Computational Systems Biology Approaches In Cancer Research

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Computational Systems Biology Approaches in Cancer Research

Inna Kuperstein,Emmanuel Barillot
Computational Systems Biology Approaches in Cancer Research Book PDF

Author : Inna Kuperstein,Emmanuel Barillot
Publisher : CRC Press
Page : 167 pages
File Size : 40,9 Mb
Release : 2019-09-09
Category : Computers
ISBN : 9781000682922

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Computational Systems Biology Approaches in Cancer Research by Inna Kuperstein,Emmanuel Barillot Pdf

Praise for Computational Systems BiologyApproaches in Cancer Research: "Complex concepts are written clearly and with informative illustrations and useful links. The book is enjoyable to read yet provides sufficient depth to serve as a valuable resource for both students and faculty." — Trey Ideker, Professor of Medicine, UC Xan Diego, School of Medicine "This volume is attractive because it addresses important and timely topics for research and teaching on computational methods in cancer research. It covers a broad variety of approaches, exposes recent innovations in computational methods, and provides acces to source code and to dedicated interactive web sites." — Yves Moreau, Department of Electrical Engineering, SysBioSys Centre for Computational Systems Biology, University of Leuven With the availability of massive amounts of data in biology, the need for advanced computational tools and techniques is becoming increasingly important and key in understanding biology in disease and healthy states. This book focuses on computational systems biology approaches, with a particular lens on tackling one of the most challenging diseases - cancer. The book provides an important reference and teaching material in the field of computational biology in general and cancer systems biology in particular. The book presents a list of modern approaches in systems biology with application to cancer research and beyond. It is structured in a didactic form such that the idea of each approach can easily be grasped from the short text and self-explanatory figures. The coverage of topics is diverse: from pathway resources, through methods for data analysis and single data analysis to drug response predictors, classifiers and image analysis using machine learning and artificial intelligence approaches. Features Up to date using a wide range of approaches Applicationexample in each chapter Online resources with useful applications’

Computational Systems Biology of Cancer

Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev
Computational Systems Biology of Cancer Book PDF

Author : Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev
Publisher : CRC Press
Page : 463 pages
File Size : 43,5 Mb
Release : 2012-08-25
Category : Science
ISBN : 9781439831441

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Computational Systems Biology of Cancer by Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev Pdf

The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models—integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencing. Offering promising insights on how to defeat cancer, the emerging field of systems biology captures the complexity of biological phenomena using mathematical and computational tools. Novel Approaches to Fighting Cancer Drawn from the authors’ decade-long work in the cancer computational systems biology laboratory at Institut Curie (Paris, France), Computational Systems Biology of Cancer explains how to apply computational systems biology approaches to cancer research. The authors provide proven techniques and tools for cancer bioinformatics and systems biology research. Effectively Use Algorithmic Methods and Bioinformatics Tools in Real Biological Applications Suitable for readers in both the computational and life sciences, this self-contained guide assumes very limited background in biology, mathematics, and computer science. It explores how computational systems biology can help fight cancer in three essential aspects: Categorising tumours Finding new targets Designing improved and tailored therapeutic strategies Each chapter introduces a problem, presents applicable concepts and state-of-the-art methods, describes existing tools, illustrates applications using real cases, lists publically available data and software, and includes references to further reading. Some chapters also contain exercises. Figures from the text and scripts/data for reproducing a breast cancer data analysis are available at www.cancer-systems-biology.net.

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 : 53,5 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.

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 : 45,6 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
Page : 484 pages
File Size : 41,6 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.

Systems Biology

Hsueh-Fen Juan,Hsuan-Cheng Huang
Systems Biology Book PDF

Author : Hsueh-Fen Juan,Hsuan-Cheng Huang
Publisher : World Scientific
Page : 339 pages
File Size : 45,7 Mb
Release : 2012
Category : Medical
ISBN : 9789814324458

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Systems Biology by Hsueh-Fen Juan,Hsuan-Cheng Huang Pdf

This volume presents an overview of recent developments in systems biology and their applications in cancer-related research. The ongoing advances in our understanding of genomics and proteomics, coupled with the development of new and more robust tools, have led to an emphasis on analyzing biological systems at multiple levels. Thus, there is a need to integrate different types of data into a comprehensive "systems" view. Written by active researchers in the emerging areas, this book gives senior undergraduate students, graduate students and new researchers an idea of where the frontiers of systems biology are and an opportunity to learn high-throughput techniques in use. One of the particular emphases of the book is to elucidate the molecular mechanisms in cancer. The discovery of biomarkers and anti-cancer drugs using systems biology approach is also extensively discussed.

Computational Systems Biology of Cancer

Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev
Computational Systems Biology of Cancer Book PDF

Author : Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev
Publisher : CRC Press
Page : 461 pages
File Size : 43,5 Mb
Release : 2012
Category : SCIENCE
ISBN : 0429093926

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Computational Systems Biology of Cancer by Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev Pdf

The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models-integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencing. Offering promising insights on how to defeat cancer, the emerging field of systems biology captures the complexity of biological phenomena using mathematical and computational tools.

Cancer Systems Biology

Edwin Wang
Cancer Systems Biology Book PDF

Author : Edwin Wang
Publisher : CRC Press
Page : 456 pages
File Size : 49,7 Mb
Release : 2010-05-04
Category : Computers
ISBN : 1439811865

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Cancer Systems Biology by Edwin Wang Pdf

The unprecedented amount of data produced with high-throughput experimentation forces biologists to employ mathematical representation and computation methods to glean meaningful information in systems-level biology. Applying this approach to the underlying molecular mechanisms of tumorigenesis, cancer researchers can uncover a series of new discov

Computational Biology

Tuan Pham
Computational Biology Book PDF

Author : Tuan Pham
Publisher : Springer Science & Business Media
Page : 309 pages
File Size : 47,8 Mb
Release : 2009-09-23
Category : Medical
ISBN : 9781441908117

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Computational Biology by Tuan Pham Pdf

This volume covers techniques in computational biology and their applications in oncology. It details advanced statistical methods, heuristic algorithms, cluster analysis, data modeling, and image and pattern analysis applied to cancer research.

Computational Systems Biology

Juergen Eilsa,Elena Herzoga,Baerbel Felder,Christian Lawerenza,Roland Eils
Computational Systems Biology Book PDF

Author : Juergen Eilsa,Elena Herzoga,Baerbel Felder,Christian Lawerenza,Roland Eils
Publisher : Elsevier Inc. Chapters
Page : 548 pages
File Size : 40,5 Mb
Release : 2013-11-26
Category : Medical
ISBN : 9780128070109

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Computational Systems Biology by Juergen Eilsa,Elena Herzoga,Baerbel Felder,Christian Lawerenza,Roland Eils Pdf

Systems biology combines experimental and computational research to facilitate understanding of complex biological processes. In this chapter we describe data repositories, data standards, modeling, and visualization tools as prerequisites for systems biology research in order to help us to better study and understand biological processes. In addition, we propose improvements of these tools providing an example application (JUMMP) developed in our laboratory. We suggest that flexibility, interoperability, and modularity of novel applications contribute to better acceptance and further development of these tools. We also emphasize that having flexible and extendable standards describing complex and incomplete biological data allow new discoveries to be incorporated in a seamless way into systems biology tools. Overall, we discuss here advances, challenges and perspectives of data, and other platforms in systems biology which we believe will continue to make an impact on biomedical research.

Computational Biology Of Cancer: Lecture Notes And Mathematical Modeling

Dominik Wodarz,Natalia Komarova
Computational Biology Of Cancer Lecture Notes And Mathematical Modeling Book PDF

Author : Dominik Wodarz,Natalia Komarova
Publisher : World Scientific
Page : 266 pages
File Size : 41,6 Mb
Release : 2005-01-24
Category : Science
ISBN : 9789814481878

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Computational Biology Of Cancer: Lecture Notes And Mathematical Modeling by Dominik Wodarz,Natalia Komarova Pdf

The book shows how mathematical and computational models can be used to study cancer biology. It introduces the concept of mathematical modeling and then applies it to a variety of topics in cancer biology. These include aspects of cancer initiation and progression, such as the somatic evolution of cells, genetic instability, and angiogenesis. The book also discusses the use of mathematical models for the analysis of therapeutic approaches such as chemotherapy, immunotherapy, and the use of oncolytic viruses.

Systems Biology in Cancer Research and Drug Discovery

Asfar S Azmi
Systems Biology in Cancer Research and Drug Discovery Book PDF

Author : Asfar S Azmi
Publisher : Springer Science & Business Media
Page : 425 pages
File Size : 43,5 Mb
Release : 2012-09-29
Category : Medical
ISBN : 9789400748194

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Systems Biology in Cancer Research and Drug Discovery by Asfar S Azmi Pdf

Systems Biology in Cancer Research and Drug Discovery provides a unique collection of chapters, by world-class researchers, describing the use of integrated systems biology and network modeling in the cancer field where traditional tools have failed to deliver expected promise. This book touches four applications/aspects of systems biology (i) in understanding aberrant signaling in cancer (ii) in identifying biomarkers and prognostic markers especially focused on angiogenesis pathways (iii) in unwinding microRNAs complexity and (iv) in anticancer drug discovery and in clinical trial design. This book reviews the state-of-the-art knowledge and touches upon cutting edge newer and improved applications especially in the area of network modeling. It is aimed at an audience ranging from students, academics, basic researcher and clinicians in cancer research. This book is expected to benefit the field of translational cancer medicine by bridging the gap between basic researchers, computational biologists and clinicians who have one ultimate goal and that is to defeat cancer.

Computational Systems Biology

Ursula Klingmüller,Marcel Schilling,Sofia Depner,Lorenza A. D’Alessandro
Computational Systems Biology Book PDF

Author : Ursula Klingmüller,Marcel Schilling,Sofia Depner,Lorenza A. D’Alessandro
Publisher : Elsevier Inc. Chapters
Page : 548 pages
File Size : 50,8 Mb
Release : 2013-11-26
Category : Medical
ISBN : 9780128070055

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Computational Systems Biology by Ursula Klingmüller,Marcel Schilling,Sofia Depner,Lorenza A. D’Alessandro Pdf

Cellular communication is mediated by extracellular stimuli that bind cellular receptors and activate intracellular signaling pathways. Principal biochemical reactions used for signal transduction are protein or lipid phosphorylation, proteolytic cleavage, protein degradation and complex formation mediated by protein-protein interactions. Within the nucleus, signaling pathways regulate transcription factor activity and gene expression. Cells differ in their competence to respond to extracellular stimuli. A deeper understanding of complex biological responses cannot be achieved by traditional approaches but requires the combination of experimental data with mathematical modeling. Following a systems biology approach, data-based mathematical models describing sub-modules of signaling pathways have been established. By combining computer simulations with experimental verification systems properties of signaling pathway including cycling behavior or threshold response could be identified. Yet, to analyze complex growth and maturation processes at a systems level and quantitatively predict the outcome of perturbations further advances in experimental and theoretical methodologies are required.

Systems Biomedicine Approaches in Cancer Research

Shailza Singh
Systems Biomedicine Approaches in Cancer Research Book PDF

Author : Shailza Singh
Publisher : Springer Nature
Page : 170 pages
File Size : 41,8 Mb
Release : 2022-08-10
Category : Science
ISBN : 9789811919534

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Systems Biomedicine Approaches in Cancer Research by Shailza Singh Pdf

This book presents the applications of systems biology and synthetic biology in cancer medicine. It highlights the use of computational and mathematical models to decipher the complexity of cancer heterogeneity. The book emphasizes the modeling approaches for predicting behavior of cancer cells, tissues in context of drug response, and angiogenesis. It introduces cell-based therapies for the treatment of various cancers and reviews the role of neural networks for drug response prediction. Further, it examines the system biology approaches for the identification of medicinal plants in cancer drug discovery. It explores the opportunities for metabolic engineering in the realm of cancer research towards development of new cancer therapies based on metabolically derived targets. Lastly, it discusses the applications of data mining techniques in cancer research. This book is an excellent guide for oncologists and researchers who are involved in the latest cancer research.

Elements of Computational Systems Biology

Huma M. Lodhi,Stephen H. Muggleton
Elements of Computational Systems Biology Book PDF

Author : Huma M. Lodhi,Stephen H. Muggleton
Publisher : John Wiley & Sons
Page : 435 pages
File Size : 43,7 Mb
Release : 2010-03-25
Category : Computers
ISBN : 9780470556740

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Elements of Computational Systems Biology by Huma M. Lodhi,Stephen H. Muggleton Pdf

Groundbreaking, long-ranging research in this emergent field that enables solutions to complex biological problems Computational systems biology is an emerging discipline that is evolving quickly due to recent advances in biology such as genome sequencing, high-throughput technologies, and the recent development of sophisticated computational methodologies. Elements of Computational Systems Biology is a comprehensive reference covering the computational frameworks and techniques needed to help research scientists and professionals in computer science, biology, chemistry, pharmaceutical science, and physics solve complex biological problems. Written by leading experts in the field, this practical resource gives detailed descriptions of core subjects, including biological network modeling, analysis, and inference; presents a measured introduction to foundational topics like genomics; and describes state-of-the-art software tools for systems biology. Offers a coordinated integrated systems view of defining and applying computational and mathematical tools and methods to solving problems in systems biology Chapters provide a multidisciplinary approach and range from analysis, modeling, prediction, reasoning, inference, and exploration of biological systems to the implications of computational systems biology on drug design and medicine Helps reduce the gap between mathematics and biology by presenting chapters on mathematical models of biological systems Establishes solutions in computer science, biology, chemistry, and physics by presenting an in-depth description of computational methodologies for systems biology Elements of Computational Systems Biology is intended for academic/industry researchers and scientists in computer science, biology, mathematics, chemistry, physics, biotechnology, and pharmaceutical science. It is also accessible to undergraduate and graduate students in machine learning, data mining, bioinformatics, computational biology, and systems biology courses.