Relevant bibliographies by topics / Systems biology / Dissertations / Theses
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Dissertations / Theses on the topic 'Systems biology'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 July 2025

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1

Xia, Tian. "Network modeling in systems biology." [Ames, Iowa : Iowa State University], 2010. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3403845.

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2

Apgar, Joshua Farley. "Experiment design for systems biology." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/61217.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2009.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (p. 219-233).<br>Mechanism-based chemical kinetic models are increasingly being used to describe biological signaling. Such models serve to encapsulate current understanding of pathways and to enable insight into complex biological processes. Despite the growing interest in these models, a number of challenges frustrate the construction of high-quality models. First, the chemical reactions that control biochemical process
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3

de, Back Walter. "Multicellular Systems Biology of Development." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-209110.

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Embryonic development depends on the precise coordination of cell fate specification, patterning and morphogenesis. Although great strides have been made in the molecular understanding of each of these processes, how their interplay governs the formation of complex tissues remains poorly understood. New techniques for experimental manipulation and image quantification enable the study of development in unprecedented detail, resulting in new hypotheses on the interactions between known components. By expressing these hypotheses in terms of rules and equations, computational modeling and simulat
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4

Dhondalay, G. K. R. "Systems biology of breast cancer." Thesis, Nottingham Trent University, 2013. http://irep.ntu.ac.uk/id/eprint/316/.

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Breast cancer, with an alarming incidence rate throughout the globe, has attracted significant investigations to identify disease specific biomarkers. Among these, oestrogen receptor (ER) occupies a central role where overexpression is a prognostic indication for breast cancer. The cross-talk between the responsible contenders of ER-associated genes potentially play an important role in the disease aetiology. Investigation of such cross talk is the focus of this thesis. The development of high throughput technologies such as expression microarrays has paved the way for investigating thousands
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5

Veliz-Cuba, Alan A. "The Algebra of Systems Biology." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/28240.

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In order to understand biochemical networks we need to know not only how their parts work but also how they interact with each other. The goal of systems biology is to look at biological systems as a whole to understand how interactions of the parts can give rise to complex dynamics. In order to do this efficiently, new techniques have to be developed. This work shows how tools from mathematics are suitable to study problems in systems biology such as modeling, dynamics prediction, reverse engineering and many others. The advantage of using mathematical tools is that there is a large num
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Folch, Fortuny Abel. "Chemometric Approaches for Systems Biology." Doctoral thesis, Universitat Politècnica de València, 2017. http://hdl.handle.net/10251/77148.

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The present Ph.D. thesis is devoted to study, develop and apply approaches commonly used in chemometrics to the emerging field of systems biology. Existing procedures and new methods are applied to solve research and industrial questions in different multidisciplinary teams. The methodologies developed in this document will enrich the plethora of procedures employed within omic sciences to understand biological organisms and will improve processes in biotechnological industries integrating biological knowledge at different levels and exploiting the software packages derived from the thesis.
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7

Kirk, Paul. "Inferential stability in systems biology." Thesis, Imperial College London, 2011. http://hdl.handle.net/10044/1/6455.

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The modern biological sciences are fraught with statistical difficulties. Biomolecular stochasticity, experimental noise, and the “large p, small n” problem all contribute to the challenge of data analysis. Nevertheless, we routinely seek to draw robust, meaningful conclusions from observations. In this thesis, we explore methods for assessing the effects of data variability upon downstream inference, in an attempt to quantify and promote the stability of the inferences we make. We start with a review of existing methods for addressing this problem, focusing upon the bootstrap and similar meth
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8

Camacho, Diogo Mayo. "In silico cell biology and biochemistry: a systems biology approach." Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/27960.

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In the post-"omic" era the analysis of high-throughput data is regarded as one of the major challenges faced by researchers. One focus of this data analysis is uncovering biological network topologies and dynamics. It is believed that this kind of research will allow the development of new mathematical models of biological systems as well as aid in the improvement of already existing ones. The work that is presented in this dissertation addresses the problem of the analysis of highly complex data sets with the aim of developing a methodology that will enable the reconstruction of a biological
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9

Falin, Lee J. "Systems Uncertainty in Systems Biology & Gene Function Prediction." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/26634.

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The widespread use of high-throughput experimental assays designed to measure the entire complement of a cells genes or gene products has led to vast stores of data which are extremely plentiful in terms of the number of items they can measure in a single sample, yet often sparse in the number of samples per experiment due to their high cost. This often leads to datasets where the number of treatment levels or time points sampled is limited, or where there are very small numbers of technical and/or biological replicates. If the goal is to use this data to infer network models, these sparse dat
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10

Uluşeker, Cansu. "A Systems and Synthetic Biology Framework for Regulatory Systems." Doctoral thesis, University of Trento, 2018. http://eprints-phd.biblio.unitn.it/3207/1/Cansu_Ulu%C5%9Feker_PhD_Thesis.pdf.

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Biological regulatory systems are complex due to their role in living organisms in modulating precise responses to changes in internal and external conditions. In this respect, mathematical models have become essential tools to address their complexity for a better understanding of their mechanisms. The vision here, based on integrating experimental and theoretical techniques, provides a systematic means to quantitatively study the characteristics of the interactions that occur in living organisms. The outcome of such an endeavour should provide insights in terms of predictions and quantifica
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11

Milewicz, Hanna. "Systems biology analyses of hematopoietic cells." Thesis, King's College London (University of London), 2013. https://kclpure.kcl.ac.uk/portal/en/theses/systems-biology-analyses-of-hematopoietic-cells(c82f6f18-0de2-4d7c-876d-989f5e999957).html.

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The focus of my thesis is to apply systems biology approaches to obtain a better understanding of complex cellular systems. In particular, my work concentrates on the function of haematological cells. The first part of the thesis applies a novel, predictive strategy to identify new regulators of a signalling pathway in human immune cells. Cdc42 is a membrane associated GTPase that is an important regulator of cytoskeleton rearrangements and is required for natural killer (NK) cell activation. Previous work had shown that Cdc42 activity oscillates during NK immune surveillance after an initial
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12

Tang, Xiaoting. "New analytical tools for systems biology." Online access for everyone, 2006. http://www.dissertations.wsu.edu/Dissertations/Fall2006/x_tang_081706.pdf.

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13

Fange, David. "Modelling Approaches to Molecular Systems Biology." Doctoral thesis, Uppsala universitet, Molekylärbiologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-132864.

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Implementation and analysis of mathematical models can serve as a powerful tool in understanding how intracellular processes in bacteria affect the bacterial phenotype. In this thesis I have implemented and analysed models of a number of different parts of the bacterium E. coli in order to understand these types of connections. I have also developed new tools for analysis of stochastic reaction-diffusion models. Resistance mutations in the E. coli ribosomes make the bacteria less susceptible to treatment with the antibiotic drug erythromycin compared to bacteria carrying wildtype ribosomes. Th
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14

Miller, David J. Ghosh Avijit. "New methods in computational systems biology /." Philadelphia, Pa. : Drexel University, 2008. http://hdl.handle.net/1860/2810.

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15

Blakes, Jonathan. "Infobiotics : computer-aided synthetic systems biology." Thesis, University of Nottingham, 2013. http://eprints.nottingham.ac.uk/13434/.

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Until very recently Systems Biology has, despite its stated goals, been too reductive in terms of the models being constructed and the methods used have been, on the one hand, unsuited for large scale adoption or integration of knowledge across scales, and on the other hand, too fragmented. The thesis of this dissertation is that better computational languages and seamlessly integrated tools are required by systems and synthetic biologists to enable them to meet the significant challenges involved in understanding life as it is, and by designing, modelling and manufacturing novel organisms, to
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16

Johnston, Hannah Elizabeth. "Systems redox biology analysis of cancer." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31348.

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The Warburg effect describes the survival advantage of cancer cells in that they can proliferate under low oxygen/hypoxic conditions via a less efficient pathway known as glycolysis. It has not yet been documented at which point, in an oxygen gradient, phenotypic changes occur. Measuring the intracellular redox potential (IRP) and its impact on cellular dynamics would provide greater insight into how disruption of redox homeostasis caused by changes in oxygen concentration leads to aberrant cell signalling and diseases such as cancer. Current techniques in measuring IRP include redox-sensitive
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17

Abraham, Brian J. "Systems biology approaches to understanding hematopoiesis." Thesis, Boston University, 2013. https://hdl.handle.net/2144/12703.

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Thesis (Ph.D.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>Understanding gene expression and the regulation thereof that confer cell type-specific (CTS) functionality holds primary importance in devising therapeutics capable of emulating these functions, especially wit
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18

Nibbe, Rod K. "Systems Biology of Human Colorectal Cancer." Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1264179836.

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19

Hudson, Corey M. "Informatic approaches to evolutionary systems biology." Thesis, University of Missouri - Columbia, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3577951.

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<p> The sheer complexity of evolutionary systems biology requires us to develop more sophisticated tools for analysis, as well as more probing and biologically relevant representations of the data. My research has focused on three aspects of evolutionary systems biology. I ask whether a gene&rsquo;s position in the human metabolic network affects the degree to which natural selection prunes variation in that gene. Using a novel orthology inference tool that uses both sequence similarity and gene synteny, I inferred orthologous groups of genes for the full genomes of 8 mammals. With these ortho
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20

Lopes, Tiago Jose da Silva. "Systems biology analysis of iron metabolism." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2011. http://dx.doi.org/10.18452/16417.

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Jede Zelle des Säugetierorganismus benötigt Eisen als Spurenelement für zahlreiche oxidativ-reduktive Elektronentransfer-Reaktionen und für Transport und Speicherung von Sauerstoff. Der Organismus unterhält daher ein komplexes Regulationsnetzwerk für die Aufnahme, Verteilung und Ausscheidung von Eisen. Die intrazelluläre Regulation in den verschiedenen Zelltypen des Körpers ist mit einer globalen hormonellen Signalstruktur verzahnt. Sowohl Eisenmangel wie Eisenüberschuss sind häufige und ernste menschliche Krankheitsbilder. Sie betreffen jede Zelle, aber auch den Organismus als Ganzes. In die
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21

Simoni, Giulia. "Modeling Startegies for Computational Systems Biology." Doctoral thesis, Università degli studi di Trento, 2020. http://hdl.handle.net/11572/254361.

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Mathematical models and their associated computer simulations are nowadays widely used in several research fields, such as natural sciences, engineering, as well as social sciences. In the context of systems biology, they provide a rigorous way to investigate how complex regulatory pathways are connected and how the disruption of these processes may contribute to the develop- ment of a disease, ultimately investigating the suitability of specific molecules as novel therapeutic targets. In the last decade, the launching of the precision medicine initiative has motivated the necessity to define
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Simoni, Giulia. "Modeling Startegies for Computational Systems Biology." Doctoral thesis, Università degli studi di Trento, 2020. http://hdl.handle.net/11572/254361.

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Mathematical models and their associated computer simulations are nowadays widely used in several research fields, such as natural sciences, engineering, as well as social sciences. In the context of systems biology, they provide a rigorous way to investigate how complex regulatory pathways are connected and how the disruption of these processes may contribute to the develop- ment of a disease, ultimately investigating the suitability of specific molecules as novel therapeutic targets. In the last decade, the launching of the precision medicine initiative has motivated the necessity to define
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23

FAILLI, MARIO. "SYSMET: SYSTEMS BIOLOGY OF MEMBRANE TRAFFICKING." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/562661.

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Studies on membrane trafficking have expanded massively over the last 40 years. During this time, research has led to an understanding of the molecular mechanisms underlying membrane trafficking pathways, providing crucial insights into several fundamental events. Although we have gained detailed knowledge about the molecular organization of membrane trafficking machineries there is a lack of a global view of its function, organization and regulation. In addition, many genes of the membrane trafficking machinery have been associated with diseases. In the majority of cases, disease manifestatio
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Aderhold, Andrej. "Machine learning in systems biology at different scales : from molecular biology to ecology." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/7030.

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Machine learning has been a source for continuous methodological advances in the field of computational learning from data. Systems biology has profited in various ways from machine learning techniques but in particular from network inference, i.e. the learning of interactions given observed quantities of the involved components or data that stem from interventional experiments. Originally this domain of system biology was confined to the inference of gene regulation networks but recently expanded to other levels of organization of biological and ecological systems. Especially the application
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Avva, Jayant. "Complex Systems Biology of Mammalian Cell Cycle Signaling in Cancer." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1295625781.

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26

Armitage, Emily Grace. "Systems biology of HIF metabolism in cancer." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/systems-biology-of-hif-metabolism-in-cancer(e237aa18-81a9-4c86-81b1-804555d3585c).html.

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Cancer is one of the most devastating human diseases that cause a vast number of mortalities worldwide each year. Cancer research is one of the largest fields in the life sciences and despite many astounding breakthroughs and contributions over the past few decades, there is still a considerable amount to unveil on the function of cancer that would improve diagnostics, prognostics and therapy. Since cancer is known to involve a wide range of processes, applying methods to study it from a systems perspective could reveal new properties of cancer. Systems biology is becoming an increasingly popu
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Kotze, Helen. "Systems biology of chemotherapy in hypoxia environments." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/systems-biology-of-chemotherapy-in-hypoxia-environments(4f0c4ff1-d90f-49a3-8190-94ec6ec106fa).html.

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Introduction: Hypoxia is found in solid cancerous tumours. The presence of hypoxia within tumours inhibits anti-cancer treatment strategies such as chemotherapy from being completely effective and it is suspected that multiple mechanisms contribute to the resistance. Methods: In this project a systems biology approach was applied to determine how the toxicity of doxorubicin is affected by hypoxia at the metabolome level. A multitude of analytical techniques were applied to analyse the intracellular metabolism of a monolayer of cancer cells (MDA-MB-231). Metabolic profiling was used to determin
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Tapinos, Avraam. "Time series data mining in systems biology." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/time-series-data-mining-in-systems-biology(5b538723-503b-4b82-959b-d4567e8d4658).html.

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Analysis of time series data constitutes an important activity in many scientific disciplines. Over the last years there has been an increase in the collection of time series data in all scientific fields and disciplines, such as the industry and engineering. Due to the increasing size of the time series datasets, new automated time series data mining techniques have been devised for comparing time series data and present information in a logical and easily comprehensible structure.In systems biology in particular, time series are used to the study biological systems. The time series represent
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Wright, Muelas Marina. "A systems biology approach to cancer metabolism." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/a-systems-biology-approach-to-cancer-metabolism(27286c8a-0281-4256-b749-2ec9bd36370f).html.

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Cancer cells have been known for some time to have very different metabolismas compared to that of normal non proliferating cells. As metabolism is involvedin almost every aspect of cell function, there has been a recent resurgence ofinterest in inhibiting cancer metabolism as a therapeutic strategy. Inhibitors thatspecifically target altered metabolic components in cancer cells are being developedas antiproliferative agents. However, many such inhibitors have not progressedinto the clinic due to limited efficacy either in vitro or in vivo. In this study weexplore the hypothesis that this is o
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Soul, Jamie. "A systems biology approach to knee osteoarthritis." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/a-systems-biology-approach-to-knee-osteoarthritis(0b229b46-7be4-4fdb-9a14-062c3dcfcf05).html.

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A hallmark of the joint disease osteoarthritis (OA) is the degradation of the articular cartilage in the affected joint, debilitating pain and decreased mobility. At present there are no disease modifying drugs for treatment of osteoarthritis. This represents a significant, unmet medical need as there is a large and increasing prevalence of OA. Using a systems biology approach, we aimed to better understand the pathogenic mechanisms of OA and ultimately aid development of therapeutics. This thesis focuses on the analysis of gene expression data from human OA cartilage obtained at total knee re
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Höghäll, Anton. "Tuning of Metaheuristics for Systems Biology Applications." Thesis, Linköping University, Department of Electrical Engineering, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-58842.

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<p>In the field of systems biology the task of finding optimal model parameters is a common procedure. The optimization problems encountered are often multi-modal, i.e., with several local optima. In this thesis, a class of algorithms for multi-modal problems called metaheuristics are studied. A downside of metaheuristic algorithms is that they are dependent on algorithm settings in order to yield ideal performance.This thesis studies an approach to tune these algorithm settings using user constructed test functions which are faster to evaluate than an actual biological model. A statistical pr
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Vyshemirsky, Vladislav. "Probabilistic reasoning and inference for systems biology." Thesis, Connect to e-thesis. Move to record for print version, 2007. http://theses.gla.ac.uk/47/.

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Thesis (Ph.D.) - University of Glasgow, 2007.<br>Ph.D. thesis submitted to the Information and Mathematical Sciences Faculty, Department of Computing Science, University of Glasgow, 2007. Includes bibliographical references. Print version also available.
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33

Pedersen, Michael. "Modular languages for systems and synthetic biology." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4602.

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Systems biology is a rapidly growing field which seeks a refined quantitative understanding of organisms, particularly studying how molecular species such as metabolites, proteins and genes interact in cells to form the complex emerging behaviour exhibited by living systems. Synthetic biology is a related and emerging field which seeks to engineer new organisms for practical purposes. Both fields can benefit from formal languages for modelling, simulation and analysis. In systems biology there is however a trade-off in the landscape of existing formal languages: some are modular but may be dif
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Koo, Andrew Jia-An. "Systems biology of endothelial mechano-activated pathways." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/80253.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, February 2013<br>"December 2012." Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Multiple signaling pathways are employed by endothelial cells to differentially respond to distinct hemodynamic environments and acquire functional phenotypes, including regulation of inflammation, angiogenesis, blood coagulation, and the vascular tone. In order to understand how these pathways interact, this thesis applies a systems biology approach through a two-step process. First, we const
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Saidi, Samir Arif. "A systems biology approach to endometrial carcinoma." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612981.

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Acharya, Lipi Rani. "Multivariate Models and Algorithms for Systems Biology." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/1364.

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Rapid advances in high-throughput data acquisition technologies, such as microarraysand next-generation sequencing, have enabled the scientists to interrogate the expression levels of tens of thousands of genes simultaneously. However, challenges remain in developingeffective computational methods for analyzing data generated from such platforms. In thisdissertation, we address some of these challenges. We divide our work into two parts. Inthe first part, we present a suite of multivariate approaches for a reliable discovery of geneclusters, often interpreted as pathway components, from molecu
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Portela, Rui Miguel Correia. "Hybrid systems biology: application to Escherichia coli." Master's thesis, Faculdade de Ciências e Tecnologia, 2011. http://hdl.handle.net/10362/6143.

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Dissertation presented to obtain a Master degree in Biotechnology<br>In complex biological systems, it is unlikely that all relevant cellular functions can be fully described either by a mechanistic (parametric) or by a statistic (nonparametric) modelling approach. Quite often, hybrid semiparametric models are the most appropriate to handle such problems. Hybrid semiparametric systems make simultaneous use of the parametric and nonparametric systems analysis paradigms to solve complex problems. The main advantage of the semiparametric over the parametric or nonparametric frameworks lies in tha
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Liu, Xin. "Probabilistic inference in models of systems biology." Thesis, University of Southampton, 2014. https://eprints.soton.ac.uk/374334/.

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In Systems Biology, it is usual to use a set of ordinary differential equations to characterize biological function at a system level. The parameters in these equations generally reflect the reaction or decay rates of a molecular species, while states characterize the concentration values of species of interest, e.g. mRNA, proteins and metabolites. Often parameter values are estimated from in vitro experiments which may not be true reflections of the in vivo environments. With internal states, some may not be accessible for experimental measurement. Hence there is interest in estimating parame
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Bosque, Chacón Gabriel. "Network Analysis and Modeling in Systems Biology." Doctoral thesis, Universitat Politècnica de València, 2017. http://hdl.handle.net/10251/79082.

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This thesis is dedicated to the study and comprehension of biological networks at the molecular level. The objectives were to analyse their topology, integrate it in a genotype-phenotype analysis, develop richer mathematical descriptions for them, study their community structure and compare different methodologies for estimating their internal fluxes. The work presented in this document moves around three main axes. The first one is the biological. Which organisms were studied in this thesis? They range from the simplest biological agents, the viruses, in this case the Potyvirus genus to prok
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Forth, Thomas. "Metabolic systems biology of the malaria parasite." Thesis, University of Leeds, 2012. http://etheses.whiterose.ac.uk/3739/.

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Quantitative one-dimensional proton NMR metabolomics is performed on growth medium samples gathered at up to ten time-points during the in vitro culture of P. falciparum in human red blood cells. From this study, exchange fluxes between the parasite-host complex and the growth medium are calculated for glucose, lactate, glycerol, glutamine, hypoxanthine, valine, leucine, isoleucine, alanine, tyrosine and phenylanaine. Carbon-source exchange fluxes are added as constraints to a new model of malaria metabolism — built using my published MetNetMaker software — consisting of 249 reactions, 143 gen
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Mizeranschi, Alexandru E. "Multiscale modelling and simulation in systems biology." Thesis, Ulster University, 2016. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737992.

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The focus of this thesis was determined by the FP7-funded e-infrastructure project Multiscale Applications on European e-Infrastructures (MAPPER). The main goal of MAPPER was to develop a distributed multiscale computing frame­work facilitating the development, deployment and use of multiscale modelling and simulation applications in various domains. MAPPER was strongly in­volved with the computing aspects of multiscale modelling and simulation. Within the MAPPER project, the research described in this thesis was focused on the development of novel (a) general multiscale modelling and simulati
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mattei, gianluca. "Tumor Microenvironment: Bioinformatics and Systems Biology Approaches." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1070301.

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Cancers develop in complex microenvironments whose importance was emerging during last years. In fact, cancer microenvironment influences tumor progression and leads to the raising of chemotherapics resistance. Thus, a shift of the focus from cancer cells to cancer cells in their environment is crucial for studying the molecular and metabolic features of tumors in physiological contexts. Within the microenvironment, cancer associated fibroblasts (CAF) are attracting the attention of scientific community since, up to date, it is clear that they are the main component involved in the organizatio
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BARDINI, ROBERTA. "A diversity-aware computational framework for systems biology." Doctoral thesis, Politecnico di Torino, 2019. http://hdl.handle.net/11583/2752792.

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Taylor, Robert James. "Systems biology of cellular signaling : quantitative experimentation and systems genetics approaches." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/7101.

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Cellular regulation is governed by dense biomolecular networks consisting of proteins, nucleotides, lipids, and metabolites that dynamically coordinate cellular decision making in the face of complex and time-varying environmental stimuli. Obtaining predictive models of these complex networks is a central goal of systems biology and requires sophisticated technologies for the acquisition and integration of many disparate data types. Recent genomic, proteomic and cellular imaging developments have greatly enabled systems-level studies, but further technological advances are needed. For instance
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Boyle, Patrick M. "Network-Scale Engineering: Systems Approaches to Synthetic Biology." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10298.

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The field of Synthetic Biology seeks to develop engineering principles for biological systems. Modular biological parts are repurposed and recombined to develop new synthetic biological devices with novel functions. The proper functioning of these devices is dependent on the cellular context provided by the host organism, and the interaction of these devices with host systems. The field of Systems Biology seeks to measure and model the properties of biological phenomena at the network scale. We present the application of systems biology approaches to synthetic biology, with particular emphasis
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Cong, Yang, and 丛阳. "Optimization models and computational methods for systems biology." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B47752841.

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Systems biology is a comprehensive quantitative analysis of the manner in which all the components of a biological system interact functionally along with time. Mathematical modeling and computational methods are indispensable in such kind of studies, especially for interpreting and predicting the complex interactions among all the components so as to obtain some desirable system properties. System dynamics, system robustness and control method are three crucial properties in systems biology. In this thesis, the above properties are studied in four different biological systems. The ou
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Chung, Hattie. "Genome evolution in structured systems." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493565.

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The evolution of a genome is shaped by spatial interactions at multiple scales. At the angstrom level, structural constraints on both RNA molecules and proteins contribute to the evolution of a gene sequence. Such optimized genes are weaved together in a particular order, out of a near-infinite number of combinations, to result in a genome. The fate of a genome is intricately linked to the evolutionary fate of its host organism; in turn, the fate of an organism is governed by where it resides in space. In this dissertation, I investigate how structure shapes the evolution of a gene, genome con
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48

Hinkelmann, Franziska Babette. "Algebraic theory for discrete models in systems biology." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/28509.

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This dissertation develops algebraic theory for discrete models in systems biology. Many discrete model types can be translated into the framework of polynomial dynamical systems (PDS), that is, time- and state-discrete dynamical systems over a finite field where the transition function for each variable is given as a polynomial. This allows for using a range of theoretical and computational tools from computer algebra, which results in a powerful computational engine for model construction, parameter estimation, and analysis methods. Formal definitions and theorems for PDS and the concept of
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Paget, Caroline Mary. "Environmental systems biology of temperature adaptation in yeast." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/environmental-systems-biology-of-temperature-adaptation-in-yeast(597a675a-aaf1-43bf-bd6c-143aeefc98be).html.

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Temperature is arguably the leading factor that drives adaptation of organisms and ecosystems. Remarkably, many sister species share the same habitat because of their different temporal or micro-spatial thermal adaptation. In this PhD, the underlying molecular mechanisms of the adaptation of closely related species to different temperatures are sought. A thermodynamic analysis was applied to a genome-scale metabolic model of S. cerevisiae at warm and cold temperatures to identify thermo-dependent reactions. Gene Ontology (GO) analysis of predicted cold-dependent reactions found that redox reac
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Regot, Rodríguez de Mier Sergi. "Systems and synthetic biology studies in Saccharomyces cerevisiae." Doctoral thesis, Universitat Pompeu Fabra, 2011. http://hdl.handle.net/10803/37475.

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A fundamental property of living cells is the ability to sense and respond appropriately to changing environmental conditions. In budding yeast (Sacharomyces cerevisiae), changes in extracellular osmotic conditions are sensed by the HOG SAPK pathway, which orchestrates the cell adaptation program required to maximize cell survival upon stress. Although most of the HOG pathway components have been described, little was known about the dynamics of the response. The aim of this thesis was to analyze the dynamic behavior of the HOG pathway. By using a chemical inhibitor and extensive signal quanti
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