System Identification Methods For Reverse Engineering Gene Regulatory Networks
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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 : 2016-01-20
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.
Proceedings Of The International Conference On Artificial Intelligence And Computer Vision Aicv2020
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Author : Aboul-Ella Hassanien
language : en
Publisher: Springer Nature
Release Date : 2020-03-23
Proceedings Of The International Conference On Artificial Intelligence And Computer Vision Aicv2020 written by Aboul-Ella Hassanien and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-23 with Technology & Engineering categories.
This book presents the proceedings of the 1st International Conference on Artificial Intelligence and Computer Visions (AICV 2020), which took place in Cairo, Egypt, from April 8 to 10, 2020. This international conference, which highlighted essential research and developments in the fields of artificial intelligence and computer visions, was organized by the Scientific Research Group in Egypt (SRGE). The book is divided into sections, covering the following topics: swarm-based optimization mining and data analysis, deep learning and applications, machine learning and applications, image processing and computer vision, intelligent systems and applications, and intelligent networks.
The International Conference On Advanced Machine Learning Technologies And Applications Amlta2019
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Author : Aboul Ella Hassanien
language : en
Publisher: Springer
Release Date : 2019-03-16
The International Conference On Advanced Machine Learning Technologies And Applications Amlta2019 written by Aboul Ella Hassanien and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-03-16 with Computers categories.
This book presents the peer-reviewed proceedings of the 4th International Conference on Advanced Machine Learning Technologies and Applications (AMLTA 2019), held in Cairo, Egypt, on March 28–30, 2019, and organized by the Scientific Research Group in Egypt (SRGE). The papers cover the latest research on machine learning, deep learning, biomedical engineering, control and chaotic systems, text mining, summarization and language identification, machine learning in image processing, renewable energy, cyber security, and intelligence swarms and optimization.
Proceedings Of The International Conference On Advanced Intelligent Systems And Informatics 2019
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Author : Aboul Ella Hassanien
language : en
Publisher: Springer Nature
Release Date : 2019-10-02
Proceedings Of The International Conference On Advanced Intelligent Systems And Informatics 2019 written by Aboul Ella Hassanien and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-10-02 with Technology & Engineering categories.
This book presents the proceedings of the 5th International Conference on Advanced Intelligent Systems and Informatics 2019 (AISI2019), which took place in Cairo, Egypt, from October 26 to 28, 2019. This international and interdisciplinary conference, which highlighted essential research and developments in the fields of informatics and intelligent systems, was organized by the Scientific Research Group in Egypt (SRGE). The book is divided into several sections, covering the following topics: machine learning and applications, swarm optimization and applications, robotic and control systems, sentiment analysis, e-learning and social media education, machine and deep learning algorithms, recognition and image processing, intelligent systems and applications, mobile computing and networking, cyber-physical systems and security, smart grids and renewable energy, and micro-grid and power systems.
Reverse Engineering
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Author : A.C. Telea
language : en
Publisher: BoD – Books on Demand
Release Date : 2012-03-07
Reverse Engineering written by A.C. Telea and has been published by BoD – Books on Demand 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.
Knowledge Discovery And Emergent Complexity In Bioinformatics
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Author : Karl Tuyls
language : en
Publisher: Springer
Release Date : 2007-05-05
Knowledge Discovery And Emergent Complexity In Bioinformatics written by Karl Tuyls and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-05-05 with Science categories.
This book constitutes the thoroughly refereed post-proceedings of the First International Workshop on Knowledge Discovery and Emergent Complexity in Bioinformatics, KDECB 2006, held in Ghent, Belgium, in May 2006, in connection with the 15th Belgium-Netherlands Conference on Machine Learning. The 12 revised full papers cover various topics in the areas of knowledge discovery and emergent complexity research in bioinformatics.
Systems Biology In Biotech Pharma
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Author : Aleš Prokop
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-01-05
Systems Biology In Biotech Pharma written by Aleš Prokop and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-01-05 with Medical categories.
The US is currently well ahead of the rest of the world in the development and application of SB and its principles especially as they pertain to basic medical research and development. This lead is largely due to its earlier start in the academic arena. However, there is evidence of rapid development in both the UK/EU and Japan, and the gap is narrowing, particularly in the UK. From an industrial point of view, the Pharmaceutical Industry based in the US and UK can capitalize on these opportunities and gain the benefits of this technology. Many educational institutions (particularly their medical divisions) at present are heavily business-oriented, realize that in this particular industrial environment, that every dollar counts.
Computational Methods In Systems Biology
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Author : Luca Bortolussi
language : en
Publisher: Springer Nature
Release Date : 2019-09-16
Computational Methods In Systems Biology written by Luca Bortolussi and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-09-16 with Computers categories.
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.
Proceedings Of The 16th International Conference On Hybrid Intelligent Systems His 2016
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Author : Ajith Abraham
language : en
Publisher: Springer
Release Date : 2017-02-21
Proceedings Of The 16th International Conference On Hybrid Intelligent Systems His 2016 written by Ajith Abraham and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-02-21 with Technology & Engineering categories.
This book presents the latest research in hybrid intelligent systems. It includes 57 carefully selected papers from the 16th International Conference on Hybrid Intelligent Systems (HIS 2016) and the 8th World Congress on Nature and Biologically Inspired Computing (NaBIC 2016), held on November 21–23, 2016 in Marrakech, Morocco. HIS - NaBIC 2016 was jointly organized by the Machine Intelligence Research Labs (MIR Labs), USA; Hassan 1st University, Settat, Morocco and University of Sfax, Tunisia. Hybridization of intelligent systems is a promising research field in modern artificial/computational intelligence and is concerned with the development of the next generation of intelligent systems. The conference’s main aim is to inspire further exploration of the intriguing potential of hybrid intelligent systems and bio-inspired computing. As such, the book is a valuable resource for practicing engineers /scientists and researchers working in the field of computational intelligence and artificial intelligence.