Study Of Gene Regulatory Networks Inference Methods From Gene Expression Data
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Study Of Gene Regulatory Networks Inference Methods From Gene Expression Data
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Author : Pau Bellot Pujalte
language : en
Publisher:
Release Date : 2017
Study Of Gene Regulatory Networks Inference Methods From Gene Expression Data written by Pau Bellot Pujalte and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
A cell is a the basic structural and functional unit of every living thing, it is protein-based an that regulates itself. The cell eats to stay alive, it grows and develops; reacting to the environment, while subjected to evolution. It also makes copies of itself. These processes are governed by chain of chemical reactions, creating a complex system. The scientific community has proposed to model the whole process with Gene Regulatory Networks (GRN). The understanding of these networks allows gaining a systems-level acknowledgment of biological organisms and also to genetically related diseases. This thesis focused on network inference from gene expression data, will contribute to this field of knowledge by studying different techniques that allows a better reconstruction of GRN. Gene expression datasets, are characterised by having thousands of noisy variables measured only with tens of samples. Moreover, these variables presents non-linear dependencies between them. Therefore, recovering a model that is capable of capturing the relationships contained in this data, constitutes a major challenge. The main contribution of this thesis is a set of fair and sound studies of different GRN inference methods and post-processing algorithms. First, we present a novel approach for inferring gene networks and we compare it with other methods. It is inspired by the concept of "variable importance" in feature selection. However, many algorithms can be proposed to infer GRNs, so there is a need to assess the quality of these algorithms. Secondly, and motivated by the fact that the previous comparison was not informative enough, we introduce a new framework for in silico performance assessment of GRN inference methods. This work has led to an open source R/Bioconductor package called NetBenchmark. Finally, and thanks to this tool we have corroborated that inferring gene regulatory networks from expression data is a tough problem. The different algorithms have some particular biases and strengths, and none of them is the best across all types of data and datasets. Therefore, we present a framework for evaluating and standardising network consensus methods to aggregate various network inferences.
Drosophila Eye Development
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Author : Kevin Moses
language : en
Publisher: Springer Science & Business Media
Release Date : 2002-03-12
Drosophila Eye Development written by Kevin Moses 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 2002-03-12 with Medical categories.
1 Kevin Moses It is now 25 years since the study of the development of the compound eye in Drosophila really began with a classic paper (Ready et al. 1976). In 1864, August Weismann published a monograph on the development of Diptera and included some beautiful drawings of the developing imaginal discs (Weismann 1864). One of these is the first description of the third instar eye disc in which Weismann drew a vertical line separating a posterior domain that included a regular pattern of clustered cells from an anterior domain without such a pattern. Weismann suggested that these clusters were the precursors of the adult ommatidia and that the line marks the anterior edge of the eye. In his first suggestion he was absolutely correct - in his second he was wrong. The vertical line shown was not the anterior edge of the eye, but the anterior edge of a moving wave of patterning and cell type specification that 112 years later (1976) Ready, Hansen and Benzer would name the "morphogenetic furrow". While it is too late to hear from August Weismann, it is a particular pleasure to be able to include a chapter in this Volume from the first author of that 1976 paper: Don Ready! These past 25 years have seen an astonishing explosion in the study of the fly eye (see Fig.
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.
Emerging Research In The Analysis And Modeling Of Gene Regulatory Networks
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Author : Ivanov, Ivan V.
language : en
Publisher: IGI Global
Release Date : 2016-06-06
Emerging Research In The Analysis And Modeling Of Gene Regulatory Networks written by Ivanov, Ivan V. and has been published by IGI Global this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-06-06 with Medical categories.
While technological advancements have been critical in allowing researchers to obtain more and better quality data about cellular processes and signals, the design and practical application of computational models of genomic regulation continues to be a challenge. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks presents a compilation of recent and emerging research topics addressing the design and use of technology in the study and simulation of genomic regulation. Exploring both theoretical and practical topics, this publication is an essential reference source for students, professionals, and researchers working in the fields of genomics, molecular biology, bioinformatics, and drug development.
Biological Network Analysis
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Author : Pietro Hiram Guzzi
language : en
Publisher: Academic Press
Release Date : 2020-05-12
Biological Network Analysis written by Pietro Hiram Guzzi and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-05-12 with Science categories.
Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource.
Emerging Technologies In Data Mining And Information Security
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Author : João Manuel R. S. Tavares
language : en
Publisher: Springer Nature
Release Date : 2021-05-04
Emerging Technologies In Data Mining And Information Security written by João Manuel R. S. Tavares and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-04 with Technology & Engineering categories.
This book features research papers presented at the International Conference on Emerging Technologies in Data Mining and Information Security (IEMIS 2020) held at the University of Engineering & Management, Kolkata, India, during July 2020. The book is organized in three volumes and includes high-quality research work by academicians and industrial experts in the field of computing and communication, including full-length papers, research-in-progress papers, and case studies related to all the areas of data mining, machine learning, Internet of things (IoT), and information security.
Modelling And Implementation Of Complex Systems
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Author : Salim Chikhi
language : en
Publisher: Springer
Release Date : 2018-11-29
Modelling And Implementation Of Complex Systems written by Salim Chikhi and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-29 with Technology & Engineering categories.
This book presents the proceedings of the fifth International Symposium on Modelling and Implementation of Complex Systems (MISC 2018). The event was held in Laghouat, Algeria, on December 16–18, 2018. The 25 papers gathered here have been selected from 109 submissions using a strict peer-review process, and address a range of topics concerning the theory and applications of networking and distributed computing, including: cloud computing and the IoT, metaheuristics and optimization, computational intelligence, software engineering and formal methods.
Analysis Of Microarray Data
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Author : Matthias Dehmer
language : en
Publisher: John Wiley & Sons
Release Date : 2008-03-17
Analysis Of Microarray Data written by Matthias Dehmer 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 2008-03-17 with Medical categories.
This book is the first to focus on the application of mathematical networks for analyzing microarray data. This method goes well beyond the standard clustering methods traditionally used. From the contents: * Understanding and Preprocessing Microarray Data * Clustering of Microarray Data * Reconstruction of the Yeast Cell Cycle by Partial Correlations of Higher Order * Bilayer Verification Algorithm * Probabilistic Boolean Networks as Models for Gene Regulation * Estimating Transcriptional Regulatory Networks by a Bayesian Network * Analysis of Therapeutic Compound Effects * Statistical Methods for Inference of Genetic Networks and Regulatory Modules * Identification of Genetic Networks by Structural Equations * Predicting Functional Modules Using Microarray and Protein Interaction Data * Integrating Results from Literature Mining and Microarray Experiments to Infer Gene Networks The book is for both, scientists using the technique as well as those developing new analysis techniques.
Advances In Biotechnology Research And Application 2011 Edition
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Author :
language : en
Publisher: ScholarlyEditions
Release Date : 2012-01-09
Advances In Biotechnology Research And Application 2011 Edition written by and has been published by ScholarlyEditions this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-01-09 with Medical categories.
Advances in Biotechnology Research and Application: 2011 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Biotechnology. The editors have built Advances in Biotechnology Research and Application: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Biotechnology in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Advances in Biotechnology Research and Application: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.