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Computational Systems Biology

Computational Systems Biology Book
Author : Andres Kriete,Roland Eils
Publisher : Academic Press
Release : 2013-12-12
ISBN : 9780124059269
Language : En, Es, Fr & De

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Book Description :

This book discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling.

Computational Systems Biology

Computational Systems Biology Book
Author : Jason McDermott,Ram Samudrala,Roger Bumgarner,Kristina Montgomery,Reneé Ireton
Publisher : Methods in Molecular Biology
Release : 2009-04
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

The recent confluence of high throughput methodology for biological data gathering, genome-scale sequencing, and computational processing power has driven a reinvention and expansion of the way we identify, infer, model, and store relationships between molecules, pathways, and cells in living organisms. In Computational Systems Biology, expert investigators contribute chapters which bring together biological data and computational and/or mathematical models of the data to aid researchers striving to create a system that provides both predictive and mechanistic information for a model organism. The volume is organized into five major sections involving network components, network inference, network dynamics, function and evolutionary system biology, and computational infrastructure for systems biology. As a volume of the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Comprehensive and up-to-date, Computational Systems Biology serves to motivate and inspire all those who wish to develop a complete description of a biological system.

Transactions on Computational Systems Biology X

Transactions on Computational Systems Biology X Book
Author : Corrado Priami,Falko Dressler,Ozgur B. Akan,Alioune Ngom
Publisher : Springer
Release : 2010-06-27
ISBN : 3540922733
Language : En, Es, Fr & De

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Book Description :

Technology is taking us to a world where myriads of heavily networked devices interact with the physical world in multiple ways, and at many levels, from the globalInternetdowntomicroandnanodevices. Manyofthesedevicesarehighly mobile and autonomous and must adapt to the surrounding environment in a totally unsupervised way. A fundamental research challenge is the design of robust decentralized c- puting systemsthat arecapableofoperating in changing environmentsandwith noisy input, and yet exhibit the desired behavior and response time, under c- straints such as energy consumption, size, and processing power. These systems should be able to adapt and learn how to react to unforeseen scenarios as well as to display properties comparable to social entities. The observation of nature has brought us many great and unforeseen concepts. Biological systems are able to handle many of these challenges with an elegance and e?ciency far beyond currenthumanartifacts. Basedonthisobservation,bio-inspiredapproacheshave been proposed as a means of handling the complexity of such systems. The goal is to obtain methods to engineer technical systems, which are of a stability and e?ciency comparable to those found in biological entities. This Special Issue on Biological and Biologically-inspired Communication contains the best papers from the Second International Conference on Bio- Inspired Models of Network, Information, and Computing Systems (BIONET- ICS 2007). The BIONETICS conference aims to bring together researchers and scientistsfromseveraldisciplines incomputerscienceandengineeringwhereb- inspired methods are investigated, as well as from bioinformatics, to deepen the information exchange and collaboration among the di?erent communities.

Transactions on Computational Systems Biology XIV

Transactions on Computational Systems Biology XIV Book
Author : Ion Petre,Erik de Vink
Publisher : Springer
Release : 2012-11-28
ISBN : 3642355242
Language : En, Es, Fr & De

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Book Description :

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This, the 14th Transactions on Computational Systems Biology volume, guest edited by Ion Petre and Erik de Vink, focuses on Computational Models for Cell Processes and features a number of carefully selected and enhanced contributions, initially presented at the CompMod workshop, which took place in Aachen, Germany, in September 2011. The papers, written from different points of view and following various approaches, cover a wide range of topics within the field of modeling and analysis of biological systems. In addition, two regular submissions deal with models of self-assembling systems and metabolic constraints on the evolution of genetic codes.

Transactions on Computational Systems Biology VI

Transactions on Computational Systems Biology VI Book
Author : Gordon Plotkin
Publisher : Springer Science & Business Media
Release : 2006-11-27
ISBN : 3540457798
Language : En, Es, Fr & De

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Book Description :

The 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing. The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval.

Elements of Computational Systems Biology

Elements of Computational Systems Biology Book
Author : Huma M. Lodhi,Stephen H. Muggleton
Publisher : John Wiley & Sons
Release : 2010-03-25
ISBN : 9780470556740
Language : En, Es, Fr & De

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Book Description :

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.

Computational Systems Biology of Cancer

Computational Systems Biology of Cancer Book
Author : Emmanuel Barillot,Laurence Calzone,Philippe Hupe,Jean-Philippe Vert,Andrei Zinovyev
Publisher : CRC Press
Release : 2012-08-25
ISBN : 1439831440
Language : En, Es, Fr & De

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Book Description :

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.

Computational Systems Biology

Computational Systems Biology Book
Author : Andres Kriete,Roland Eils
Publisher : Academic Press
Release : 2013-11-26
ISBN : 0124059384
Language : En, Es, Fr & De

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Book Description :

This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.

Formal Methods for Computational Systems Biology

Formal Methods for Computational Systems Biology Book
Author : Marco Bernardo,Pierpaolo Degano,Gianluigi Zavattaro
Publisher : Springer Science & Business Media
Release : 2008-05-20
ISBN : 3540688927
Language : En, Es, Fr & De

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Book Description :

This book presents a set of 14 papers accompanying the lectures of leading researchers given at the 8th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008, held in Bertinoro, Italy in June 2008. SFM 2008 was devoted to formal techniques for computational systems biology and covered several aspects of the field, including computational models, calculi and logics for biological systems, and verification and simulation methods. The first part of this volume comprises nine papers based on regular lectures, the second part of this volume comprises five papers based on talks given by people involved in the Italian BISCA research project on Bio-Inspired Systems and Calculi with Applications.

Computational Systems Biology Approaches in Cancer Research

Computational Systems Biology Approaches in Cancer Research Book
Author : Inna Kuperstein,Emmanuel Barillot
Publisher : CRC Press
Release : 2019-09-09
ISBN : 1000682927
Language : En, Es, Fr & De

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Book Description :

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’

Transactions on Computational Systems Biology VIII

Transactions on Computational Systems Biology VIII Book
Author : Corrado Priami
Publisher : Springer
Release : 2007-11-06
ISBN : 9783540766384
Language : En, Es, Fr & De

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Book Description :

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences. It supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. The six papers selected for this special issue cover a broad range of topics.

Computational Methods in Systems Biology

Computational Methods in Systems Biology Book
Author : Ezio Bartocci,Pietro Lio,Nicola Paoletti
Publisher : Springer
Release : 2016-09-27
ISBN : 9783319451763
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 14th International Conference on Computational Methods in Systems Biology, CMSB 2016, held in Cambridge, UK, in September 2016. The 20 full papers, 3 tool papers and 9 posters presented were carefully reviewed and selected from 37 regular paper submissions. The topics include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology.

Transactions on Computational Systems Biology VII

Transactions on Computational Systems Biology VII Book
Author : Anna Ingolfsdottir,Bud Mishra,Hanne Riis Nielson
Publisher : Springer Science & Business Media
Release : 2006-11-13
ISBN : 3540488375
Language : En, Es, Fr & De

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Book Description :

This volume, the 7th in the Transactions on Computational Systems Biology series, contains a fully refereed and carefully selected set of papers from two workshops: BioConcur 2004 held in London, UK in August 2004 and BioConcur 2005 held in San Francisco, CA, USA in August 2005. The 8 papers chosen for this special issue are devoted to various aspects of computational methods, algorithms, and techniques in bioinformatics.

Transactions on Computational Systems Biology IX

Transactions on Computational Systems Biology IX Book
Author : Corrado Priami
Publisher : Springer
Release : 2011-01-10
ISBN : 3540887652
Language : En, Es, Fr & De

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Book Description :

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This issue contains four highly detailed papers. The first paper focuses on quantitative aspects of the bgl operon for E.coli. The second contribution deals with ecosystem transitions affecting phenotype expressions and selection mechanisms. The third paper presents the Stochastic Calculus of Looping Sequences (SCLS) suitable for the description of microbiological systems, such as cellular pathways, and their evolution. The final contribution describes the use of biological transactions to make atomic sequences of interactions in the BlenX language.

Computational Methods in Systems Biology

Computational Methods in Systems Biology Book
Author : Alessandro Abate,Tatjana Petrov,Verena Wolf
Publisher : Springer
Release : 2020-10-01
ISBN : 9783030603267
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 18th International Conference on Computational Methods in Systems Biology, CMSB 2020, held in Konstanz, Germany, in September 2020.* The 17 full papers and 5 tool papers were carefully reviewed and selected from 30 submissions. In addition 3 abstracts of invited talks and 2 tutorials have been included in this volume. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; computational approaches for synthetic biology; and case studies in systems and synthetic biology. * The conference was held virtually due to the COVID-19 pandemic.

Transactions on Computational Systems Biology V

Transactions on Computational Systems Biology V Book
Author : Tony Hu,Yi Pan,Tsau Young Lin
Publisher : Springer Science & Business Media
Release : 2006-07-31
ISBN : 3540360484
Language : En, Es, Fr & De

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Book Description :

The 5th Transactions on Computational Systems Biology collects carefully chosen and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing held in Beijing, China, in July 2005. The 9 papers in this special issue cover various aspects of computational methods, algorithms and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval.

Transactions on Computational Systems Biology XIII

Transactions on Computational Systems Biology XIII Book
Author : Corrado Priami,Ralph-Johan Back,Ion Petre,Erik de Vink
Publisher : Springer Science & Business Media
Release : 2011-03-28
ISBN : 3642197477
Language : En, Es, Fr & De

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Book Description :

This book covers Computational Models for Cell Processes, featuring enhanced contributions from the CompMod workshop (2009). Covers a wide range of topics in systems biology, addressing the dynamics and the computational principles of this emerging field.

An Introduction to Computational Systems Biology

An Introduction to Computational Systems Biology Book
Author : Karthik Raman
Publisher : CRC Press
Release : 2021-05-30
ISBN : 0429944527
Language : En, Es, Fr & De

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Book Description :

This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks—a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity that will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling Covers a broad spectrum of modelling, from static networks to dynamic models and constraint-based models Thoughtful exercises to test and enable understanding of concepts State-of-the-art chapters on exciting new developments, like community modelling and biological circuit design Emphasis on coding and software tools for systems biology Companion website featuring lecture videos, figure slides, codes, supplementary exercises, further reading, and appendices: https://ramanlab.github.io/SysBioBook/ An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.

Computational Methods in Systems Biology

Computational Methods in Systems Biology Book
Author : Luca Bortolussi,Guido Sanguinetti
Publisher : Springer
Release : 2019-09-17
ISBN : 9783030313036
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 17th International Conference on Computational Methods in Systems Biology, CMSB 2019, held in Trieste, Italy, in September 2019. The 14 full papers, 7 tool papers and 11 posters were carefully reviewed and selected from 53 submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; computational approaches for synthetic biology; and case studies in systems and synthetic biology.