Gene Network Inference
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Gene Network Inference
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Author : Alberto Fuente
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-01-03
Gene Network Inference written by Alberto Fuente 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 2014-01-03 with Science categories.
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.
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.
Computational Modeling Of Gene Regulatory Networks
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Author : Hamid Bolouri
language : en
Publisher: Imperial College Press
Release Date : 2008
Computational Modeling Of Gene Regulatory Networks written by Hamid Bolouri and has been published by Imperial College Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Medical categories.
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.
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.
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.
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.
Unsupervised Gene Regulatory Network Inference On Microarray Data
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Author : Nidhi Radia
language : en
Publisher:
Release Date : 2015
Unsupervised Gene Regulatory Network Inference On Microarray Data written by Nidhi Radia and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
Obtaining gene regulatory networks (GRNs) from expression data is a challenging and crucial task. Many computational methods and algorithms have been developed to infer gene networks for gene expression data, which are usually obtained from microarray experiments. A gene network is a method to depict the relation among clusters of genes. To infer gene networks, the unsupervised method is used in this study. The two types of data used are time-series data and steady-state data. The data is analyzed using various tools containing different algorithms and concepts. GRNs from time-series data tools are obtained using the Time-delayed Algorithm for the Reconstruction of Accurate Cellular Networks (TD-ARACNe), the Bayesian Network Inference with Java Objects (BANJO), and causality. For steady-state data tools such as ARACNe, Gene Network Inference with Ensemble of trees (GENIE3), Context Likelihood or Relatedness Network (CLR), and Maximum Relevance Minimum Redundancy (MRNET) are used. The performance of time-series data as well as steady-state data based tool algorithms is compared by calculating their accuracy. The accuracy is calculated by comparing gene interactions between predicted and true networks. From the experimental studies it was found that the TD-ARACNe gives the highest accuracy on time-series gene expression data while for steady-state data, the ARACNe tool gives the highest accuracy. Overall, these analyses suggest that the suitability of the tools depends on the types of gene expression data available.
Computational Methods For Single Cell Data Analysis
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Author : Guo-Cheng Yuan
language : en
Publisher: Humana Press
Release Date : 2019-02-14
Computational Methods For Single Cell Data Analysis written by Guo-Cheng Yuan and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-02-14 with Science categories.
This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. 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, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.
Network Inference In Molecular Biology
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Author : Jesse M. Lingeman
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-05-24
Network Inference In Molecular Biology written by Jesse M. Lingeman 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 2012-05-24 with Computers categories.
Inferring gene regulatory networks is a difficult problem to solve due to the relative scarcity of data compared to the potential size of the networks. While researchers have developed techniques to find some of the underlying network structure, there is still no one-size-fits-all algorithm for every data set. Network Inference in Molecular Biology examines the current techniques used by researchers, and provides key insights into which algorithms best fit a collection of data. Through a series of in-depth examples, the book also outlines how to mix-and-match algorithms, in order to create one tailored to a specific data situation. Network Inference in Molecular Biology is intended for advanced-level students and researchers as a reference guide. Practitioners and professionals working in a related field will also find this book valuable.
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.