Download or read book Gene Regulatory Networks written by Guido Sanguinetti and published by Humana. This book was released on 2018-12-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores recent techniques for the computational inference of gene regulatory networks (GRNs). The chapters in this book cover topics such as methods to infer GRNs from time-varying data; the extraction of causal information from biological data; GRN inference from multiple heterogeneous data sets; non-parametric and hybrid statistical methods; the joint inference of differential networks; and mechanistic models of gene regulation dynamics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, descriptions of recently developed methods for GRN inference, applications of these methods on real and/ or simulated biological data, and step-by-step tutorials on the usage of associated software tools. Cutting-edge and thorough, Gene Regulatory Networks: Methods and Protocols is an essential tool for evaluating the current research needed to further address the common challenges faced by specialists in this field.
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.
Download or read book Probabilistic Boolean Networks written by Ilya Shmulevich and published by SIAM. This book was released on 2010-01-21 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.
Download or read book Plant Gene Regulatory Networks written by Kerstin Kaufmann and published by Humana. This book was released on 2017-06-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents protocols that analyze and explore gene regulatory networks (GRNs) at different levels in plants. This book is divided into two parts: Part I introduces different experimental techniques used to study genes and their regulatory interactions in plants. Part II highlights different computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. This part of the book also provides information on essential database resources that grant access to gene-regulatory and molecular interactions in different plant genomes, with a specific focus on Arabidopsis thaliana. 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. Thorough and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols is a valuable resource for scientists and researchers interested in expanding their knowledge of GRNs.
Download or read book Gene Network Inference written by Alberto Fuente and published by Springer Science & Business Media. This book was released on 2014-01-03 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.
Download or read book Computational Modeling Of Gene Regulatory Networks A Primer written by Hamid Bolouri and published by World Scientific Publishing Company. This book was released on 2008-08-13 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./a
Download or read book Gene Regulatory Networks written by and published by Academic Press. This book was released on 2020-05-22 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene Regulatory Networks, Volume 139 in the Current Topics in Developmental Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors. Topics in this release include Mouse hindbrain GRN, Xenopus endoderm GRN – organogenesis, Vertebrate limb GRN, The notochord gene regulatory network in chordate evolution: conservation and divergence from Ciona to vertebrates, Ciona early embryo GRNs, Boolean logic models, Modeling GRN response to morphogen gradient, GRN architecture, Theory of GRN evolution, Evolution of fly segmentation GRNs, GRN evolution in echinoderms, Evolution of network specificity, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Current Topics in Developmental Biology series Includes the latest information on gene regulatory networks
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.
Download or read book The Regulatory Genome written by Eric H. Davidson and published by Elsevier. This book was released on 2010-07-19 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. - The only book in the market that is solely devoted to the genomic regulatory code for animal development - Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding - Presents a comprehensive treatment of molecular control elements that determine the function of genes - Provides a comparative treatment of development, based on principles rather than description of developmental processes - Considers the evolutionary processes in terms of the structural properties of gene regulatory networks - Includes 42 full-color descriptive figures and diagrams
Download or read book Ingenious Genes written by Roger Sansom and published by MIT Press. This book was released on 2011-09-30 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: A proposal for a new model of the evolution of gene regulation networks and development that draws on work from artificial intelligence and philosophy of mind. Each of us is a collection of more than ten trillion cells, busy performing tasks crucial to our continued existence. Gene regulation networks, consisting of a subset of genes called transcription factors, control cellular activity, producing the right gene activities for the many situations that the multiplicity of cells in our bodies face. Genes working together make up a truly ingenious system. In this book, Roger Sansom investigates how gene regulation works and how such a refined but simple system evolved. Sansom describes in detail two frameworks for understanding gene regulation. The first, developed by the theoretical biologist Stuart Kauffman, holds that gene regulation networks are fundamentally systems that repeat patterns of gene expression. Sansom finds Kauffman's framework an inadequate explanation for how cells overcome the difficulty of development. Sansom proposes an alternative: the connectionist framework. Drawing on work from artificial intelligence and philosophy of mind, he argues that the key lies in how multiple transcription factors combine to regulate a single gene, acting in a way that is qualitatively consistent. This allows the expression of genes to be finely tuned to the variable microenvironments of cells. Because of the nature of both development and its evolution, we can gain insight into the developmental process when we identify gene regulation networks as the controllers of development. The ingenuity of genes is explained by how gene regulation networks evolve to control development.
Download or read book Plant Gene Regulatory Networks written by Kerstin Kaufmann and published by Springer Nature. This book was released on with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Emerging Research in the Analysis and Modeling of Gene Regulatory Networks written by Ivanov, Ivan V. and published by IGI Global. This book was released on 2016-06-06 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Genomic Control Process written by Isabelle S. Peter and published by Academic Press. This book was released on 2015-01-21 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. - Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life - Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework - Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature - Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type - Demonstrates the causal power of system-level understanding of genomic control process - Conceptually organizes a constellation of complex and diverse biological phenomena - Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models - Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome
Download or read book Evolution of Gene Regulatory Networks in Plant Development written by Federico Valverde and published by Frontiers Media SA. This book was released on 2018-02-15 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.
Download or read book Plant Systems Biology written by Sacha Baginsky and published by Springer Science & Business Media. This book was released on 2007-06-25 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.
Download or read book Systems Immunology and Infection Microbiology written by Bor-Sen Chen and published by Academic Press. This book was released on 2021-03-16 with total page 673 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Immunology and Infection Microbiology provides a large amount of biological system models, diagrams and flowcharts to illustrate development procedures and help users understand the results of systems immunology and infection microbiology. Chapters discuss systems immunology, systems infection microbiology, systematic inflammation and immune responses in restoration and regeneration process, systems' innate and adaptive immunity in infection process, systematic genetic and epigenetic pathogenic/defensive mechanism during bacterial infection on human cells is introduced, and the systematic genetic and epigenetic pathogenic/defensive mechanisms during viral infection on human cells. This book provides new big data-driven and systems-driven systems immunology and infection microbiology to researchers applying systems biology and bioinformatics in their work. It is also invaluable to several members of biomedical field who are interested in learning more about those approaches. Encompasses one applicable example in every chapter to illustrate the solution procedure from big data mining, network modeling, host/pathogen cross-talk detection, drug target identification and systems drug design Presents flowcharts to represent the development procedure of systematic immunology and infection in a very clear format Contains 100 color diagrams to help readers understand the related biological networks, their corresponding mechanisms, and significant network biomarkers for therapeutic drug design
Download or read book Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays written by Mehmet Eren Ahsen and published by Birkhäuser. This book was released on 2015-02-25 with total page 104 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
