Reverse Engineering Gene Regulatory Networks
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Reverse Engineering Of Regulatory Networks
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Author : Sudip Mandal
language : en
Publisher: Springer Nature
Release Date : 2023-10-06
Reverse Engineering Of Regulatory Networks written by Sudip Mandal and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-10-06 with Technology & Engineering categories.
This volume details the development of updated dry lab and wet lab based methods for the reconstruction of Gene regulatory networks (GRN). Chapters guide readers through culprit genes, in-silico drug discovery techniques, genome-wide ChIP-X data, high-Throughput Transcriptomic Data Exome Sequencing, Next-Generation Sequencing, Fuorescence Spectroscopy, data analysis in Bioinformatics, Computational Biology, and S-system based modeling of GRN. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Reverse Engineering of Regulatory Networks aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.
Reverse Engineering Gene Regulatory Networks
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Author : Vincenzo Belcastro
language : en
Publisher:
Release Date : 2010
Reverse Engineering Gene Regulatory Networks written by Vincenzo Belcastro and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with Genetic regulation categories.
Linking The Genes
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Author : ALBERTO. DE LA FUENTE
language : en
Publisher:
Release Date : 2018
Linking The Genes written by ALBERTO. DE LA FUENTE and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with categories.
Towards Reverse Engineering Gene Regulatory Networks
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Author : Thomas Schlitt
language : en
Publisher:
Release Date : 2004
Towards Reverse Engineering Gene Regulatory Networks written by Thomas Schlitt and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
System Identification Methods For Reverse Engineering Gene Regulatory Networks
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Author : Zhen Wang
language : en
Publisher:
Release Date : 2010
System Identification Methods For Reverse Engineering Gene Regulatory Networks written by Zhen Wang and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
With the advent of high throughput measurement technologies, large scale gene expression data are available for analysis. Various computational methods have been introduced to analyze and predict meaningful molecular interactions from gene expression data. Such patterns can provide an understanding of the regulatory mechanisms in the cells. In the past, system identification algorithms have been extensively developed for engineering systems. These methods capture the dynamic input/output relationship of a system, provide a deterministic model of its function, and have reasonable computational requirements. In this work, two system identification methods are applied for reverse engineering of gene regulatory networks. The first method is based on an orthogonal search; it selects terms from a predefined set of gene expression profiles to best fit the expression levels of a given output gene. The second method consists of a few cascades, each of which includes a dynamic component and a static component. Multiple cascades are added in a parallel to reduce the difference of the estimated expression profiles with the actual ones. Gene regulatory networks can be constructed by defining the selected inputs as the regulators of the output. To assess the performance of the approaches, a temporal synthetic dataset is developed. Methods are then applied to this dataset as well as the Brainsim dataset, a popular simulated temporal gene expression data. Furthermore, the methods are also applied to a biological dataset in yeast Saccharomyces Cerevisiae. This dataset includes 14 cell-cycle regulated genes; their known cell cycle pathway is used as the target network structure, and the criteria sensitivity, precision, and specificity are calculated to evaluate the inferred networks through these two methods. Resulting networks are also compared with two previous studies in the literature on the same dataset.
Evolutionary Computation In Gene Regulatory Network Research
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Author : Hitoshi Iba
language : en
Publisher: John Wiley & Sons
Release Date : 2016-02-23
Evolutionary Computation In Gene Regulatory Network Research written by Hitoshi Iba and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-02-23 with Computers categories.
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.
Reverse Engineering
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Author : A.C. Telea
language : en
Publisher: IntechOpen
Release Date : 2012-03-07
Reverse Engineering written by A.C. Telea and has been published by IntechOpen this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-03-07 with Computers categories.
Reverse engineering encompasses a wide spectrum of activities aimed at extracting information on the function, structure, and behavior of man-made or natural artifacts. Increases in data sources, processing power, and improved data mining and processing algorithms have opened new fields of application for reverse engineering. In this book, we present twelve applications of reverse engineering in the software engineering, shape engineering, and medical and life sciences application domains. The book can serve as a guideline to practitioners in the above fields to the state-of-the-art in reverse engineering techniques, tools, and use-cases, as well as an overview of open challenges for reverse engineering researchers.
Probabilistic Boolean Networks
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Author : Ilya Shmulevich
language : en
Publisher: SIAM
Release Date : 2010-01-01
Probabilistic Boolean Networks written by Ilya Shmulevich and has been published by SIAM this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-01-01 with Mathematics categories.
This is the first comprehensive treatment of probabilistic Boolean networks (PBNs), an important model class for studying genetic regulatory networks. This book covers basic model properties, including the relationships between network structure and dynamics, steady-state analysis, and relationships to other model classes." "Researchers in mathematics, computer science, and engineering are exposed to important applications in systems biology and presented with ample opportunities for developing new approaches and methods. The book is also appropriate for advanced undergraduates, graduate students, and scientists working in the fields of computational biology, genomic signal processing, control and systems theory, and computer science.
Evolutionary Computation In Gene Regulatory Network Research
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Author : Hitoshi Iba
language : en
Publisher: John Wiley & Sons
Release Date : 2016-01-20
Evolutionary Computation In Gene Regulatory Network Research written by Hitoshi Iba and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-01-20 with Computers categories.
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.
Analysis Of Deterministic Cyclic Gene Regulatory Network Models With Delays
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Author : Mehmet Eren Ahsen
language : en
Publisher: Birkhäuser
Release Date : 2015-02-25
Analysis Of Deterministic Cyclic Gene Regulatory Network Models With Delays written by Mehmet Eren Ahsen and has been published by Birkhäuser this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-02-25 with Science categories.
This brief examines a deterministic, ODE-based model for gene regulatory networks (GRN) that incorporates nonlinearities and time-delayed feedback. An introductory chapter provides some insights into molecular biology and GRNs. The mathematical tools necessary for studying the GRN model are then reviewed, in particular Hill functions and Schwarzian derivatives. One chapter is devoted to the analysis of GRNs under negative feedback with time delays and a special case of a homogenous GRN is considered. Asymptotic stability analysis of GRNs under positive feedback is then considered in a separate chapter, in which conditions leading to bi-stability are derived. Graduate and advanced undergraduate students and researchers in control engineering, applied mathematics, systems biology and synthetic biology will find this brief to be a clear and concise introduction to the modeling and analysis of GRNs.