Analysis Of 3d Genome Organization And Gene Regulation In Mammalian Cells

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Analysis of 3D Genome Organization and Gene Regulation in Mammalian Cells

Author : Siddarth Gautham Selvaraj
Publisher :
ISBN 13 : 9781321138146
Total Pages : 156 pages
Book Rating : 4.1/5 (381 download)

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Book Synopsis Analysis of 3D Genome Organization and Gene Regulation in Mammalian Cells by : Siddarth Gautham Selvaraj

Download or read book Analysis of 3D Genome Organization and Gene Regulation in Mammalian Cells written by Siddarth Gautham Selvaraj and published by . This book was released on 2014 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure of the genome plays a key role in gene regulation. For example, while highly compacted heterochromatin drives gene silencing, open euchromatin facilitates gene activation. Nevertheless, how chromatin folds within these structures and consequently how it controls access to genomic content is poorly understood. Recent advances in high-throughput sequencing have provided valuable tools, such as Hi-C, for the study of chromatin structure. Using Hi-C datasets, I developed a hidden markov based algorithm to identify self-interacting patterns of chromatin structure termed topological domains. These mega-base sized domains are pervasive throughout the genome and are highly conserved among humans and mouse. At a higher resolution, topological domains encompass individual chromatin interactions between regulatory elements and its target gene. Therefore, in order to mechanistically understand gene regulation, it is essential to elucidate the functional relationship among regulatory elements and their target genes. By exploiting the sequence diversity between homologous chromosomes, it is possible to delineate this relationship. However, this requires the knowledge of haplotypes, which has traditionally been difficult to obtain. As the Hi-C protocol preferentially recovers DNA variants on the same chromosome, I invented HaploSeq to reconstruct chromosome-scale haplotypes. HaploSeq can generate haplotypes with ~99.5% accuracy for >95% of alleles in mouse and 98% accuracy for ~81% of alleles in humans, thus solving a long-standing problem in genetics. By integrating the knowledge of haplotypes, we queried the relationship between regulatory elements and gene expression in human embryonic stem cells and a panel of differentiated cell-types. Across the 5 cell lineages examined, I identified a total of 24% of genes that showed allelic bias in gene expression. While most of the allelic-genes had a correlating allelic-promoter chromatin state, ~29% of genes were exceptions suggesting other mechanisms of gene regulation. Accordingly, I then analyzed histone-acetylation marks to identify 1589 allelic enhancers. By predicting chromatin interactions using Hi-C, we observed allelic enhancers to be spatially proximal to allelic genes, suggesting cooperative activity among genome sequence, structure, and function. Taken together, our studies suggest that gene regulation is facilitated and coordinated by genome structure.

Plant Chromatin Dynamics

Author : Marian Bemer
Publisher : Humana
ISBN 13 : 9781493984510
Total Pages : 0 pages
Book Rating : 4.9/5 (845 download)

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Book Synopsis Plant Chromatin Dynamics by : Marian Bemer

Download or read book Plant Chromatin Dynamics written by Marian Bemer and published by Humana. This book was released on 2018-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into three sections detail the profiling of chromatin features in relation to epigenetic regulation, investigate the interaction between chromatin modifications and gene regulation, and explore the 3D spatial organization of the chromatin inside the nucleus. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Plant Chromatin Dynamics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Computational Methods for Analyzing and Modeling Gene Regulation and 3D Genome Organization

Author : Anastasiya Belyaeva
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (125 download)

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Book Synopsis Computational Methods for Analyzing and Modeling Gene Regulation and 3D Genome Organization by : Anastasiya Belyaeva

Download or read book Computational Methods for Analyzing and Modeling Gene Regulation and 3D Genome Organization written by Anastasiya Belyaeva and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological processes from differentiation to disease progression are governed by gene regulatory mechanisms. Currently large-scale omics and imaging data sets are being collected to characterize gene regulation at every level. Such data sets present new opportunities and challenges for extracting biological insights and elucidating the gene regulatory logic of cells. In this thesis, I present computational methods for the analysis and integration of various data types used for cell profiling. Specifically, I focus on analyzing and linking gene expression with the 3D organization of the genome. First, I describe methodologies for elucidating gene regulatory mechanisms by considering multiple data modalities. I design a computational framework for identifying colocalized and coregulated chromosome regions by integrating gene expression and epigenetic marks with 3D interactions using network analysis. Then, I provide a general framework for data integration using autoencoders and apply it for the integration and translation between gene expression and chromatin images of naive T-cells. Second, I describe methods for analyzing single modalities such as contact frequency data, which measures the spatial organization of the genome, and gene expression data. Given the important role of the 3D genome organization in gene regulation, I present a methodology for reconstructing the 3D diploid conformation of the genome from contact frequency data. Given the ubiquity of gene expression data and the recent advances in single-cell RNA-sequencing technologies as well as the need for causal modeling of gene regulatory mechanisms, I then describe an algorithm as well as a software tool, difference causal inference (DCI), for learning causal gene regulatory networks from gene expression data. DCI addresses the problem of directly learning differences between causal gene regulatory networks given gene expression data from two related conditions. Finally, I shift my focus from basic biology to drug discovery. Given the current COVID19 pandemic, I present a computational drug repurposing platform that enables the identification of FDA approved compounds for drug repurposing and investigation of potential causal drug mechanisms. This framework relies on identifying drugs that reverse the signature of the infection in the space learned by an autoencoder and then uses causal inference to identify putative drug mechanisms.

Long-Range Control of Gene Expression

Author : Veronica van Heyningen
Publisher : Academic Press
ISBN 13 : 0080877818
Total Pages : 415 pages
Book Rating : 4.0/5 (88 download)

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Book Synopsis Long-Range Control of Gene Expression by : Veronica van Heyningen

Download or read book Long-Range Control of Gene Expression written by Veronica van Heyningen and published by Academic Press. This book was released on 2011-09-02 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer

HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing

Author : Oldenburg Oldenburg Press
Publisher :
ISBN 13 : 9781523764426
Total Pages : 40 pages
Book Rating : 4.7/5 (644 download)

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Book Synopsis HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing by : Oldenburg Oldenburg Press

Download or read book HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing written by Oldenburg Oldenburg Press and published by . This book was released on 2016-01-29 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.

Eucaryotic Gene Regulation

Author : Richard Axel
Publisher : Elsevier
ISBN 13 : 0323143504
Total Pages : 682 pages
Book Rating : 4.3/5 (231 download)

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Book Synopsis Eucaryotic Gene Regulation by : Richard Axel

Download or read book Eucaryotic Gene Regulation written by Richard Axel and published by Elsevier. This book was released on 2012-12-02 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: Eukaryotic Gene Regulation covers the aspects and mechanisms of gene regulation of selected eukaryotes, such as yeast, Drosophila, and insect. This book is organized into eight parts, encompassing 52 chapters. The majority of the chapters are presented in an experimental manner containing an abstract, methods, results and discussion, and conclusion. This book first gives a short overview of the evolutionary role of interspersion in eukaryotic genes. It then presents considerable chapters on control of gene expression in yeast; gene mutation and isolation; structure and function; and analysis. Part III focuses on genetic and DNA sequence analysis in Drosophila. It includes discussions on allelic complementation and transvection, genetic organization, histone gene, and gene transcription. Part IV examines cell lineage; gene expression and sequences; and protein synthesis of insects, sea urchin, and mammalian cells. This is followed by discussions on structure and expression of specific eukaryotic genes from chicken, rat, rabbit, and human. Topics on the transfer of genetic information within and between cells and the structure and function of chromosome are significantly considered in Parts VI and VII. Genes evaluated in these sections include heavy chain immunoglobulin, light chain, beta-globin, and dihydrofolate reductase. Furthermore, this book describes the in vitro transcription and the factors involved; internal organization and mechanism of assembly of nucleosome; and chromatin structure. The concluding section focuses on aspects of viral genome expression including gene regulation, synthesis, processing, and alternative RNA splicing. Research biologists, geneticists, scientists, teachers, and students will greatly benefit from this book.

The Nucleus

Author : Ronald Hancock
Publisher : Humana Press
ISBN 13 : 9781588299772
Total Pages : 360 pages
Book Rating : 4.2/5 (997 download)

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Book Synopsis The Nucleus by : Ronald Hancock

Download or read book The Nucleus written by Ronald Hancock and published by Humana Press. This book was released on 2008-08-28 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although our understanding of the structure and activities of the cell nucleus and of the nanomachines which it contains is increasing rapidly, much remains to be learned. The application and continuing development of the new, powerful biochemical and biophysical methodologies described here are essential in this quest. In The Nucleus, researchers from more than forty leading international laboratories describe state-of-the-art methods for isolating nuclei and their components and for studying their structure and activities, including some pathology-associated features. Volume I: Nuclei and Subnuclear Structures presents an overview of features of the intranuclear environment, followed by the most recent procedures for isolating nuclei from a wide range of cell types including muscle cells, yeast, oocytes, cells with polytene nuclei, Arabidopsis, trypanosomes, and dinoflagellates. The latest methods are described for isolating and working with nucleoli, constitutive heterochromatin, pathology-associated inclusions, and chromatin and for examining glycosylation, sumoylation, and ADP-ribosylation of nuclear proteins. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain lists of necessary materials and reagents, readily reproducible protocols, and tips for troubleshooting and avoiding known pitfalls. The Nucleus, Volume I: Nuclei and Subnuclear Structures is an essential reference for scientists who are working on our rapidly growing understanding of the cell nucleus and its activities.

Hi-C Data Analysis

Author : Silvio Bicciato
Publisher : Humana
ISBN 13 : 9781071613924
Total Pages : 0 pages
Book Rating : 4.6/5 (139 download)

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Book Synopsis Hi-C Data Analysis by : Silvio Bicciato

Download or read book Hi-C Data Analysis written by Silvio Bicciato and published by Humana. This book was released on 2022-09-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.

Introduction to Epigenetics

Author : Renato Paro
Publisher : Springer Nature
ISBN 13 : 3030686701
Total Pages : 215 pages
Book Rating : 4.0/5 (36 download)

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Book Synopsis Introduction to Epigenetics by : Renato Paro

Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease

Data-driven Mechanistic Modeling of 3D Human Genome

Author : Yifeng Qi (Scientist in chemistry)
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (134 download)

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Book Synopsis Data-driven Mechanistic Modeling of 3D Human Genome by : Yifeng Qi (Scientist in chemistry)

Download or read book Data-driven Mechanistic Modeling of 3D Human Genome written by Yifeng Qi (Scientist in chemistry) and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis is organized as follows. In the first chapter, we introduce a computational model to simulate chromatin structure and dynamics. The model defines chromatin states by taking one-dimensional genomics and epigenomics data as input and quantitatively learns interacting patterns between these states using experimental contact data. Once learned, the model is able to make de novo predictions of 3D chromatin structures at five-kilo-base resolution across different cell types. The manuscript associated with this study is published in PLoS Computational Biology, 15.6, e1007024 (2019).

Fluorescence In Situ Hybridization (FISH) - Application Guide

Author : Thomas Liehr
Publisher : Springer Science & Business Media
ISBN 13 : 3540705813
Total Pages : 447 pages
Book Rating : 4.5/5 (47 download)

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Book Synopsis Fluorescence In Situ Hybridization (FISH) - Application Guide by : Thomas Liehr

Download or read book Fluorescence In Situ Hybridization (FISH) - Application Guide written by Thomas Liehr and published by Springer Science & Business Media. This book was released on 2008-11-26 with total page 447 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a unique source of information on the present state of the exciting field of molecular cytogenetics and how it can be applied in research and diagnostics. The basic techniques of fluorescence in situ hybridization and primed in situ hybridization (PRINS) are outlined, the multiple approaches and probe sets that are now available for these techniques are described, and applications of them are presented in 36 chapters by authors from ten different countries around the world. The book not only provides the reader with basic and background knowledge on the topic, but also gives detailed protocols that show how molecular cytogenetics is currently performed by specialists in this field. The FISH Application Guide initially provides an overview of the (historical) development of molecular cytogenetics, its basic procedures, the equipment required, and probe generation. The book then describes tips and tricks for making different tissues available for molecular cytogenetic studies. These are followed by chapters on various multicolor FISH probe sets, their availability, and their pot- tial for use in combination with other approaches. The possible applications that are shown encompass the characterization of marker chromosomes, cryptic cytogenetic aberrations and epigenetic changes in humans by interphase and metaphase cyto- netics, studies of nuclear architecture, as well as the application of molecular cytogenetics to zoology, botany and microbiology.

Molecular Biology of The Cell

Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)

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Book Synopsis Molecular Biology of The Cell by : Bruce Alberts

Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

CELL GEOMETRY.

Author : G. V. SHIVASHANKAR
Publisher :
ISBN 13 : 9781138628564
Total Pages : pages
Book Rating : 4.6/5 (285 download)

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Book Synopsis CELL GEOMETRY. by : G. V. SHIVASHANKAR

Download or read book CELL GEOMETRY. written by G. V. SHIVASHANKAR and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Genomics with R

Author : Altuna Akalin
Publisher : CRC Press
ISBN 13 : 1498781861
Total Pages : 462 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Computational Genomics with R by : Altuna Akalin

Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

The Mouse Nervous System

Author : Charles Watson
Publisher : Academic Press
ISBN 13 : 0123694973
Total Pages : 815 pages
Book Rating : 4.1/5 (236 download)

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Book Synopsis The Mouse Nervous System by : Charles Watson

Download or read book The Mouse Nervous System written by Charles Watson and published by Academic Press. This book was released on 2011-11-28 with total page 815 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Mouse Nervous System provides a comprehensive account of the central nervous system of the mouse. The book is aimed at molecular biologists who need a book that introduces them to the anatomy of the mouse brain and spinal cord, but also takes them into the relevant details of development and organization of the area they have chosen to study. The Mouse Nervous System offers a wealth of new information for experienced anatomists who work on mice. The book serves as a valuable resource for researchers and graduate students in neuroscience. Systematic consideration of the anatomy and connections of all regions of the brain and spinal cord by the authors of the most cited rodent brain atlases A major section (12 chapters) on functional systems related to motor control, sensation, and behavioral and emotional states A detailed analysis of gene expression during development of the forebrain by Luis Puelles, the leading researcher in this area Full coverage of the role of gene expression during development and the new field of genetic neuroanatomy using site-specific recombinases Examples of the use of mouse models in the study of neurological illness

Chromosome Structure and Aberrations

Author : Tariq Ahmad Bhat
Publisher : Springer
ISBN 13 : 8132236734
Total Pages : 377 pages
Book Rating : 4.1/5 (322 download)

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Book Synopsis Chromosome Structure and Aberrations by : Tariq Ahmad Bhat

Download or read book Chromosome Structure and Aberrations written by Tariq Ahmad Bhat and published by Springer. This book was released on 2017-02-08 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a compilation of various chapters contributed by a group of leading researchers from different countries and covering up to date information based on published reports and personal experience of authors in the field of cytogenetics. Beginning with the introduction of chromosome, the subsequent chapters on organization of genetic material, karyotype evolution, structural and numerical variations in chromosomes, B-chromosomes and chromosomal aberrations provide an in-depth knowledge and easy understanding of the subject matter. A special feature of the book is the inclusion of a series of chapters on various types of chromosomal aberrations and their impact on breeding behaviour and crop improvement. The possible mechanism, their consequences and role in genetic analysis has been emphasized in these chapters. A few chapters have also been dedicated on various techniques routinely used in the laboratory by students and researchers. Each chapter ends with an extensive bibliography so that the students and researchers may find it relevant to consult more literature on the subject than a book of this size can offer. The book is intended to fulfill the needs of undergraduate and post graduate students of botany, zoology and agriculture besides, teachers and researchers engaged in the field of genetics, cytogenetics, and molecular genetics. In general the readers will find each chapter of the book informative and easy to understand.

Recent Advances in Learning and Control

Author : Vincent D. Blondel
Publisher : Springer Science & Business Media
ISBN 13 : 1848001541
Total Pages : 283 pages
Book Rating : 4.8/5 (48 download)

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Book Synopsis Recent Advances in Learning and Control by : Vincent D. Blondel

Download or read book Recent Advances in Learning and Control written by Vincent D. Blondel and published by Springer Science & Business Media. This book was released on 2008-01-11 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is composed of invited papers on learning and control. The contents form the proceedings of a workshop held in January 2008, in Hyderabad that honored the 60th birthday of Doctor Mathukumalli Vidyasagar. The 14 papers, written by international specialists in the field, cover a variety of interests within the broader field of learning and control. The diversity of the research provides a comprehensive overview of a field of great interest to control and system theorists.