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Modeling Transcriptional Regulation
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Book Synopsis Modeling Transcriptional Regulation by : SHAHID MUKHTAR
Download or read book Modeling Transcriptional Regulation written by SHAHID MUKHTAR and published by Humana. This book was released on 2021-07-13 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides methods and techniques used in construction of global transcriptional regulatory networks in diverse systems, various layers of gene regulation and mathematical as well as computational modeling of transcriptional gene regulation. 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, Modeling Transcriptional Regulation: Methods and Protocols aims to provide an in depth understanding of new techniques in transcriptional gene regulation for specialized audience.
Book Synopsis Modeling Transcriptional Regulation by : Shahid M. Mukhtar
Download or read book Modeling Transcriptional Regulation written by Shahid M. Mukhtar and published by . This book was released on 2021 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides methods and techniques used in construction of global transcriptional regulatory networks in diverse systems, various layers of gene regulation and mathematical as well as computational modeling of transcriptional gene regulation. 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, Modeling Transcriptional Regulation: Methods and Protocols aims to provide an in depth understanding of new techniques in transcriptional gene regulation for specialized audience.
Book Synopsis Computational Modeling of Gene Regulatory Networks by : Hamid Bolouri
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.
Book Synopsis Theoretical and Applied Aspects of Systems Biology by : Fabricio Alves Barbosa da Silva
Download or read book Theoretical and Applied Aspects of Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer. This book was released on 2018-06-21 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.
Book Synopsis Transcription Factor Regulatory Networks by : Etsuko Miyamoto-Sato
Download or read book Transcription Factor Regulatory Networks written by Etsuko Miyamoto-Sato and published by Humana Press. This book was released on 2014-06-14 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription Factor Regulatory Methods details various techniques ranging from cutting-edge to general techniques use to study transcription factor regulatory networks. 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 practical, Transcription Factor Regulatory Methods aids scientists in the further study into post-genomic or the personal genomic era.
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.
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:
Book Synopsis Integrative Modeling for Genome-wide Regulation of Gene Expression by : Zhengqing Ouyang
Download or read book Integrative Modeling for Genome-wide Regulation of Gene Expression written by Zhengqing Ouyang and published by Stanford University. This book was released on 2010 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput genomics has been increasingly generating the massive amount of genome-wide data. With proper modeling methodologies, we can expect to archive a more comprehensive understanding of the regulatory mechanisms of biological systems. This work presents integrative approaches for the modeling and analysis of gene regulatory systems. In mammals, gene expression regulation is combinatorial in nature, with diverse roles of regulators on target genes. Microarrays (such as Exon Arrays) and RNA-Seq can be used to quantify the whole spectrum of RNA transcripts. ChIP-Seq is being used for the identification of transcription factor (TF) binding sites and histone modification marks. RNA interference (RNAi), coupled with gene expression profiles, allow perturbations of gene regulatory systems. Our approaches extract useful information from those genome-wide measurements for effectively modeling the logic of gene expression regulation. We present a predictive model for the prediction of gene expression from ChIP-Seq signals, based on quantitative modeling of regulator-gene association strength, principal component analysis, and regression-based model selection. We demonstrate the combinatorial regulation of TFs, and their power for explaining genome-wide gene expression variation. We also illustrate the roles of covalent histone modification marks on predicting gene expression and their regulation by TFs. We present a dynamical model of gene expression profiling, and derive the perturbed behaviors of the ordinary differential equation (ODE) system. Based on that, we present a regularized multivariate regression method for inferring the gene regulatory network of a stable cell type. We model the sparsity and stability of the network by a regularization approach. We applied the approaches to both a simulation data set and the RNAi perturbation data in mouse embryonic stem cells.
Book Synopsis Systems Biology of Transcription Regulation by : Ekaterina Shelest
Download or read book Systems Biology of Transcription Regulation written by Ekaterina Shelest and published by Frontiers Media SA. This book was released on 2016-09-09 with total page 191 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches. Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks. Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic.
Book Synopsis Probabilistic Boolean Networks by : Ilya Shmulevich
Download or read book Probabilistic Boolean Networks written by Ilya Shmulevich and published by SIAM. This book was released on 2010-01-01 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Gene Regulatory Networks by : Guido Sanguinetti
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.
Book Synopsis Genomic Control Process by : Isabelle Peter
Download or read book Genomic Control Process written by Isabelle Peter and published by Academic Press. This book was released on 2015-01-21 with total page 460 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 Complex Networks written by Eli Ben-Naim and published by Springer Science & Business Media. This book was released on 2004-09-01 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is devoted to the applications of techniques from statistical physics to the characterization and modeling of complex networks. The first two parts of the book concern theory and modeling of networks, the last two parts survey applications to a wide variety of natural and artificial networks. The tutorial reviews that form this book are aimed at students and newcomers to the field, and will also constitute a modern and comprehensive reference for experts. To this aim, all contributions have been carefully peer-reviewed not only for scientific content but also for self-consistency and readability.
Download or read book Models of Life written by Kim Sneppen and published by Cambridge University Press. This book was released on 2014-10-02 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of current models of biological systems, reflecting the major advances that have been made over the past decade.
Book Synopsis Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays by : Mehmet Eren Ahsen
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 94 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.
Book Synopsis Gene Network Inference by : Alberto Fuente
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 130 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.
Book Synopsis Transcriptomics and Gene Regulation by : Jiaqian Wu
Download or read book Transcriptomics and Gene Regulation written by Jiaqian Wu and published by Springer. This book was released on 2015-11-17 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on modern computational and statistical tools for translational gene expression and regulation research to improve prognosis, diagnostics, prediction of severity, and therapies for human diseases. It introduces some of state of the art technologies as well as computational and statistical tools for translational bioinformatics in the areas of gene transcription and regulation, including the tools for next generation sequencing analyses, alternative spicing, the modeling of signaling pathways, network analyses in predicting disease genes, as well as protein and gene expression data integration in complex human diseases etc. The book is particularly useful for researchers and students in the field of molecular biology, clinical biology and bioinformatics, as well as physicians etc. Dr. Jiaqian Wu is assistant professor in the Vivian L. Smith Department of Neurosurgery and Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Centre, Houston, TX, USA.
