Tesi sul tema "Modul biologi"
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Nygren, Kristiina. "Evolutionary Consequences of Reproductive Strategies : Testing Theory on Sex and Reproductive Gene Evolution in the Fungal Model Neurospora". Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-152953.
Testo completoBorrvall, Charlotte. "Biodiversity and Species Extinctions in Model Food Webs". Doctoral thesis, Linköping : Department of Physics, Chemistry and Biology, Linköping University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-6660.
Testo completoMarín, de Mas Igor Bartolomé. "Development and application of novel model-driven and data-driven approaches to study metabolism in the framework of systems medicine". Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/296313.
Testo completoLa presente tesis doctoral se centra en el desarrollo de herramientas computacionales que permitan el estudio de los mecanismos moleculares que ocurren dentro de la célula. Mas específicamente estudia el metabolismo celular desde diferentes puntos de vista usando y desarrollando métodos computacionales basados en diversas metodologías. Así pues en un primer capitulo se desarrolla un método basado en el analista de los flujos metabólicos en estado no estacional isotópico utilizando modelos cinéticos para estudiar el fenómeno de la canalización metabólica en hepatocitos. Este fenómeno modifica la topología metabólica alterando el fenotipo. Nuestro método nos permitió discriminar varios modelos con distintas topología prediciendo la existencia de canalización metabólica en la glucólisis. En el segundo capitulo se desarrolló un método para analizar el metabolismo tumoral teniendo en cuenta la heterogeneidad de poblaciones. En concreto estudiamos dos subpoblaciones extraídas de una linea celular de cáncer de próstata. Para ello utilizamos un modelo a gran escala de todo el metabolismo celular humano. El análisis reflejó la existencia de diferencias notables a nivel de vías metabólicas concretas, confiriendo a cada subpoblacion sensibilidades distintas a diferentes fármacos. En esta linea se demostró que mientras las células PC-3M eran sensibles al etomoxir e insensibles al calcitriol, las PC-3S presentaban una sensibilidad opuesta. En el tercero y ultimo capitulo de la tesis desarrollamos un nuevo método computacional que integra aproximaciones probabilísticas y mecanicistas para integrar diferentes tipos de datos en un análisis basado en modelos discretos. Para ello utilizamos como caso de concepto el estudio de la adaptación anómala al entrenamiento de pacientes con EPOC. El análisis reveló diferencias importantes a nivel de metabolismo energético en comparación con el grupo control.
Ferrández, Roldán Alfonso. "Deconstruction of the cardiopharyngeal gene regulatory network in appendicularians, a paradigmatic study of Oikopleura dioica as an evolutionary knockout model". Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/672832.
Testo completoMACEDO, JOSE ANTONIO FERNANDES DE. "A CONCEPTUAL MODEL FOR MOLECULAR BIOLOGY". PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2005. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=7939@1.
Testo completoGenomic and molecular biology projects are generating knowledge data whose volume and complexity are unparalleled in this research area. In addition, data and knoweledge sources produced and used by research groups have terminological differences (synonyms, aliases and formulae), syntactic differences (file structure, separators and spelling) and semantic differences (intra- and interdisciplinary homonyms). In this context, data management techniques play a fundamental role for biological applications development because it offers adequate abstractions to desing, implement, access and manage data, in order to generate knowledge. In this work, we study the representation problems presentd in traditional languages. Following, we raise the main requiremants for a new conceptual data model specially conceived for molecular biology. Finally, we propose a new conceptual data model with special types of constructor tryng to solve some of the representation problems discurssed before. In addition, we formalize our proposed model using first-order logic and we use this logical description to infer some properties that may help database designer during the elaboration of database schema.
Browning, Alexander P. "Model complexity in biology and bioengineering". Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/227787/1/Alexander_Browning_Thesis.pdf.
Testo completoJohannes, Eleanor M. "Voice, disability and inclusion: a case study of biology learners with cerebral palsy". Thesis, University of the Western Cape, 2006. http://etd.uwc.ac.za/index.php?module=etd&.
Testo completoZiehm, Matthias Fritz. "Computational biology of longevity in model organisms". Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648888.
Testo completoNylander, Johan A. A. "Bayesian Phylogenetics and the Evolution of Gall Wasps". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3996.
Testo completoPaulsen, Jon Rune. "Optimal Information Retrieval Model for Molecular Biology Information". Thesis, Norwegian University of Science and Technology, Department of Computer and Information Science, 2007. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-8718.
Testo completoSearch engines for biological information are not a new technology. Since the 1960s computers have emerged as an important tool for biologists. Online Mendelian Inheritance in Man (OMIM) is a comprehensive catalogue containing approximately 14 000 records with information about human genes and genetic disorders. An approach called Latent Semantic Indexing (LSI) was introduced in 1990 that is based on Singular Value Decomposition (SVD). This approach improved the information retrieval and reduced the storage requirements. This thesis applies LSI on the collection of OMIM records. To further improve the retrieval effectiveness and efficiency, the author propose a clustering method based on the standard k-means algorithm, called Two step k-means. Both the standard k-means and the Two step k-means algorithms are tested and compared with each other.
Santos, Elmer Buluran. "Biologic response to papillomavirus DNA in COPV model". Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621132.
Testo completoLi, Yifei. "Nonlinear diffusion in mathematical biology". Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/234381/1/Yifei_Li_Thesis.pdf.
Testo completoCoskun, Sarp Arda. "PATHCASE-SB MODEL SIMULATION AND MODEL COMPOSITION TOOLS FOR SYSTEMS BIOLOGY MODELS". Case Western Reserve University School of Graduate Studies / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=case1328556115.
Testo completoFoguet, Coll Carles. "Development of model-driven approaches for metabolic flux analysis and anticancer drug discovery". Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668644.
Testo completoJin, Wang. "Investigating the reproducibility of in vitro cell biology assays using mathematical models". Thesis, Queensland University of Technology, 2017. https://eprints.qut.edu.au/109790/1/Wang_Jin_Thesis.pdf.
Testo completoDemattè, Lorenzo. "Scaling up Systems Biology: Model Construction, Simulation and Visualization". Doctoral thesis, Università degli studi di Trento, 2010. https://hdl.handle.net/11572/369136.
Testo completoDematté, Lorenzo. "Scaling up Systems Biology: Model Construction, Simulation and Visualization". Doctoral thesis, University of Trento, 2010. http://eprints-phd.biblio.unitn.it/258/1/PhD-Thesis.pdf.
Testo completoVogel, Ivan. "Aplikace pro zpracování dat z oblasti evoluční biologie". Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2011. http://www.nusl.cz/ntk/nusl-235533.
Testo completoVeliz-Cuba, Alan A. "The Algebra of Systems Biology". Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/28240.
Testo completoPh. D.
Naruse, Kiyoshi, Mitsuru Sakaizumi e Akihiro Shima. "Medaka as a model organism for research in experimental biology". Laboratory of Freshwater Fish Stocks Bioscience Center Nagoya University, 1994. http://hdl.handle.net/2237/13792.
Testo completoKarlstädt, Anja [Verfasser]. "A systems biology approach to model cardiomyocyte metabolism / Anja Karlstädt". Berlin : Medizinische Fakultät Charité - Universitätsmedizin Berlin, 2013. http://d-nb.info/1043197656/34.
Testo completoKonieczka, Jay, Kevin Drew, Alex Pine, Kevin Belasco, Sean Davey, Tatiana Yatskievych, Richard Bonneau e Parker Antin. "BioNetBuilder2.0: bringing systems biology to chicken and other model organisms". BioMed Central, 2009. http://hdl.handle.net/10150/610006.
Testo completothis engine translates between alternate gene names as well as between orthologs in multiple species. Additionally, BioNetBuilder is now implemented to be part of the Gaggle, thereby allowing seamless communication of interaction data to any software implementing the widely used Gaggle software. Using BioNetBuilder, we constructed a chicken interactome possessing 72,000 interactions among 8,140 genes directly in the Cytoscape environment. In this paper, we present a tutorial on how to do so and analysis of a specific use case.CONCLUSION:BioNetBuilder 2.0 provides numerous user-friendly systems biology tools that were otherwise inaccessible to researchers in chicken genomics, as well as other model systems. We provide a detailed tutorial spanning all required steps in the analysis. BioNetBuilder 2.0, the tools for maintaining its data bases, standard operating procedures for creating local copies of its back-end data bases, as well as all of the Gaggle and Cytoscape codes required, are open-source and freely available at http://err.bio.nyu.edu/cytoscape/bionetbuilder/ webcite.
Hinneburg, Detlef, e Nicole Mölders. "A mesoscale atmospheric model combining meteorology, chemistry, biology, and heterogeneity". Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-213743.
Testo completoEin mesoskaliges nicht-hydrostatisches Atmosphärenmodell ist um ein Chemie-TransportModul (CTM) zur Berücksichtigung der Triaden-Komponenten NO, N02 und 03 sowie um ein Verfahren zur verfeinerten Auflösung der topographischen Unterlage (explicit surface-subgrid modul ESSM) erweitert worden. CTM: Die simulierten zeitabhängigen Konzentrationsfelder sind das Resultat folgender modellierter Prozesse: Anthropogene Emission in verschiedenen Höhenschichten, biogene Emission, trockene Deposition (Rezeption), die speziellen chemischen Umwandlungen, turbulente Diffusion und passiver Transport. Da der Schwerpunkt der Prozesse und die höchsten Konzentrationsgradienten innerhalb der bodennahen ersten Modellschicht vorliegen, werden die Berechnungen in dieser Schicht auf einem verfeinerten vertikalen Untergitter durchgeführt. ESSM: Unabhängig von den Eigenheiten des CTM wird für alle untergrundbezogenen meteorologischen Größen ein regelmäßiges horizontales Untergitter zwecks Berücksichtigung des subskalig aufgelösten topographischen Untergrundes eingeführt. Auf diesem Untergitter werden in den bisherigen Näherungen alle Oberflächenflüsse für Impuls, fühlbare und latente Wärme, langwellige Strahlung, der Bodenwärmefluß, die Bodenfeuchte sowie die Energiebilanz am Boden berechnet. Die über die Untergitterzellen gemittelten Werte dienen den weiteren Berechnungen im normalen Modellgitter als die erforderlichen Randwerte. Innerhalb des CTM führt die ESSM-Methode zu einer Überlagerung des vertikalen CTM-Untergitters mit dem horizontalen Untergitter des ESSM. Erste Simulationsergebnisse, die dem derzeitigen Stand in der Realisierung des ESSM entsprechen, erbringen teilweise stark veränderte Depositionsraten infolge der Berücksichtigung der horizontal feiner aufgelösten Topographie
Hinneburg, Detlef, e Nicole Mölders. "A mesoscale atmospheric model combining meteorology, chemistry, biology, and heterogeneity". Wissenschaftliche Mitteilungen des Leipziger Instituts für Meteorologie ; 12 = Meteorologische Arbeiten aus Leipzig ; 4 (1999), S. 44-58, 1999. https://ul.qucosa.de/id/qucosa%3A15094.
Testo completoEin mesoskaliges nicht-hydrostatisches Atmosphärenmodell ist um ein Chemie-TransportModul (CTM) zur Berücksichtigung der Triaden-Komponenten NO, N02 und 03 sowie um ein Verfahren zur verfeinerten Auflösung der topographischen Unterlage (explicit surface-subgrid modul ESSM) erweitert worden. CTM: Die simulierten zeitabhängigen Konzentrationsfelder sind das Resultat folgender modellierter Prozesse: Anthropogene Emission in verschiedenen Höhenschichten, biogene Emission, trockene Deposition (Rezeption), die speziellen chemischen Umwandlungen, turbulente Diffusion und passiver Transport. Da der Schwerpunkt der Prozesse und die höchsten Konzentrationsgradienten innerhalb der bodennahen ersten Modellschicht vorliegen, werden die Berechnungen in dieser Schicht auf einem verfeinerten vertikalen Untergitter durchgeführt. ESSM: Unabhängig von den Eigenheiten des CTM wird für alle untergrundbezogenen meteorologischen Größen ein regelmäßiges horizontales Untergitter zwecks Berücksichtigung des subskalig aufgelösten topographischen Untergrundes eingeführt. Auf diesem Untergitter werden in den bisherigen Näherungen alle Oberflächenflüsse für Impuls, fühlbare und latente Wärme, langwellige Strahlung, der Bodenwärmefluß, die Bodenfeuchte sowie die Energiebilanz am Boden berechnet. Die über die Untergitterzellen gemittelten Werte dienen den weiteren Berechnungen im normalen Modellgitter als die erforderlichen Randwerte. Innerhalb des CTM führt die ESSM-Methode zu einer Überlagerung des vertikalen CTM-Untergitters mit dem horizontalen Untergitter des ESSM. Erste Simulationsergebnisse, die dem derzeitigen Stand in der Realisierung des ESSM entsprechen, erbringen teilweise stark veränderte Depositionsraten infolge der Berücksichtigung der horizontal feiner aufgelösten Topographie.
Patitucci, Cecilia. "PPARy, a new player in hepatic metabolic adaptation from mouse model to human liver cancer". Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCB056/document.
Testo completoTumorigenesis is influenced by genetic and environmental factors. Overnutrition leads to obesity and fatty liver disease, contributing to increase diabetes incidence worldwide. Diabetes and obesity are independent risk factors for liver cancer development (El-Serag et al., Clin Gastroenterol Hepatol, 2006). This PhD project elucidates the molecular mechanisms linking activated insulin signalling pathway, fatty liver disease and liver cancer development and proposes novel therapeutic strategies. The hepatocytes-specific deletion of tumour suppressor Phosphatase and tensin homolog (PTEN) is a model of steatosis-associated liver cancer (Horie et al., J Clin Invest, 2004). Using this model of activated PI3K/mTOR signalling, our laboratory discovered that the nuclear receptor transcription factor Proliferator-Activated Receptor gamma (PPARγ) is induced in PTEN-null liver. My group demonstrated that in the liver PPARγ contributes to steatosis and aerobic glycolysis. Its activity specifically requires a downstream effector in the PI3K/mTOR pathway, the serine/threonine-specific protein kinase AKT2 (Panasyuk et al., Nat Comm, 2012). Based on these observations, we hypothesized that PPARγ might be an important regulator of pathological growth and development of steatohepatitis-associated liver adenocarcinomas. In my PhD work, I demonstrated that PPARγ expression and activity is essential for liver cancer in PTEN mutants. Moreover, PPARγ is induced in human samples of Hepatocellular Carcinoma (HCC) characterized by poor differentiation accompanied by the activation of PI3K/AKT pathway. We could attribute to PPARγ a specific role in tumour formation as it is required for abnormal liver growth and steatosis in mice at pre-tumoral age. In addition, deletion of PPARγ in PTEN mutants protected animals form liver tumorigenesis placing PPARγ downstream of activated AKT2. Analysing human samples of pre-carcinoma lesions characterized by high steatotic rate, we demonstrated that PPARγ transcript levels are increased in a specific subgroup of adenomas characterized by loss-of-function mutations in the Hepatocyte Nuclear Factor 1α (HNF1α). We identified HNF1α as a novel direct negative regulator of PPARγ transcription. We also revealed HNF1α expression and activity inhibited by AKT2 and thereby inducing PPARγ pro-tumorigenic action. Finally, the sensitivity of PPARγ to natural and exogenous ligands encouraged us to perform treatments to pharmacologically modulate PPARγ activity. Further activation of PPARγ with its synthetic ligand pioglitazione dramatically aggravates liver disease. While PPARγ inhibition by selective antagonist SR2595 allowed to reduce the pre-tumoral and tumoral signs of PTEN-null mice. In sum, our studies in men and mice reveal a novel pro-tumorigenic network of transcription factors HNF1α and PPARγ downstream of activated insulin signalling pathway, suggesting possible strategies for treatment of a subgroup of steatohepatitis-associated liver cancer
Schutte, Brian J. "Biology and ecology of Ambrosia Trifida L. seedling emergence". The Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=osu1181937971.
Testo completoKallner, Bastviken Sofia. "Nitrogen removal in treatment wetlands : Factors influencing spatial and temporal variations". Doctoral thesis, Linköpings universitet, Ekologi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-7564.
Testo completoÖsterman, Hanna. "Olfactory performance and neuropathology in the Tg6799 strain of Alzheimer’s disease model mice". Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56816.
Testo completoYao, Xuefei. "High Forest or Wood Pasture: A model of Large Herbivores' impact on European Lowland Vegetation". Thesis, Linköping University, Linköping University, Linköping University, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-57429.
Testo completoNatural forest dynamics is a foundational topic of forest science. A new Wood Pasture hypothesis considering large herbivore as driving force in forest ecosystem is now challenging the traditional High Forest hypothesis, in which vegetation is regarded as main driving force. In this study, a model-based approach is applied to investigate differences between these two hypotheses and the determine factors in the system. A theoretical landscape of 1 km²formed by 100*100 cells is set up with 100 vegetation patches and free moving herbivores on. Our null hypothesis that herbivores make no difference in vegetation dynamics especially at canopy level is rejected. It is found that synchronization of herbivore behaviors is the most influencing factor of how a landscape might be shaped. It is also found that landscape could be a mosaic of both high forest and wood pasture depends on large herbivore’s herd size.
Tashakor, Ghazal. "Scalable agent-based model simulation using distributed computing on system biology". Doctoral thesis, Universitat Autònoma de Barcelona, 2021. http://hdl.handle.net/10803/671332.
Testo completoEl modelado basado en agentes es una herramienta computacional muy útil que permite simular un comportamiento complejo utilizando reglas tanto en escalas micro como macro. La complejidad de este tipo de modelado radica en la definición de las reglas que tendrán los agentes para definir los elementos estructurales o los patrones de comportamiento estáticos y/o dinámicos. La presente tesis aborda la definición de modelos complejos de redes biológicas que representan células cancerosas para obtener comportamientos sobre diferentes escenarios mediante simulación y conocer la evolución del proceso de metástasis para usuarios no expertos en sistemas de cómputo. Además se desarrolla una prueba de concepto de cómo incorporar técnicas de análisis de redes dinámicas y de aprendizaje automático en los modelos basados en agentes a partir del desarrollo de un sistema de simulación federado para mejorar el proceso de toma de decisiones. Para el desarrollo de esta tesis se han tenido que abordar, desde el punto de vista de la simulación, la representación de redes biológicas complejas basadas en grafos e investigar como integrar la topología y funciones de este tipo de redes interactuando un modelo basado en agentes. En este objetivo, se ha utilizado el modelo ABM como base para la construcción, agrupamiento y clasificación de los elementos de la red y que representan la estructura de una red biológica compleja y escalable. La simulación de un modelo complejo de múltiples escalas y múltiples agentes, proporciona una herramienta útil para que un científico, no-experto en computación, pueda ejecutar un modelo complejo paramétrico y utilizarlo como herramienta de análisis de escenarios o predicción de variaciones según los diferentes perfiles de pacientes considerados. El desarrollo se ha centrado en un modelo de tumor basado en agentes que ha evolucionado desde un modelo ABM simple y bien conocido, al cual se le han incorporado las variables y dinámicas referenciadas por el Hallmarks of Cancer, a un modelo complejo basado en grafos. Este modelo, basado en grafos, se utiliza para representar a diferentes niveles de interacción y dinámicas dentro de las células en la evolución de un tumor que permite diferentes grado de representaciones (a nivel molecular/celular). Todo ello se ha puesto en funcionamiento en un entorno de simulación y se ha creado un flujo de trabajo (workflow) para construir una red escalable compleja basada en un escenario de crecimiento tumoral y donde se aplican técnicas dinámicas para conocer el crecimiento de la red tumoral sobre diferentes patrones. La experimentación se ha realizado utilizando el entorno de simulación desarrollado considerado la ejecución de modelos para diferentes perfiles de pacientes, como muestra de su funcionalidad, para calcular parámetros de interés para el experto no-informático como por ejemplo la evolución del volumen del tumor. El entorno ha sido diseñado para descubrir y clasificar subgrafos del modelo de tumor basado en agentes, que permitirá distribuir los modelos en un sistema de cómputo de altas prestaciones y así poder analizar escenarios complejos y/o diferentes perfiles de pacientes con patrones tumorales con un alto número de células cancerosas en un tiempo reducido.
Agent-based modeling is a very useful computational tool to simulate complex behavior using rules at micro and macro scales. This type of modeling’s complexity is in defining the rules that the agents will have to define the structural elements or the static and dynamic behavior patterns. This thesis considers the definition of complex models of biological networks that represent cancer cells obtain behaviors on different scenarios by means of simulation and to know the evolution of the metastatic process for non-expert users of computer systems. Besides, a proof of concept has been developed to incorporate dynamic network analysis techniques and machine learning in agent-based models based on developing a federated simulation system to improve the decision-making process. For this thesis’s development, the representation of complex biological networks based on graphs has been analyzed, from the simulation point of view, to investigate how to integrate the topology and functions of this type of networks interacting with an agent-based model. For this purpose, the ABM model has been used as a basis for the construction, grouping, and classification of the network elements representing the structure of a complex and scalable biological network. The simulation of complex models with multiple scales and multiple agents provides a useful tool for a scientist, non-computer expert to execute a complex parametric model and use it to analyze scenarios or predict variations according to the different patient’s profiles. The development has focused on an agent-based tumor model that has evolved from a simple and well-known ABM model. The variables and dynamics referenced by the Hallmarks of Cancer have been incorporated into a complex model based on graphs. Based on graphs, this model is used to represent different levels of interaction and dynamics within cells in the evolution of a tumor with different degrees of representations (at the molecular/cellular level). A simulation environment and workflow have been created to build a complex, scalable network based on a tumor growth scenario. In this environment, dynamic techniques are applied to know the tumor network’s growth using different patterns. The experimentation has been carried out using the simulation environment developed considering the execution of models for different patient profiles, as a sample of its functionality, to calculate parameters of interest for the non-computer expert, such as the evolution of the tumor volume. The environment has been designed to discover and classify subgraphs of the agent-based tumor model to execute these models in a high-performance computer system. These executions will allow us to analyze complex scenarios and different profiles of patients with tumor patterns with a high number of cancer cells in a short time.
Tervonen, V. (Virpi). "Salmon cardiac peptide (sCP): a new model for natriuretic peptide biology". Doctoral thesis, University of Oulu, 2001. http://urn.fi/urn:isbn:9514264932.
Testo completoDeshpande, Abhishek. "Beyond the two-state model of switching in biology and computation". Thesis, Imperial College London, 2018. http://hdl.handle.net/10044/1/62626.
Testo completoRichardson, Jennifer. "Zebrafish as a model of BRAFV600E melanoma subtypes and Nevus biology". Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/6493.
Testo completoPrescott, Thomas Paul. "Large-scale layered systems and synthetic biology : model reduction and decomposition". Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:205a18fb-b21f-4148-ba7d-3238f4b1f25b.
Testo completoFeist, Adam Michael. "Model-driven metabolic engineering of Escherichia coli a systems biology approach /". Diss., [La Jolla] : University of California, San Diego, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3354731.
Testo completoTitle from first page of PDF file (viewed June 2, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
Gay, Steven. "Subgraph Epimorphisms : Theory and Application to Model Reductions in Systems Biology". Sorbonne Paris Cité, 2015. http://www.theses.fr/2015USPCC265.
Testo completoThis thesis develops a framework of graph morphisms and applies it to model reduction in systems biology. We are interested in the following problem: the collection of systems biology models is growing, but there is no formai relation between models in this collection. Thus, the task of organizing the existing models, essential for model refinement and coupling, is left to the modeler. In mathematical biology, model reduction techniques have been studied for a long time, however these techniques are far too restrictive to be applied on the scales required by systems biology. We propose a model reduction framework based solely on graphs, allowing to organize models in a partial order. Systems biology models will be represented by their reaction graphs. To capture the process of reduction itself, we study a particular kind of graph morphisms: subgraph epimorphisms, which allow both vertex merging and deletion. We first analyze the partial order emerging from the merge/delete graph operations, then develop tools to solve computational problems raised by this framework, and finally show both the computational feasibility of the approach and the accuracy of the reaction graphs/subgraph epimorphisms framework on a large repository of systems biology models
Frenkel, Martin. "Light, stress and herbivory : from photoprotection to trophic interactions using Arabidopsis thaliana as a model organism". Doctoral thesis, Umeå : Department of Ecology and Environmental Science, Umeå University, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1651.
Testo completoMurphy, Ryan John. "Mechanochemical and experimental models in mathematical biology". Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/228428/1/Ryan%20John_Murphy_Thesis.pdf.
Testo completoBoman, Erik. "Olfactory and cognitive abilities in two strains of Alzheimer`s disease model mice". Thesis, Linköping University, Department of Physics, Chemistry and Biology, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-19200.
Testo completoThe present study assessed olfactory and cognitive abilities in two strains of Alzheimer’s disease (AD) model mice and in healthy control mice over a four month time period. To this end an operant conditioning paradigm using an automated olfactometer and a spatial learning test with non-olfactory cues were employed and data on olfactory learning and memory, discrimination, and sensitivity as well as spatial learning and memory were collected. The mice were between 6 to 7 month old at the beginning of the study and 9 to 10 months old at the end of the data collection, that is, in the age range when the animals are supposed to display marked neuroanatomical changes typical of AD. The results demonstrate that there were no systematic differences in olfactory performance and spatial learning and memory abilities of AD model mice and the control mice up to the age they were tested. Further, there was no indication of an age-related decline in performance in any of the mouse strains across the testing period. Several reasons might account for the observed lack of difference in olfactory and cognitive performance between the mouse strains tested here: the AD model mice might not develop amyloid plaques and neurofibrillary tangles at all or they might develop them later than stated by the supplier. Alternatively, the AD model mice may have developed AD-typical neuroanatomical changes but these do not, or not yet, affect their olfactory performance and/or spatial learning and memory capabilities. Ongoing data collection will help to evaluate which of these explanations holds true.
Nangu, Bongiwe B. "Teaching in English and Isixhosa: code-switching in grade 11 Biology classes at a school in Khayelitsha". Thesis, University of the Western Cape, 2006. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_7339_1242696871.
Testo completoThis study explored the use of code-switching in Biology classes at high school level, how it is used in the teaching and learning situation and its effect on the learners' performance in the subject. Grade 11 was chosen as it precedes the last year at high school.
Chen, Daphne Wei-chen. "Integrative modelling of glucocorticoid induced apoptosis with a systems biology approach". Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/integrative-modelling-of-glucocorticoid-induced-apoptosis-with-a-systems-biology-approach(a05039a1-f3e3-44d2-959e-0fade52a28a1).html.
Testo completoPastor, André [Verfasser]. "Membranadsorber-Modul zur Aufarbeitung ungeklärter Bioprozessmedien / André Pastor". Hannover : Technische Informationsbibliothek (TIB), 2016. http://d-nb.info/1128922665/34.
Testo completoROSAS, ILIANA NICOLE. "MODEL BASED INQUIRY IN AN INTRODUCTORY MOLECULAR AND CELLULAR BIOLOGY LABORATORY SETTING". Thesis, The University of Arizona, 2016. http://hdl.handle.net/10150/613566.
Testo completoGhosh, Krishnendu. "Formal Analysis of Automated Model Abstractions under Uncertainty: Applications in Systems Biology". University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1330024977.
Testo completoToni, Tina. "Approximate Bayesian computation for parameter inference and model selection in systems biology". Thesis, Imperial College London, 2010. http://hdl.handle.net/10044/1/11481.
Testo completoWang, Zhi. "Module-Based Analysis for "Omics" Data". Thesis, North Carolina State University, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3690212.
Testo completoThis thesis focuses on methodologies and applications of module-based analysis (MBA) in omics studies to investigate the relationships of phenotypes and biomarkers, e.g., SNPs, genes, and metabolites. As an alternative to traditional single–biomarker approaches, MBA may increase the detectability and reproducibility of results because biomarkers tend to have moderate individual effects but significant aggregate effect; it may improve the interpretability of findings and facilitate the construction of follow-up biological hypotheses because MBA assesses biomarker effects in a functional context, e.g., pathways and biological processes. Finally, for exploratory “omics” studies, which usually begin with a full scan of a long list of candidate biomarkers, MBA provides a natural way to reduce the total number of tests, and hence relax the multiple-testing burdens and improve power.
The first MBA project focuses on genetic association analysis that assesses the main and interaction effects for sets of genetic (G) and environmental (E) factors rather than for individual factors. We develop a kernel machine regression approach to evaluate the complete effect profile (i.e., the G, E, and G-by-E interaction effects separately or in combination) and construct a kernel function for the Gene-Environmental (GE) interaction directly from the genetic kernel and the environmental kernel. We use simulation studies and real data applications to show improved performance of the Kernel Machine (KM) regression method over the commonly adapted PC regression methods across a wide range of scenarios. The largest gain in power occurs when the underlying effect structure is involved complex GE interactions, suggesting that the proposed method could be a useful and powerful tool for performing exploratory or confirmatory analyses in GxE-GWAS.
In the second MBA project, we extend the kernel machine framework developed in the first project to model biomarkers with network structure. Network summarizes the functional interplay among biological units; incorporating network information can more precisely model the biological effects, enhance the ability to detect true signals, and facilitate our understanding of the underlying biological mechanisms. In the work, we develop two kernel functions to capture different network structure information. Through simulations and metabolomics study, we show that the proposed network-based methods can have markedly improved power over the approaches ignoring network information.
Metabolites are the end products of cellular processes and reflect the ultimate responses of biology system to genetic variations or environment exposures. Because of the unique properties of metabolites, pharmcometabolomics aims to understand the underlying signatures that contribute to individual variations in drug responses and identify biomarkers that can be helpful to response predictions. To facilitate mining pharmcometabolomic data, we establish an MBA pipeline that has great practical value in detection and interpretation of signatures, which may potentially indicate a functional basis for the drug response. We illustrate the utilities of the pipeline by investigating two scientific questions in aspirin study: (1) which metabolites changes can be attributed to aspirin intake, and (2) what are the metabolic signatures that can be helpful in predicting aspirin resistance. Results show that the MBA pipeline enables us to identify metabolic signatures that are not found in preliminary single-metabolites analysis.
Cossa, Eugenia Flora Rosa. "A case study of practical work in a cell biology course at the Eduardo Mondlane University in Mozambique". Thesis, University of the Western Cape, 2007. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_1757_1228307542.
Testo completoThis study was carried out with the assumption that practical work does contribute to the teaching and learning of cell biology at Eduardo Mondlane University in Mozambique. In this regard, the main purpose of this study was to investigate the impact of practical work in the teaching and learning of cell biology concepts, specifically focussing on cell divisions concepts. It also aimed at determining the students' perceptions of the role of practical work in the learning of cell biology. On the other hand, the study sought also to understand the lecturers' practical work teaching experiences and views regarding the cell biology practical work.
Lott, Paul Christian. "StochHMM| A Flexible Hidden Markov Model Framework". Thesis, University of California, Davis, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3602142.
Testo completoIn the era of genomics, data analysis models and algorithms that provide the means to reduce large complex sets into meaningful information are integral to further our understanding of complex biological systems. Hidden Markov models comprise one such data analysis technique that has become the basis of many bioinformatics tools. Its relative success is primarily due to its conceptually simplicity and robust statistical foundation. Despite being one of the most popular data analysis modeling techniques for classification of linear sequences of data, researchers have few available software options to rapidly implement the necessary modeling framework and algorithms. Most tools are still hand-coded because current implementation solutions do not provide the required ease or flexibility that allows researchers to implement models in non-traditional ways. I have developed a free hidden Markov model C++ library and application, called StochHMM, that provides researchers with the flexibility to apply hidden Markov models to unique sequence analysis problems. It provides researchers the ability to rapidly implement a model using a simple text file and at the same time provide the flexibility to adapt the model in non-traditional ways. In addition, it provides many features that are not available in any current HMM implementation tools, such as stochastic sampling algorithms, ability to link user-defined functions into the HMM framework, and multiple ways to integrate additional data sources together to make better predictions. Using StochHMM, we have been able to rapidly implement models for R-loop prediction and classification of methylation domains. The R-loop predictions uncovered the epigenetic regulatory role of R-loops at CpG promoters and protein coding genes 3' transcription termination. Classification of methylation domains in multiple pluripotent tissues identified epigenetics gene tracks that will help inform our understanding of epigenetic diseases.
Maqungo, Monique Nonceba. "Physiological and cellular characterization of a plant natriuretic peptide". Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&.
Testo completofor example, at least four different signal pathways have been identified for water-deficit stress (Shinozaki and Yamaguchi-Shinozaki, 1997
Xiong et al., 2002). Different forms of stress may activate or utilize the same components, including proteins and other signaling molecules. Signaling molecules such as jasmonic acid (JA) are involved in multiple stress response and development in plants (Creelman and Mullet, 1995, 1997
Turner et al., 2002). However it is the specific combination of various components of the signaling network coupled with spatial and temporal factors that allows the plant to mount a directed response to any given stress factors. Systemic defense responses thus provide an attractive model for the study of cell-to-to cell signal transduction pathways that operates over long distances (Lucas and Lee, 2004).
Cellular and physiological evidence suggest the presence of a novel class of systemic mobile plant molecule that is recognized by antibodies against vertebrate atrial natriuretic peptides (ANPs). It has been demonstrated that a recombinant Arabidopsis thaliana natriuretic peptide analogue (AtPNP-A) molecule can induce osmoticumdependent water uptake into protoplast at nanomolar concentrations thus affecting cell volume and hence plant growth. In this study we confirm that active recombinant protein causes swelling in Arabidopsis mesophyll cell protoplasts (MCPs).
Buckalew, Richard L. "Mathematical Models in Cell Cycle Biology and Pulmonary Immunity". Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1395242276.
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