Reverse Engineering of Regulatory Networks

Reverse Engineering of Regulatory Networks PDF

Author: Sudip Mandal

Publisher: Springer Nature

Published: 2023-11-07

Total Pages: 331

ISBN-13: 1071634615

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This volume details the development of updated dry lab and wet lab based methods for the reconstruction of Gene regulatory networks (GRN). Chapters guide readers through culprit genes, in-silico drug discovery techniques, genome-wide ChIP-X data, high-Throughput Transcriptomic Data Exome Sequencing, Next-Generation Sequencing, Fuorescence Spectroscopy, data analysis in Bioinformatics, Computational Biology, and S-system based modeling of GRN. 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 cutting-edge, Reverse Engineering of Regulatory Networks aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

Gene Network Inference

Gene Network Inference PDF

Author: Alberto Fuente

Publisher: Springer Science & Business Media

Published: 2014-01-03

Total Pages: 135

ISBN-13: 3642451616

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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.

Reverse Engineering Biological Networks

Reverse Engineering Biological Networks PDF

Author: Gustavo Stolovitzky

Publisher: Wiley-Blackwell

Published: 2007-12-26

Total Pages: 308

ISBN-13:

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"This volume is the result of a workshop entitled Dialogue on Reverse Engineering Assessment and Methods (DREAM) held on September 7-8, 2006, at Wave Hill, New York"--P [vii].

Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays

Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays PDF

Author: Mehmet Eren Ahsen

Publisher: Birkhäuser

Published: 2015-02-25

Total Pages: 104

ISBN-13: 3319156063

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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.

Reverse Engineering

Reverse Engineering PDF

Author: A.C. Telea

Publisher: IntechOpen

Published: 2012-03-07

Total Pages: 294

ISBN-13: 9789535101581

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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.

Reverse Engineering of RNA Regulatory Networks

Reverse Engineering of RNA Regulatory Networks PDF

Author: David Nellinger Adamson

Publisher:

Published: 2013

Total Pages: 141

ISBN-13:

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Understanding gene regulation is of central importance to biology because controlling when, where, and how genes are expressed accounts for a large proportion of the complexity and organization of living systems. While for many years RNA was largely thought of as the middleman for converting genetic information into biochemically active proteins, it has become increasingly clear that RNAs are also major players gene regulation. This thesis examines the functional properties of regulatory RNAs in the context of bacterial RNA networks. More specifically, the three studies presented here examine signaling dynamics and crosstalk within the CsrA and Hfq-dependent small RNA regulatory systems; each of these systems (i) contain non-coding RNAs which regulate the translation of multiple target messenger RNAs, (ii) have central roles in coordinating their cells' adaptation to environmental change, and (iii) are evolutionarily conserved across a wide range of bacterial species. In this work, a combination of synthetic biology and mathematical modeling are brought to bear to uncover the operational behavior and potential of the these two model RNA networks.

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