A Practical Guide To Cancer Systems Biology

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A Practical Guide To Cancer Systems Biology

Juan Hsueh-fen,Huang Hsuan-cheng
A Practical Guide To Cancer Systems Biology Book PDF

Author : Juan Hsueh-fen,Huang Hsuan-cheng
Publisher : World Scientific
Page : 152 pages
File Size : 45,9 Mb
Release : 2017-11-29
Category : Medical
ISBN : 9789813229167

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A Practical Guide To Cancer Systems Biology by Juan Hsueh-fen,Huang Hsuan-cheng Pdf

Systems biology combines computational and experimental approaches to analyze complex biological systems and focuses on understanding functional activities from a systems-wide perspective. It provides an iterative process of experimental measurements, data analysis, and computational simulation to model biological behavior. This book provides explained protocols for high-throughput experiments and computational analysis procedures central to cancer systems biology research and education. Readers will learn how to generate and analyze high-throughput data, therapeutic target protein structure modeling and docking simulation for drug discovery. This is the first practical guide for students and scientists who wish to become systems biologists or utilize the approach for cancer research. Contents: Introduction to Cancer Systems Biology (Hsueh-Fen Juan and Hsuan-Cheng Huang)Transcriptome Analysis: Library Construction (Hsin-Yi Chang and Hsueh-Fen Juan)Quantitative Proteome: The Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) (Yi-Hsuan Wu and Hsueh-Fen Juan)Phosphoproteome: Sample Preparation (Chia-Wei Hu and Hsueh-Fen Juan)Transcriptomic Data Analysis: RNA-Seq Analysis Using Galaxy (Chia-Lang Hsu and Chantal Hoi Yin Cheung)Proteomic Data Analysis: Functional Enrichment (Hsin-Yi Chang and Hsueh-Fen Juan)Phosphorylation Data Analysis (Chia-Lang Hsu and Wei-Hsuan Wang)Pathway and Network Analysis (Chen-Tsung Huang and Hsueh-Fen Juan)Dynamic Modeling (Yu-Chao Wang)Protein Structure Modeling (Chia-Hsien Lee and Hsueh-Fen Juan)Docking Simulation (Chia-Hsien Lee and Hsueh-Fen Juan) Readership: Graduate students and researchers entering the cancer systems biology field. Keywords: Systems Biology;Transcriptomics;Proteomics;Network Biology;Dynamic Modeling;Protein Structure Modeling;Docking Simulation;BioinformaticsReview: Key Features: Written by two active researchers in the fieldCovers both experimental and computational areas in cancer systems biologyStep-by-step instructions help beginners who are interested in creating biological data and analyzing the data by themselvesReaders will gain the skills to generate and analyze omics data and discover potential therapeutic targets and drug candidates

Cancer Systems Biology, Bioinformatics and Medicine

Alfredo Cesario,Frederick Marcus
Cancer Systems Biology Bioinformatics and Medicine Book PDF

Author : Alfredo Cesario,Frederick Marcus
Publisher : Springer Science & Business Media
Page : 484 pages
File Size : 52,7 Mb
Release : 2011-08-21
Category : Medical
ISBN : 9400715676

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Cancer Systems Biology, Bioinformatics and Medicine by Alfredo Cesario,Frederick Marcus Pdf

This teaching monograph on systems approaches to cancer research and clinical applications provides a unique synthesis, by world-class scientists and doctors, of laboratory, computational, and clinical methods, thereby establishing the foundations for major advances not possible with current methods. Specifically, the book: 1) Sets the stage by describing the basis of systems biology and bioinformatics approaches, and the clinical background of cancer in a systems context; 2) Summarizes the laboratory, clinical, data systems analysis and bioinformatics tools, along with infrastructure and resources required; 3) Demonstrates the application of these tools to cancer research; 4) Extends these tools and methods to clinical diagnosis, drug development and treatment applications; and 5) Finishes by exploring longer term perspectives and providing conclusions. This book reviews the state-of-the-art, and goes beyond into new applications. It is written and highly referenced as a textbook and practical guide aimed at students, academics, doctors, clinicians, industrialists and managers in cancer research and therapeutic applications. Ideally, it will set the stage for integration of available knowledge to optimize communication between basic and clinical researchers involved in the ultimate fight against cancer, whatever the field of specific interest, whatever the area of activity within translational research.

Introduction to Bioinformatics with R

Edward Curry
Introduction to Bioinformatics with R Book PDF

Author : Edward Curry
Publisher : CRC Press
Page : 311 pages
File Size : 48,9 Mb
Release : 2020-11-02
Category : Mathematics
ISBN : 9781351015301

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Introduction to Bioinformatics with R by Edward Curry Pdf

In biological research, the amount of data available to researchers has increased so much over recent years, it is becoming increasingly difficult to understand the current state of the art without some experience and understanding of data analytics and bioinformatics. An Introduction to Bioinformatics with R: A Practical Guide for Biologists leads the reader through the basics of computational analysis of data encountered in modern biological research. With no previous experience with statistics or programming required, readers will develop the ability to plan suitable analyses of biological datasets, and to use the R programming environment to perform these analyses. This is achieved through a series of case studies using R to answer research questions using molecular biology datasets. Broadly applicable statistical methods are explained, including linear and rank-based correlation, distance metrics and hierarchical clustering, hypothesis testing using linear regression, proportional hazards regression for survival data, and principal component analysis. These methods are then applied as appropriate throughout the case studies, illustrating how they can be used to answer research questions. Key Features: · Provides a practical course in computational data analysis suitable for students or researchers with no previous exposure to computer programming. · Describes in detail the theoretical basis for statistical analysis techniques used throughout the textbook, from basic principles · Presents walk-throughs of data analysis tasks using R and example datasets. All R commands are presented and explained in order to enable the reader to carry out these tasks themselves. · Uses outputs from a large range of molecular biology platforms including DNA methylation and genotyping microarrays; RNA-seq, genome sequencing, ChIP-seq and bisulphite sequencing; and high-throughput phenotypic screens. · Gives worked-out examples geared towards problems encountered in cancer research, which can also be applied across many areas of molecular biology and medical research. This book has been developed over years of training biological scientists and clinicians to analyse the large datasets available in their cancer research projects. It is appropriate for use as a textbook or as a practical book for biological scientists looking to gain bioinformatics skills.

Cancer Systems Biology, Bioinformatics and Medicine

Alfredo Cesario,Frederick Marcus
Cancer Systems Biology Bioinformatics and Medicine Book PDF

Author : Alfredo Cesario,Frederick Marcus
Publisher : Springer
Page : 484 pages
File Size : 54,8 Mb
Release : 2011-08-21
Category : Medical
ISBN : 9400715668

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Cancer Systems Biology, Bioinformatics and Medicine by Alfredo Cesario,Frederick Marcus Pdf

This teaching monograph on systems approaches to cancer research and clinical applications provides a unique synthesis, by world-class scientists and doctors, of laboratory, computational, and clinical methods, thereby establishing the foundations for major advances not possible with current methods. Specifically, the book: 1) Sets the stage by describing the basis of systems biology and bioinformatics approaches, and the clinical background of cancer in a systems context; 2) Summarizes the laboratory, clinical, data systems analysis and bioinformatics tools, along with infrastructure and resources required; 3) Demonstrates the application of these tools to cancer research; 4) Extends these tools and methods to clinical diagnosis, drug development and treatment applications; and 5) Finishes by exploring longer term perspectives and providing conclusions. This book reviews the state-of-the-art, and goes beyond into new applications. It is written and highly referenced as a textbook and practical guide aimed at students, academics, doctors, clinicians, industrialists and managers in cancer research and therapeutic applications. Ideally, it will set the stage for integration of available knowledge to optimize communication between basic and clinical researchers involved in the ultimate fight against cancer, whatever the field of specific interest, whatever the area of activity within translational research.

Bioinformatics and Systems Biology

Frederick Marcus
Bioinformatics and Systems Biology Book PDF

Author : Frederick Marcus
Publisher : Springer Science & Business Media
Page : 296 pages
File Size : 47,7 Mb
Release : 2008-07-22
Category : Science
ISBN : 9783540783534

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Bioinformatics and Systems Biology by Frederick Marcus Pdf

Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.

Bioinformatics

Andreas D. Baxevanis,B. F. Francis Ouellette
Bioinformatics Book PDF

Author : Andreas D. Baxevanis,B. F. Francis Ouellette
Publisher : John Wiley & Sons
Page : 504 pages
File Size : 47,6 Mb
Release : 2004-03-24
Category : Computers
ISBN : 9780471461012

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Bioinformatics by Andreas D. Baxevanis,B. F. Francis Ouellette Pdf

"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edition includes: All new end-of-chapter Web resources, bibliographies, andproblem sets Accompanying Web site containing the answers to the problems,as well as links to relevant Web resources New coverage of comparative genomics, large-scale genomeanalysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics andgenomics Bioinformatics: A Practical Guide to the Analysis of Genesand Proteins, Second Edition is essential reading forresearchers, instructors, and students of all levels in molecularbiology and bioinformatics, as well as for investigators involvedin genomics, positional cloning, clinical research, andcomputational biology.

A Practical Guide to Human Cancer Genetics

S. V. Hodgson,E. R. Maher
A Practical Guide to Human Cancer Genetics Book PDF

Author : S. V. Hodgson,E. R. Maher
Publisher : Cambridge University Press
Page : 258 pages
File Size : 46,8 Mb
Release : 1993-02-25
Category : Medical
ISBN : 0521401283

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A Practical Guide to Human Cancer Genetics by S. V. Hodgson,E. R. Maher Pdf

This extensively up-dated and expanded edition provides the busy clinician with an essential overview of the latest developments in human cancer genetics - an area that has made significant advances since publication of the first edition. The opening section presents the principles of cancer genetics and introduces the basic concepts and mechanisms of tumorigenesis and inherited predisposition to cancer. The second part of the book provides information, on a systems basis, on the incidence, significance and management of predisposition to individual cancers. The final section then deals with specific inherited cancer syndromes, giving practical guidance on clinical investigation, screening and management of affected patients and relatives at risk. Up-to-date details of the genetic mapping of inherited cancer syndromes and the molecular genetic changes in individual cancers are also provided. Finally, an appendix provides a helpful revision guide to the fundamental principles of genetics. This practical and clear account will benefit clinicians and research workers in oncology, genetics, surgery and general medicine.

Phase I Cancer Clinical Trials

Elizabeth A. Eisenhauer,Christopher Twelves,Marc Buyse
Phase I Cancer Clinical Trials Book PDF

Author : Elizabeth A. Eisenhauer,Christopher Twelves,Marc Buyse
Publisher : Oxford University Press
Page : 352 pages
File Size : 48,9 Mb
Release : 2015-03-20
Category : Medical
ISBN : 9780199359035

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Phase I Cancer Clinical Trials by Elizabeth A. Eisenhauer,Christopher Twelves,Marc Buyse Pdf

Phase I trials are a critical first step in the study of novel cancer therapeutic approaches. Their primary goals are to identify the recommended dose, schedule and pharmacologic behavior of new agents or new combinations of agents and to describe the adverse effects of treatment. In cancer therapeutics, such studies have particular challenges. Due to the nature of the effects of treatment, most such studies are conducted in patients with advanced malignancy, rather than in healthy volunteers. Further, the endpoints of these trials are usually measures adverse effects rather than molecular target or anti-tumor effects. These factors render the design, conduct, analysis and ethical aspects of phase I cancer trials unique. As the only comprehensive book on this topic, Phase I Cancer Clinical Trials is a useful resource for oncology trainees or specialists interested in understanding cancer drug development. New to this edition are chapters on Phase 0 Trials and Immunotherapeutics, and updated information on the process, pitfalls, and logistics of Phase I Trials

Metabolomics

Taylor & Francis Group
Metabolomics Book PDF

Author : Taylor & Francis Group
Publisher : CRC Press
Page : 290 pages
File Size : 44,6 Mb
Release : 2021-12-13
Category : Electronic
ISBN : 1032242639

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Metabolomics by Taylor & Francis Group Pdf

This book covers Metabolomics, the scientific study of the chemical processes of the metabolic system. It is based on a course taught to masters and postgraduate students of bioinformatics and statistics at the European Bioinformatics Institute at Cambridge.

Statistical Genomics

Ewy Mathé,Sean Davis
Statistical Genomics Book PDF

Author : Ewy Mathé,Sean Davis
Publisher : Humana
Page : 0 pages
File Size : 44,6 Mb
Release : 2016-03-24
Category : Medical
ISBN : 1493935763

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Statistical Genomics by Ewy Mathé,Sean Davis Pdf

This volume expands on statistical analysis of genomic data by discussing cross-cutting groundwork material, public data repositories, common applications, and representative tools for operating on genomic data. Statistical Genomics: Methods and Protocols is divided into four sections. The first section discusses overview material and resources that can be applied across topics mentioned throughout the book. The second section covers prominent public repositories for genomic data. The third section presents several different biological applications of statistical genomics, and the fourth section highlights software tools that can be used to facilitate ad-hoc analysis and data integration. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible analysis protocols, and tips on troubleshooting and avoiding known pitfalls. Through and practical, Statistical Genomics: Methods and Protocols, explores a range of both applications and tools and is ideal for anyone interested in the statistical analysis of genomic data.

MicroRNA Cancer Regulation

Ulf Schmitz,Olaf Wolkenhauer,Julio Vera
MicroRNA Cancer Regulation Book PDF

Author : Ulf Schmitz,Olaf Wolkenhauer,Julio Vera
Publisher : Springer Science & Business Media
Page : 352 pages
File Size : 47,9 Mb
Release : 2013-02-03
Category : Medical
ISBN : 9789400755901

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MicroRNA Cancer Regulation by Ulf Schmitz,Olaf Wolkenhauer,Julio Vera Pdf

This edited reflects the current state of knowledge about the role of microRNAs in the formation and progression of solid tumours. The main focus lies on computational methods and applications, together with cutting edge experimental techniques that are used to approach all aspects of microRNA regulation in cancer. We are sure that the emergence of high-throughput quantitative techniques will make this integrative approach absolutely necessary in the near future. This book will be a resource for researchers starting out with cancer microRNA research, but is also intended for the experienced researcher who wants to incorporate concepts and tools from systems biology and bioinformatics into his work. Bioinformaticians and modellers are provided with a general perspective on microRNA biology in cancer, and the state-of-the-art in computational microRNA biology.

Gynecologic Radiation Oncology: A Practical Guide

Patricia Eifel,Ann H. Klopp
Gynecologic Radiation Oncology A Practical Guide Book PDF

Author : Patricia Eifel,Ann H. Klopp
Publisher : Lippincott Williams & Wilkins
Page : 352 pages
File Size : 44,9 Mb
Release : 2016-07-13
Category : Medical
ISBN : 9781496362452

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Gynecologic Radiation Oncology: A Practical Guide by Patricia Eifel,Ann H. Klopp Pdf

Offering practical approaches to common clinical problems, Gynecologic Radiation Oncology: A Practical Guide compiles the extensive clinical experience of Drs. Patricia J. Eifel and Ann H. Klopp from MD Anderson Cancer Center into one user-friendly volume. This reference addresses practical aspects of the field: how to evaluate the role of radiation therapy in various clinical settings, how to explain the rationale for treatment recommendations to referring physicians and patients, when and how to apply various external beam and brachytherapy techniques to address specific clinical problems, and how to monitor and manage patients during and after treatment. The book focuses on the following items, which can have immediate application to the treatment of patients with gynecologic cancers.

Metabolomics

Ron Wehrens,International Agency for Research on Can
Metabolomics Book PDF

Author : Ron Wehrens,International Agency for Research on Can
Publisher : CRC Press
Page : 313 pages
File Size : 51,6 Mb
Release : 2019-08-19
Category : Mathematics
ISBN : 9781315353487

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Metabolomics by Ron Wehrens,International Agency for Research on Can Pdf

Metabolomics is the scientific study of the chemical processes in a living system, environment and nutrition. It is a relatively new omics science, but the potential applications are wide, including medicine, personalized medicine and intervention studies, food and nutrition, plants, agriculture and environmental science. The topics presented and discussed in this book are based on the European Molecular Biology Organization (EMBO) practical courses in metabolomics bioinformatics taught to those working in the field, from masters to postgraduate students, PhDs, postdoctoral and early PIs. The book covers the basics and fundamentals of data acquisition and analytical technologies, but the primary focus is data handling and data analysis. The mentioning and usage of a particular data analysis tool has been avoided; rather, the focus is on the concepts and principles of data processing and analysis. The material has been class-tested and includes lots of examples, computing and exercises. Key Features: Provides an overview of qualitative /quantitative methods in metabolomics Offers an introduction to the key concepts of metabolomics, including experimental design and technology Covers data handling, processing, analysis, data standards and sharing Contains lots of examples to illustrate the topics Includes contributions from some of the leading researchers in the field of metabolomics with extensive teaching experiences

Epidemiology of Endocrine Tumors

Jahangir Moini,Craig Badolato,Raheleh Ahangari
Epidemiology of Endocrine Tumors Book PDF

Author : Jahangir Moini,Craig Badolato,Raheleh Ahangari
Publisher : Elsevier
Page : 570 pages
File Size : 54,5 Mb
Release : 2021-03-03
Category : Medical
ISBN : 9780128232668

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Epidemiology of Endocrine Tumors by Jahangir Moini,Craig Badolato,Raheleh Ahangari Pdf

Epidemiology of Endocrine Tumors brings current data and clinical research into one source for a multidisciplinary audience. The book discusses the prevalence, incidence, etiology, pathology, diagnosis and treatment of various endocrine tumors. With clear and focused writing, it is essential reading for healthcare professionals, endocrinologists, oncologists, and public health professionals. Users will be able to bridge the knowledge gap that exists in the comprehensive coverage surrounding the epidemiology of endocrine tumors. Globally, the prevalence and incidence of endocrine tumors is high. This audience needs a treatise where they can gain a broad overview of endocrine tumors with a focus on epidemiology. Supplies information about the epidemiology of various endocrine tumors, both benign and malignant, to endocrinologists, oncologists and related health care professionals Focuses on the impact upon costs and patient deaths due to complications of these tumors Describes how endocrine tumors affect various age groups and ethnicities, discussing the prevention of endocrine tumors Presents chapters on Cancer Problem, Specific Endocrine Tumors, Prevention, Detection and Diagnosis, and Treatment of Endocrine Tumors Provides review questions with an answer key and detailed glossary

Computational Genomics with R

Altuna Akalin
Computational Genomics with R Book PDF

Author : Altuna Akalin
Publisher : CRC Press
Page : 462 pages
File Size : 42,9 Mb
Release : 2020-12-16
Category : Mathematics
ISBN : 9781498781862

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Computational Genomics with R by Altuna Akalin Pdf

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.