly developing discipline, and, thus, will ultimately contribute to deciphering the roles of non-canonical DNA nucleotides in different biological systems.
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Parasite Genomics

This detailed book provides a comprehensive series of innovative research techniques and methodologies applied to the parasite genomics research area, all applying different approaches to analyzing parasite genomes and furthering the study ...

Author: Luis M. de Pablos

Publisher: Humana

ISBN: 1071616803

Category: Medical

Page: 336

View: 330

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This detailed book provides a comprehensive series of innovative research techniques and methodologies applied to the parasite genomics research area, all applying different approaches to analyzing parasite genomes and furthering the study of genetic complexity and the mechanisms of regulation. Beginning with chapters on novel sequencing and the bioinformatics pipeline, the volume continues by exploring diagnostic approaches using genomic tools, host-parasite interactions, as well as the genomics of parasite-derived extracellular vesicles. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Parasite Genomics: Methods and Protocols creates a detailed picture of genomic approaches for researchers seeking a better understanding of characterizing parasite nucleic acid content.
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Protein Supersecondary Structures

This second edition volume expands on the previous edition with an update on the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins.

Author: Alexander E. Kister

Publisher: Humana Press

ISBN: 1493991604

Category: Science

Page: 438

View: 486

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This second edition volume expands on the previous edition with an update on the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Chapters in this book discuss topics such as sequence and structural features of different SSS elements; software used for the automatic annotation of secondary structure elements in proteins; the new developments in secondary and SSS prediction and the modern approaches for energy landscape calculation; protein misfolding and amyloid structural formation; analysis of ‘transformer proteins’; discovery of the structure of the hydrophobic nucleus; and discussions of the main principles of protein structures formation. The contributing authors of the volume are the eminent experts in the field of protein research and bioinformatics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Protein Supersecondary Structures: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about the relationship between amino acids sequences and protein structures, the evolution of proteins and the dynamics of protein formation.
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Proteomics

This volume aims to provide protocols on a wide range of biochemical methods, analytical approaches, and bioinformatics tools developed to analyze the proteome.

Author: Lucio Comai

Publisher: Humana

ISBN: 1493982907

Category: Science

Page: 371

View: 804

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This volume aims to provide protocols on a wide range of biochemical methods, analytical approaches, and bioinformatics tools developed to analyze the proteome. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Proteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.
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Bioinformatics Methods in Clinical Research

Informative and ground-breaking, Bioinformatics Methods in Clinical Research establishes a much-needed bridge between theory and practice, making it an indispensable resource for bioinformatics researchers.

Author: Rune Matthiesen

Publisher: Humana Press

ISBN: 1617796700

Category: Science

Page: 390

View: 417

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Integrated bioinformatics solutions have become increasingly valuable in past years, as technological advances have allowed researchers to consider the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes, and as the costs of such techniques have begun to lessen. In Bioinformatics Methods in Clinical Research, experts examine the latest developments impacting clinical omics, and describe in great detail the algorithms that are currently used in publicly available software tools. Chapters discuss statistics, algorithms, automated methods of data retrieval, and experimental consideration in genomics, transcriptomics, proteomics, and metabolomics. Composed in the highly successful Methods in Molecular BiologyTM series format, each chapter contains a brief introduction, provides practical examples illustrating methods, results, and conclusions from data mining strategies wherever possible, and includes a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Informative and ground-breaking, Bioinformatics Methods in Clinical Research establishes a much-needed bridge between theory and practice, making it an indispensable resource for bioinformatics researchers.
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