Investigating Complexity In Transcriptome Expression Regulation And Evolution Using Mathematical Modeling
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Investigating Complexity In Transcriptome Expression Regulation And Evolution Using Mathematical Modeling
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Author : Nicholas Louis Panchy
language : en
Publisher:
Release Date : 2017
Investigating Complexity In Transcriptome Expression Regulation And Evolution Using Mathematical Modeling written by Nicholas Louis Panchy and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with Electronic dissertations categories.
Mathematical Models And Algorithms For Genetic Regulatory Networks
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Author : Shuqin Zhang
language : en
Publisher: Open Dissertation Press
Release Date : 2017-01-27
Mathematical Models And Algorithms For Genetic Regulatory Networks written by Shuqin Zhang and has been published by Open Dissertation Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-01-27 with categories.
This dissertation, "Mathematical Models and Algorithms for Genetic Regulatory Networks" by Shuqin, Zhang, 張淑芹, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled MATHEMATICAL MODELS AND ALGORITHMS FOR GENETIC REGULATORY NETWORKS submitted by ZHANG Shu-Qin for the degree of Doctor of Philosophy at The University of Hong Kong in August 2007 Genetic regulatory network is an important research topic in bioinformat- ics, which considers the on-o(R) switches and rheostats of a cell operating at the gene level. Mathematical modeling and computation are indispensable in such studies, especially for the complex patterns of behavior which needs high indus- trialpayo(R)sandisdiculttogettheinformationthroughexperimentalmethods. Booleannetworks(BNs)andprobabilisticBooleannetworks(PBNs)areproposed to model the interactions among the genes and have received much attention in the biophysics community. The study in this thesis is based on the BN and PBN models. With the BN model, several algorithms using gene ordering and feedback vertex sets are devel- opedtoidentifysingletonattractorsandsmallattractorswhichcorrespondtocell types and cell states. The average case time complexities of some proposed al- gorithms are analyzed. Extensive computational experiments are also performed which are in good agreement with the theoretical results. A simple and complete proofforshowingthatndinganattractorwiththeshortestperiodisNP-hardis given. Finding global states incoming to a specied global state is useful for the preprocessingofndingasequenceofcontrolactionsinBooleannetworksandfor identifying the basin of attraction for a given attractor. This problem is shown to be NP-hard in general. New algorithms based on the algorithms for ndingsmall attractors are developed, which are much faster than the naive exhaustive search-based algorithm. Based on the PBN model, an ecient method for the construction of the sparse transition probability matrix is proposed. Power method is then applied to compute the steady-state probability distribution. With this method, the sensitivity of the steady-state distribution to the inuences of input genes, gene connections and Boolean functions is studied. Simulation results are given to illustrate the method and to demonstrate the steady-state analysis. An approxi- mation method is proposed to further reduce the time complexity for computing the steady-state probability distribution by neglecting some BNs with very small probabilities during the construction of the transition probability matrix. An error analysis of this approximation method is givenand theoretical result on the distribution of BNs in a PBN with at most two Boolean functions for one gene is also presented. Numerical experiments are given to demonstrate the eciency of the proposed method. The ultimate goal of studying the long-term behavior of the genetic regula- tory network is to study the control strategies such that the system can go into the desirable states with larger probabilities. A control model is also proposed for gene intervention here. The problem is formulated as a minimization prob- lem with integer variables to minimize the amount of control cost for a genetic network over a given period of time such that the probabilities of obtaining the target states are as large as possible. Experimental results show that the pro- posed formulation is ecient and e(R)ective for solving the control problem of gene intervention. DOI: 10.5353/th_b3884282 Subjects: Genetics - Mathematical models Algorithms Bioinformatics
Inference Of Gene Regulation From Expression Data
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Author : Angela Grassi
language : en
Publisher:
Release Date : 2011
Inference Of Gene Regulation From Expression Data written by Angela Grassi and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Plant Single Cell Type Systems Biology
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Author : Marc Libault
language : en
Publisher: Frontiers Media SA
Release Date : 2016-09-06
Plant Single Cell Type Systems Biology written by Marc Libault and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-09-06 with Botany categories.
The phenotype of a plant in response to a stress condition is the reflection of the molecular responses in different cell-types composing the plant. The multicellular complexity represents a challenge when accessing specific responses of each cell or cell type composing the plant. To overcome this difficulty and allow the clear characterization of the plant cell molecular mechanisms, the research community is now focusing on studying a single cell and single cell-types. The isolation of plant single cells is limited by the cell wall that confers the rigidity of the plant and its overall structure. Various methods have been developed for isolating plant cells (e.g. laser capture microdissection; cell sorting of Green Fluorescent Protein (GFP)-tagged protoplasts, differential protoplastization of cells such as guard cells, isolation of easily accessible cell types such as cotton fiber, pollen cells, trichomes and root hair cells). The development of these innovative approaches to isolate single plant cells or cell-types combined with the application of sensitive and high-throughput technologies allows a better analysis of the developmental processes and response to environmental stresses. Ultimately, single plant cell and cell-type biology will lead to establishment of more reliable and accurate -molecular regulatory networks at the resolution of basic life unit. The goal of this Research Topic is to cover new technological and biological advances in the study of plant single cell, cell-type and systems biology.
Metabiology
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Author : Arturo Carsetti
language : en
Publisher: Springer Nature
Release Date : 2019-11-07
Metabiology written by Arturo Carsetti and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-11-07 with Technology & Engineering categories.
In the context of life sciences, we are constantly confronted with information that possesses precise semantic values and appears essentially immersed in a specific evolutionary trend. In such a framework, Nature appears, in Monod’s words, as a tinkerer characterized by the presence of precise principles of self-organization. However, while Monod was obliged to incorporate his brilliant intuitions into the framework of first-order cybernetics and a theory of information with an exclusively syntactic character such as that defined by Shannon, research advances in recent decades have led not only to the definition of a second-order cybernetics but also to an exploration of the boundaries of semantic information. As H. Atlan states, on a biological level "the function self-organizes together with its meaning". Hence the need to refer to a conceptual theory of complexity and to a theory of self-organization characterized in an intentional sense. There is also a need to introduce, at the genetic level, a distinction between coder and ruler as well as the opportunity to define a real software space for natural evolution. The recourse to non-standard model theory, the opening to a new general semantics, and the innovative definition of the relationship between coder and ruler can be considered, today, among the most powerful theoretical tools at our disposal in order to correctly define the contours of that new conceptual revolution increasingly referred to as metabiology. This book focuses on identifying and investigating the role played by these particular theoretical tools in the development of this new scientific paradigm. Nature "speaks" by means of mathematical forms: we can observe these forms, but they are, at the same time, inside us as they populate our organs of cognition. In this context, the volume highlights how metabiology appears primarily to refer to the growth itself of our instruments of participatory knowledge of the world.
Gene Quantification
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Author : Francois Ferre
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
Gene Quantification written by Francois Ferre 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 2012-12-06 with Medical categories.
Geneticists and molecular biologists have been interested in quantifying genes and their products for many years and for various reasons (Bishop, 1974). Early molecular methods were based on molecular hybridization, and were devised shortly after Marmur and Doty (1961) first showed that denaturation of the double helix could be reversed - that the process of molecular reassociation was exquisitely sequence dependent. Gillespie and Spiegelman (1965) developed a way of using the method to titrate the number of copies of a probe within a target sequence in which the target sequence was fixed to a membrane support prior to hybridization with the probe - typically a RNA. Thus, this was a precursor to many of the methods still in use, and indeed under development, today. Early examples of the application of these methods included the measurement of the copy numbers in gene families such as the ribosomal genes and the immunoglo bulin family. Amplification of genes in tumors and in response to drug treatment was discovered by this method. In the same period, methods were invented for estimating gene num bers based on the kinetics of the reassociation process - the so-called Cot analysis. This method, which exploits the dependence of the rate of reassociation on the concentration of the two strands, revealed the presence of repeated sequences in the DNA of higher eukaryotes (Britten and Kohne, 1968). An adaptation to RNA, Rot analysis (Melli and Bishop, 1969), was used to measure the abundance of RNAs in a mixed population.
Glucocorticoid Signaling
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Author : Jen-Chywan Wang
language : en
Publisher: Springer
Release Date : 2015-07-27
Glucocorticoid Signaling written by Jen-Chywan Wang and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07-27 with Science categories.
This timely volume provides a comprehensive overview of glucocorticoids and their role in regulating many aspects of physiology and their use in the treatment of disease. The book is broken into four sections that begin by giving a general introduction to glucocorticoids and a brief history of the field. The second section will discuss the effects of glucocorticoids on metabolism, while the third section will cover the effects of glucocorticoids on key tissues. The final section will discuss general topics, such as animal models in glucocorticoid research and clinical implications of glucocorticoid research. Featuring chapters from leaders in the field, this volume will be of interest to both researchers and clinicians.
Machine Learning And Mathematical Models For Single Cell Data Analysis
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Author : Le Ou-Yang
language : en
Publisher: Frontiers Media SA
Release Date : 2022-11-29
Machine Learning And Mathematical Models For Single Cell Data Analysis written by Le Ou-Yang and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-29 with Science categories.
Genomic And Epigenomic Biomarkers Of Toxicology And Disease
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Author : Saura C. Sahu
language : en
Publisher: John Wiley & Sons
Release Date : 2022-04-21
Genomic And Epigenomic Biomarkers Of Toxicology And Disease written by Saura C. Sahu and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-04-21 with Science categories.
Genomic and Epigenomic Biomarkers of Toxicology and Disease The latest developments in biomarker research applicable to toxicology and medicine Research on genomic and epigenomic biomarkers is developing rapidly with cutting-edge studies scattered throughout the academic literature, making the status of ongoing scientific activity in this area difficult to ascertain. Genomic and Epigenomic Biomarkers of Toxicology and Disease: Clinical and Therapeutic Actions delivers a comprehensive and authoritative compilation of up-to-date developments in the application of genomic and epigenomic biomarkers to toxicology, disease prevention, cancer detection, therapeutics, gene therapy, and other areas. With contributions from a collection of internationally recognized investigators, this edited volume offers unique insights into current trends and future directions of research in the discussed areas. Combining state-of-the-art information on genomic and epigenomic biomarkers from a range of specialists from around the world, this monograph includes: A thorough introduction to microRNAs as non-invasive biomarkers of toxicity and chemical hazard Comprehensive explorations of extracellular vesicle-associated miRNAs as toxic biomarkers, as well as transcriptomic applications in toxicology and medicine Practical discussions of circulating miRNAs as biomarkers of metal exposure, as well as microRNAs biomarkers of malignant mesothelioma In-depth examinations of the role of noncoding RNAs in innate immune responses perturbed by environmental arsenic with a focus on microRNAs Perfect for researchers, toxicologists, risk assessors, and regulators, Genomic and Epigenomic Biomarkers of Toxicology and Disease: Clinical and Therapeutic Actions will also earn a place in the libraries of graduate students with an interest in biomarkers, toxicology, agriculture, or the environment.
Multi Omics Strategies To Analyze Complex Agronomic Traits In Plants
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Author : Lin Chen
language : en
Publisher: Frontiers Media SA
Release Date : 2023-11-01
Multi Omics Strategies To Analyze Complex Agronomic Traits In Plants written by Lin Chen and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-11-01 with Science categories.