Computational Genetic Regulatory Networks: Evolvable, Self-organizing Systems

Computational Genetic Regulatory Networks: Evolvable, Self-organizing Systems

Author: Johannes F. Knabe

Publisher: Springer

Published: 2012-08-14

Total Pages: 125

ISBN-13: 3642302963

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Genetic Regulatory Networks (GRNs) in biological organisms are primary engines for cells to enact their engagements with environments, via incessant, continually active coupling. In differentiated multicellular organisms, tremendous complexity has arisen in the course of evolution of life on earth. Engineering and science have so far achieved no working system that can compare with this complexity, depth and scope of organization. Abstracting the dynamics of genetic regulatory control to a computational framework in which artificial GRNs in artificial simulated cells differentiate while connected in a changing topology, it is possible to apply Darwinian evolution in silico to study the capacity of such developmental/differentiated GRNs to evolve. In this volume an evolutionary GRN paradigm is investigated for its evolvability and robustness in models of biological clocks, in simple differentiated multicellularity, and in evolving artificial developing 'organisms' which grow and express an ontogeny starting from a single cell interacting with its environment, eventually including a changing local neighbourhood of other cells. These methods may help us understand the genesis, organization, adaptive plasticity, and evolvability of differentiated biological systems, and may also provide a paradigm for transferring these principles of biology's success to computational and engineering challenges at a scale not previously conceivable.


Book Synopsis Computational Genetic Regulatory Networks: Evolvable, Self-organizing Systems by : Johannes F. Knabe

Download or read book Computational Genetic Regulatory Networks: Evolvable, Self-organizing Systems written by Johannes F. Knabe and published by Springer. This book was released on 2012-08-14 with total page 125 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic Regulatory Networks (GRNs) in biological organisms are primary engines for cells to enact their engagements with environments, via incessant, continually active coupling. In differentiated multicellular organisms, tremendous complexity has arisen in the course of evolution of life on earth. Engineering and science have so far achieved no working system that can compare with this complexity, depth and scope of organization. Abstracting the dynamics of genetic regulatory control to a computational framework in which artificial GRNs in artificial simulated cells differentiate while connected in a changing topology, it is possible to apply Darwinian evolution in silico to study the capacity of such developmental/differentiated GRNs to evolve. In this volume an evolutionary GRN paradigm is investigated for its evolvability and robustness in models of biological clocks, in simple differentiated multicellularity, and in evolving artificial developing 'organisms' which grow and express an ontogeny starting from a single cell interacting with its environment, eventually including a changing local neighbourhood of other cells. These methods may help us understand the genesis, organization, adaptive plasticity, and evolvability of differentiated biological systems, and may also provide a paradigm for transferring these principles of biology's success to computational and engineering challenges at a scale not previously conceivable.

Evolutionary Computation in Gene Regulatory Network Research

Evolutionary Computation in Gene Regulatory Network Research

Author: Hitoshi Iba

Publisher: John Wiley & Sons

Published: 2016-02-23

Total Pages: 464

ISBN-13: 1118911512

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Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.


Book Synopsis Evolutionary Computation in Gene Regulatory Network Research by : Hitoshi Iba

Download or read book Evolutionary Computation in Gene Regulatory Network Research written by Hitoshi Iba and published by John Wiley & Sons. This book was released on 2016-02-23 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.

Computational Modeling of Gene Regulatory Networks

Computational Modeling of Gene Regulatory Networks

Author: Hamid Bolouri

Publisher: Imperial College Press

Published: 2008

Total Pages: 341

ISBN-13: 1848162200

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This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.


Book Synopsis Computational Modeling of Gene Regulatory Networks by : Hamid Bolouri

Download or read book Computational Modeling of Gene Regulatory Networks written by Hamid Bolouri and published by Imperial College Press. This book was released on 2008 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.

Applications of Evolutionary Computation

Applications of Evolutionary Computation

Author: Cecilia Di Chio

Publisher: Springer

Published: 2010-04-03

Total Pages: 644

ISBN-13: 3642122396

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Evolutionary Computation (EC) techniques are e?cient, nature-inspired me- ods based on the principles of natural evolution and genetics. Due to their - ciency and simple underlying principles, these methods can be used for a diverse rangeofactivitiesincludingproblemsolving,optimization,machinelearningand pattern recognition. A large and continuously increasing number of researchers and professionals make use of EC techniques in various application domains. This volume presents a careful selection of relevant EC examples combined with a thorough examination of the techniques used in EC. The papers in the volume illustrate the current state of the art in the application of EC and should help and inspire researchers and professionals to develop e?cient EC methods for design and problem solving. All papers in this book were presented during EvoApplications 2010, which included a range of events on application-oriented aspects of EC. Since 1998, EvoApplications — formerly known as EvoWorkshops— has provided a unique opportunity for EC researchers to meet and discuss application aspects of EC and has been an important link between EC research and its application in a variety of domains. During these 12 years, new events have arisen, some have disappeared,whileothershavematuredtobecomeconferencesoftheirown,such as EuroGP in 2000, EvoCOP in 2004, and EvoBIO in 2007. And from this year, EvoApplications has become a conference as well.


Book Synopsis Applications of Evolutionary Computation by : Cecilia Di Chio

Download or read book Applications of Evolutionary Computation written by Cecilia Di Chio and published by Springer. This book was released on 2010-04-03 with total page 644 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evolutionary Computation (EC) techniques are e?cient, nature-inspired me- ods based on the principles of natural evolution and genetics. Due to their - ciency and simple underlying principles, these methods can be used for a diverse rangeofactivitiesincludingproblemsolving,optimization,machinelearningand pattern recognition. A large and continuously increasing number of researchers and professionals make use of EC techniques in various application domains. This volume presents a careful selection of relevant EC examples combined with a thorough examination of the techniques used in EC. The papers in the volume illustrate the current state of the art in the application of EC and should help and inspire researchers and professionals to develop e?cient EC methods for design and problem solving. All papers in this book were presented during EvoApplications 2010, which included a range of events on application-oriented aspects of EC. Since 1998, EvoApplications — formerly known as EvoWorkshops— has provided a unique opportunity for EC researchers to meet and discuss application aspects of EC and has been an important link between EC research and its application in a variety of domains. During these 12 years, new events have arisen, some have disappeared,whileothershavematuredtobecomeconferencesoftheirown,such as EuroGP in 2000, EvoCOP in 2004, and EvoBIO in 2007. And from this year, EvoApplications has become a conference as well.

Evolutionary Computation in Gene Regulatory Network Research

Evolutionary Computation in Gene Regulatory Network Research

Author: Hitoshi Iba

Publisher: John Wiley & Sons

Published: 2016-01-20

Total Pages: 464

ISBN-13: 1119079772

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Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.


Book Synopsis Evolutionary Computation in Gene Regulatory Network Research by : Hitoshi Iba

Download or read book Evolutionary Computation in Gene Regulatory Network Research written by Hitoshi Iba and published by John Wiley & Sons. This book was released on 2016-01-20 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.

Computational Evolution of Neural and Morphological Development

Computational Evolution of Neural and Morphological Development

Author: Yaochu Jin

Publisher: Springer Nature

Published: 2023-07-14

Total Pages: 302

ISBN-13: 9819918545

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This book provides a basic yet unified overview of theory and methodologies for evolutionary developmental systems. Based on the author’s extensive research into the synergies between various approaches to artificial intelligence including evolutionary computation, artificial neural networks, and systems biology, it also examines the inherent links between biological intelligence and artificial intelligence. The book begins with an introduction to computational algorithms used to understand and simulate biological evolution and development, including evolutionary algorithms, gene regulatory network models, multi-cellular models for neural and morphological development, and computational models of neural plasticity. Chap. 2 discusses important properties of biological gene regulatory systems, including network motifs, network connectivity, robustness and evolvability. Going a step further, Chap. 3 presents methods for synthesizing regulatory motifs from scratch and creating more complex regulatory dynamics by combining basic regulatory motifs using evolutionary algorithms. Multi-cellular growth models, which can be used to simulate either neural or morphological development, are presented in Chapters 4 and 5. Chap. 6 examines the synergies and coupling between neural and morphological evolution and development. In turn, Chap. 7 provides preliminary yet promising examples of how evolutionary developmental systems can help in self-organized pattern generation, referred to as morphogenetic self-organization, highlighting the great potentials of evolutionary developmental systems. Finally, Chap. 8 rounds out the book, stressing the importance and promise of the evolutionary developmental approach to artificial intelligence. Featuring a wealth of diagrams, graphs and charts to aid in comprehension, this book offers a valuable asset for graduate students, researchers and practitioners who are interested in pursuing a different approach to artificial intelligence.


Book Synopsis Computational Evolution of Neural and Morphological Development by : Yaochu Jin

Download or read book Computational Evolution of Neural and Morphological Development written by Yaochu Jin and published by Springer Nature. This book was released on 2023-07-14 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a basic yet unified overview of theory and methodologies for evolutionary developmental systems. Based on the author’s extensive research into the synergies between various approaches to artificial intelligence including evolutionary computation, artificial neural networks, and systems biology, it also examines the inherent links between biological intelligence and artificial intelligence. The book begins with an introduction to computational algorithms used to understand and simulate biological evolution and development, including evolutionary algorithms, gene regulatory network models, multi-cellular models for neural and morphological development, and computational models of neural plasticity. Chap. 2 discusses important properties of biological gene regulatory systems, including network motifs, network connectivity, robustness and evolvability. Going a step further, Chap. 3 presents methods for synthesizing regulatory motifs from scratch and creating more complex regulatory dynamics by combining basic regulatory motifs using evolutionary algorithms. Multi-cellular growth models, which can be used to simulate either neural or morphological development, are presented in Chapters 4 and 5. Chap. 6 examines the synergies and coupling between neural and morphological evolution and development. In turn, Chap. 7 provides preliminary yet promising examples of how evolutionary developmental systems can help in self-organized pattern generation, referred to as morphogenetic self-organization, highlighting the great potentials of evolutionary developmental systems. Finally, Chap. 8 rounds out the book, stressing the importance and promise of the evolutionary developmental approach to artificial intelligence. Featuring a wealth of diagrams, graphs and charts to aid in comprehension, this book offers a valuable asset for graduate students, researchers and practitioners who are interested in pursuing a different approach to artificial intelligence.

Self-Organizing Systems

Self-Organizing Systems

Author: Christian Bettstetter

Publisher: Springer

Published: 2011-02-03

Total Pages: 125

ISBN-13: 3642191673

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This book constitutes the refereed proceedings of the 5th International Workshop on Self-Organizing Systems, IWSOS 2011, held in Karlsruhe, Germany, in February 2011. The 9 revised full papers presented together with 1 invited paper were carefully selected from 25 initial submissions. It was the 5th workshop in a series of multidisciplinary events dedicated to self-organization in networked systems with main focus on communication and computer networks. The papers address theoretical aspects of self-organization as well as applications in communication and computer networks and robot networks.


Book Synopsis Self-Organizing Systems by : Christian Bettstetter

Download or read book Self-Organizing Systems written by Christian Bettstetter and published by Springer. This book was released on 2011-02-03 with total page 125 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 5th International Workshop on Self-Organizing Systems, IWSOS 2011, held in Karlsruhe, Germany, in February 2011. The 9 revised full papers presented together with 1 invited paper were carefully selected from 25 initial submissions. It was the 5th workshop in a series of multidisciplinary events dedicated to self-organization in networked systems with main focus on communication and computer networks. The papers address theoretical aspects of self-organization as well as applications in communication and computer networks and robot networks.

Bio-Inspired Self-Organizing Robotic Systems

Bio-Inspired Self-Organizing Robotic Systems

Author: Yan Meng

Publisher: Springer

Published: 2011-05-11

Total Pages: 273

ISBN-13: 364220760X

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Self-organizing approaches inspired from biological systems, such as social insects, genetic, molecular and cellular systems under morphogenesis, and human mental development, has enjoyed great success in advanced robotic systems that need to work in dynamic and changing environments. Compared with classical control methods for robotic systems, the major advantages of bio-inspired self-organizing robotic systems include robustness, self-repair and self-healing in the presence of system failures and/or malfunctions, high adaptability to environmental changes, and autonomous self-organization and self-reconfiguration without a centralized control. “Bio-inspired Self-organizing Robotic Systems” provides a valuable reference for scientists, practitioners and research students working on developing control algorithms for self-organizing engineered collective systems, such as swarm robotic systems, self-reconfigurable modular robots, smart material based robotic devices, unmanned aerial vehicles, and satellite constellations.


Book Synopsis Bio-Inspired Self-Organizing Robotic Systems by : Yan Meng

Download or read book Bio-Inspired Self-Organizing Robotic Systems written by Yan Meng and published by Springer. This book was released on 2011-05-11 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: Self-organizing approaches inspired from biological systems, such as social insects, genetic, molecular and cellular systems under morphogenesis, and human mental development, has enjoyed great success in advanced robotic systems that need to work in dynamic and changing environments. Compared with classical control methods for robotic systems, the major advantages of bio-inspired self-organizing robotic systems include robustness, self-repair and self-healing in the presence of system failures and/or malfunctions, high adaptability to environmental changes, and autonomous self-organization and self-reconfiguration without a centralized control. “Bio-inspired Self-organizing Robotic Systems” provides a valuable reference for scientists, practitioners and research students working on developing control algorithms for self-organizing engineered collective systems, such as swarm robotic systems, self-reconfigurable modular robots, smart material based robotic devices, unmanned aerial vehicles, and satellite constellations.

Self-Organizing Systems

Self-Organizing Systems

Author: Christian Bettstetter

Publisher:

Published: 2011-03-30

Total Pages: 128

ISBN-13: 9783642191688

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Book Synopsis Self-Organizing Systems by : Christian Bettstetter

Download or read book Self-Organizing Systems written by Christian Bettstetter and published by . This book was released on 2011-03-30 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Handbook of Research on Computational Methodologies in Gene Regulatory Networks

Handbook of Research on Computational Methodologies in Gene Regulatory Networks

Author: Das, Sanjoy

Publisher: IGI Global

Published: 2009-10-31

Total Pages: 740

ISBN-13: 1605666866

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"This book focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization"--Provided by publisher.


Book Synopsis Handbook of Research on Computational Methodologies in Gene Regulatory Networks by : Das, Sanjoy

Download or read book Handbook of Research on Computational Methodologies in Gene Regulatory Networks written by Das, Sanjoy and published by IGI Global. This book was released on 2009-10-31 with total page 740 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization"--Provided by publisher.