Dissertations / Theses on the topic 'Network pathway'
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Isik, Zerrin. "Network Structure Based Pathway Enrichment System To Analyze Pathway Activities." Phd thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12612951/index.pdf.
Full textWang, Chen. "From network to pathway: integrative network analysis of genomic data." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/77121.
Full textPh. D.
Gao, Yipeng. "Transformation Pathway Network Analysis for Martensitic Transformations." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385978073.
Full textOgris, Christoph. "Global functional association network inference and crosstalk analysis for pathway annotation." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-146703.
Full textAt the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.
Eguchi, Akihiro. "Neural network modelling of the primate ventral visual pathway." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:99277b9c-00ee-45e3-8adb-47190d716912.
Full textChou, I.-Chun. "Parameter estimation and network identification in metabolic pathway systems." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26513.
Full textCommittee Chair: Voit, Eberhard O.; Committee Member: Borodovsky, Mark; Committee Member: Butera, Robert; Committee Member: Kemp, Melissa; Committee Member: Park, Haesun. Part of the SMARTech Electronic Thesis and Dissertation Collection.
Oswal, Vipul Kantilal. "Pathway Pioneer: Heterogenous Server Architecture for Scientific Visualization and Pathway Search in Metabolic Network Using Informed Search." DigitalCommons@USU, 2014. https://digitalcommons.usu.edu/etd/2775.
Full textStoney, Ruth. "Using pathway networks to model context dependent cellular function." Thesis, University of Manchester, 2018. https://www.research.manchester.ac.uk/portal/en/theses/using-pathway-networks-to-model-context-dependent-cellular-function(562db48d-5e8b-40bb-8457-47c9a3455f9c).html.
Full textKaur, Dipendra. "Mapping and Filling Metabolic Pathway Holes." Digital Archive @ GSU, 2008. http://digitalarchive.gsu.edu/biology_theses/14.
Full textLiu, Boqi. "The gene regulatory network in the anterior neural plate border of ascidian embryos." Kyoto University, 2020. http://hdl.handle.net/2433/253119.
Full textDosi, Harsh. "Patway Pioneer: A Web-Based Metabolic Network Layout Extension." DigitalCommons@USU, 2014. https://digitalcommons.usu.edu/etd/2797.
Full textJin, Ying. "New Algorithms for Mining Network Datasets: Applications to Phenotype and Pathway Modeling." Diss., Virginia Tech, 2009. http://hdl.handle.net/10919/40493.
Full textPh. D.
Rivera, Corban G. "Automatic Reconstruction of the Building Blocks of Molecular Interaction Networks." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/28752.
Full text- cellular wiring diagrams can be decomposed into overlapping modules, where each module is a set of coherently-interacting molecules and
- a cell responds to a stress or a stimulus by appropriately modulating the activities of a subset of these modules.
- Given a wiring diagram and genome-wide gene expression data measured after the application of a stress or in a disease state, compute the active network of molecular interactions perturbed by the stress or the disease.
- Given the active networks for multiple stresses, stimuli, or diseases, compute a set of network legos, which are molecular modules with the property that each active network can be expressed as an appropriate combination of a subset of modules.
Ph. D.
Self, Roland. "Unilateral termination of psychotherapy and the Decision Action Pathway Interactive Network (DAPIN) model." Thesis, University of Hull, 2003. http://hydra.hull.ac.uk/resources/hull:12375.
Full textGuo, Chongye. "An integrated approach for the investigation and analysis of signalling networks in azoospermia : biological network analysis for the discovery of intracellular signalling pathway alterations associated with azoospermia." Thesis, University of Bradford, 2014. http://hdl.handle.net/10454/7343.
Full textBécavin, Christophe. "Dimensionaly reduction and pathway network analysis of transcriptome data : application to T-cell characterization." Paris, Ecole normale supérieure, 2010. http://www.theses.fr/2010ENSUBS02.
Full textLi, Lei. "The mechanism and network of BES1 mediated transcriptional regulation in Brassinosteroids (BR) pathway in Arabidopsis." [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:3403814.
Full textCaccamise, Lauren M. "Regulation of a Differentiation MAPK Pathway by a Novel Integrated Signaling Network and Multiple Sensors." Thesis, State University of New York at Buffalo, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3725898.
Full textFilamentous growth is a cell differentiation program utilized by Saccharomyces cerevisiae to respond to nutrient limitation in the environment. This process is principally controlled by a mitogen-activated protein kinase (MAPK) pathway but is also impacted by a number of other pathways including Ras2p-cAMP-PKA, Target of Rapamycin, Rim101, and mitochondrial retrograde. Using a high-throughput genetic screening approach in conjunction with directed gene-deletion analysis, I have identified 97 new regulators of the filamentous growth MAPK pathway. These new regulators created new connections to the filamentous growth MAPK pathway as well as extended previously known connections. I have linked several of the pathways governing filamentous growth together as part of an integrated signaling network by showing that these pathways regulate each other’s transcriptional targets. This network indicates an intricate level of communication and coordination among these pathways that has not been previously appreciated. I show that proper coordination of the filamentous growth MAPK pathway is essential for proper morphogenesis and this is a potential reason for the many inputs used to control this response. The filamentous growth MAPK pathway is also regulated by three transmembrane proteins – Msb2p, Sho1p, and Opy2p. Here these three proteins are compared to determine that they have specific functions in regulating filamentous growth. The three proteins exhibit different localization patterns and rates of turnover from the plasma membrane. I show that the Rim101 pathway affects the filamentous growth MAPK pathway independently of the ESCRT pathway which shares components with the Rim101 pathway. Additionally, I have shown that overexpression of the arrestin protein Aly1p results in mislocalized Msb2p and diminished pathway activity.
Aita, Ada. "Genetics in TNF-TNFR pathway: a complex network causing spondyloarthritis and conditioning response to therapy." Doctoral thesis, Università degli studi di Padova, 2017. http://hdl.handle.net/11577/3425710.
Full textIntroduzione. Le spondiloartriti sieronegative (SpA) sono un gruppo di malattie infiammatorie croniche risultanti da una complessa interazione tra fattori genetici (tra cui, HLA-B27 è il maggior predisponente) e ambientali. Ed è tale interazione ad indurre l'attivazione di processi autoinfiammatori e la disregolazione del sistema immunitario caratterizzanti la malattia. In molti casi, una diagnosi precoce ed un adeguato monitoraggio dell’ attività di malattia risultano difficili a causa della sovrapposizione delle caratteristiche cliniche tra le diverse forme. Il ritardo nella diagnosi e conseguentemente nel trattamento, è inoltre dovuto al fatto che, gli indici d’infiammazione comunemente utilizzati nella pratica clinica, la velocità di eritrosedimentazione (VES) ed la proteina C-reattiva (PCR), sono nella norma in almeno metà dei pazienti con chiara espressione dell’attività di malattia. Il ritardo nella diagnosi conferisce a questi pazienti un carico sintomatico importante ed una perdita di funzione durante gli anni di vita produttiva. Pertanto, forte attenzione è attualmente rivolta all’identificazione di marcatori biochimici e genetici utili alla diagnosi e di fattori prognostici necessari a valutare l'efficacia del trattamento. Tra i fattori genetici predisponenti, è noto il ruolo di HLA-B27, che contribuisce però solo per il 20-30% all'ereditarietà totale, mentre il complesso maggiore di istocompatibilità (MHC) rappresenta circa il 40-50% del rischio genetico di sviluppare la patologia. Questo dato ha suggerito il probabile coinvolgimento di altri geni nel meccanismo patogenetico. Studi di associazione genetica hanno permesso di identificare un certo numero di altri geni, associati alla patologia, sia nel locus MHC che in altri loci. In questo contesto, di grande interesse è lo studio della genetica di TNF-α, considerato il ruolo di tale citochina nel propagare e perdurare dell'infiammazione. Sebbene numerosi studi abbiano dimostrato l’associazione tra i polimorfismi di geni coinvolti nella via del segnale del TNF-α (es. TNFA, TNFSF15, TNFR1 e TRADD) e la patologia di SpA, i risultati sono discordanti. Di grande interesse sono anche le varianti del MEFV gene, coinvolto nella patogenesi della malattia autoinfiammatoria Febbre Mediterranea Familiare (FMF). Studi recenti hanno, infatti, dimostrato che le SpA, ed in particolare la spondilite anchilosante (AS), sono molto comuni tra i pazienti affetti da FMF e che questi pazienti possono presentarsi con AS come unica manifestazione. Questo studio, condotto su 91 pazienti e 223 controlli, provenienti da una regione italiana del Nord-Est, si propone di identificare fattori bioumorali (biochimici ed ematologici) e genetici al fine di supportare i processi diagnostici e prognostici (risposta alla terapia). In particolare, oltre ai parametri biochimici ed ematologici, è stato valutato se polimorfismi nella regione del promotore del gene TNFA, o dei geni TNFRSF1A e MEFV, possano concorrere con l’allele HLA-B27 all’aumento del rischio di sviluppare la malattia e/o nel predire la risposta agli inibitori del TNF-α. Metodi. La popolazione studiata comprendeva 91 pazienti con diagnosi di SpA (età media ± deviazione standard: 52.1 ± 12.5 anni; 57 maschi, 34 femmine) e 223 donatori di sangue (età media ± deviazione standard: 46 ± 11 anni; 146 maschi, 77 femmine) provenienti dalla Regione Veneto, una regione italiana del Nord-Est. Tra i pazienti, 36 presentavano AS e 55 artrite psoriasica (PsA), con diagnosi formulata sulla base dei criteri rispettivamente di New York e CASPAR. Il protocollo di questo studio è stato approvato dal Comitato Etico Istituzionale locale dell’Università-Azienda Ospedaliera di Padova, Italia (Prot.n. 3024P / 13), e tutti i soggetti arruolati hanno firmato un consenso informato prima di partecipare allo studio. Per ciascun soggetto arruolato, sono stati raccolti i dati demografici e fisiologici, la storia clinica e familiare. Sono stati raccolti poi, campioni di sangue, al fine di valutare l’emocromo e la VES, e di determinare i livelli di PCR, acido urico, prealbumina, alanina aminotransferasi (ALT) e glucosio. L’analisi molecolare dei geni MEFV (esoni 2,3,5 e 10) e TNFRSF1A (esoni 2,3,4 e 6) è avvenuta mediante sequenziamento diretto. La determinazione degli alleli HLA-B27 e dei polimorfismi del gene TNFA (-1031T>C;-857C>T;-376G>A;-308G>A;-238G>A) è stata condotta mediante PCR in Real-Time. La determinazione degli alleli HLA-CW6 è avvenuta mediante un test genetico molecolare CE-IVD, disponibile in commercio, che adotta la tecnologia microarray. L’analisi statistica è stata effettuata utilizzando il software STATA (versione 13.1). Risultati. Un maggior numero di cellule polimorfonucleate circolanti e livelli di PCR più elevati sono stati rilevati nei pazienti affetti da SpA rispetto ai controlli. Inoltre, i pazienti affetti da PsA hanno mostrato livelli più elevati di ALT, non solo rispetto ai controlli, ma anche rispetto a pazienti affetti da AS. In ogni caso tali indici non erano molto elevati e spesso risultavano compresi entro gli intervalli di riferimento. Come atteso, gli alleli HLA-B27 sono risultati associati all’AS (χ2=120.1; p<0.0001). Sebbene una frequenza leggermente maggiore degli alleli HLA-CW6 sia stata osservata tra i pazienti con AS (circa il 6%) o PsA (circa il 13%) rispetto ai controlli (circa 4%), la differenza non è risultata essere statisticamente significativa. Nessuno dei polimorfismi del gene TNFA è risultato singolarmente associato alla diagnosi SpA, né a quella di AS o PsA, se valutate indipendentemente. Sono stati, poi, statisticamente dedotti gli aplotipi derivanti dalle coppie di combinazioni dei cinque polimorfismi studiati. Gli aplotipi più frequenti nei controlli sono stati selezionati come aplotipi di riferimento, e solo l’aplotipo -1031C/-308G è risultato significativamente associato con l’AS (p=0.015) esercitando in questa malattia un ruolo protettivo (odds ratio: 0.43; intervallo di confidenza al 95%: 0.22- 0.85). Tre polimorfismi sono stati identificati nel gene TNFRSF1A e tra questi, solo i polimorfismi R92Q (Frequenza dell’allele minore- MAF = 0.034) e c.625 + 10A> G (MAF = 0.479) sono stati selezionati a causa del potenziale ruolo funzionale. Entrambi i polimorfismi non sono risultati associati con la diagnosi di SpA (χ2 = 1.073 e p = 0.300 per R92Q; χ2 = 4.721 e p = 0.094 per c.625 + 10A> G). Il polimorfismo c.625 + 10A> G è però, risultato essere associato con la risposta alla terapia con anti-TNF, valutato sulla base di un punteggio BASDAI inferiore / uguale o superiore a 4, a 10 mesi dall’inizio della terapia (p = 0.031). Ventuno polimorfismi sono stati identificati nel gene MEFV e tra questi, 10 noti per il potenziale significato funzionale. Tali varianti alleliche sono risultate estremamente rare nella nostra popolazione (MAF <0.025) ad eccezione di R202Q (MAF = 0.27). Nessun polimorfismo è risultato essere associato con la diagnosi SpA (p> 0.05). Conclusioni. In conclusione, i risultati di questo studio suggeriscono il ruolo rilevante della genetica della via del segnale TNF-TNFR nel complesso sistema che induce la patogenesi di SpA e condiziona la risposta alla terapia. Il gene TNFA, nella popolazione oggetto di studio, si è dimostrato un fattore predisponente per lo sviluppo di SpA, ma soprattutto di AS. Al contrario, la genetica del gene MEFV non sembra mostrare alcun impatto in questo gruppo di malattie. L'aplotipo TNFA-1031C/-308G, potenzialmente associato alla produzione di livelli più bassi di TNF-α, sembra esercitare un ruolo protettivo nella patogenesi di AS, mentre è emerso che il polimorfismo c.625 TNFRSF1A + 10A> G costituisce un potenziale fattore predittivo di risposta alla terapia con anti-TNFα.
Jiang, Xiaoshan. "A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli." Thesis, Virginia Tech, 2012. http://hdl.handle.net/10919/42523.
Full textMaster of Science
Howells, Christopher Corey. "The Modeling and Analysis of the Apoptotic BAD/tBID/BAK Pathway as a Chemical Reaction Network." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/26915.
Full textPh. D.
Gu, Jinghua. "Novel Monte Carlo Approaches to Identify Aberrant Pathways in Cancer." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/51950.
Full textPh. D.
Motianlifu, Muzhapaer. "Expansion of Reaction Network Flux Analysis toward including Life Cycle Assessment and Ecosystem Services." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1492635223149177.
Full textWashbrook, Simon Richard. "The development of an experimental pathway for the synthesis of organic sequential interpenetrating polymer network (IPN) microgel dispersions." Thesis, Loughborough University, 1998. https://dspace.lboro.ac.uk/2134/13742.
Full textHamidi, Perchehkolaei Seyyed Babak. "Bit Optimized Reconfigurable Network (BORN): A New Pathway Towards Implementing a Fully Integrated Band-Switchable CMOS Power Amplifier." Diss., North Dakota State University, 2020. https://hdl.handle.net/10365/32133.
Full textStatello, Luisa. "Specific Alterations of miRNA Transcriptome and Global Network Structure in Colorectal Cancer After Inhibition of MAPK/ERK Signaling Pathway." Doctoral thesis, Università di Catania, 2013. http://hdl.handle.net/10761/1343.
Full textHänzelmann, Sonja 1981. "Pathway-centric approaches to the analysis of high-throughput genomics data." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/108337.
Full textEn l'última dècada, la biologia molecular ha evolucionat des d'una perspectiva reduccionista cap a una perspectiva a nivell de sistemes que intenta desxifrar les complexes interaccions entre els components cel•lulars. Amb l'aparició de les tecnologies d'alt rendiment actualment és possible interrogar genomes sencers amb una resolució sense precedents. La dimensió i la naturalesa desestructurada d'aquestes dades ha posat de manifest la necessitat de desenvolupar noves eines i metodologies per a convertir aquestes dades en coneixement biològic. Per contribuir a aquest repte hem explotat l'abundància de dades genòmiques procedents d'instruments d'alt rendiment i disponibles públicament, i hem desenvolupat mètodes bioinformàtics focalitzats en l'extracció d'informació a nivell de via molecular en comptes de fer-ho al nivell individual de cada gen. En primer lloc, hem desenvolupat GSVA (Gene Set Variation Analysis), un mètode que facilita l'organització i la condensació de perfils d'expressió dels gens en conjunts. GSVA possibilita anàlisis posteriors en termes de vies moleculars amb dades d'expressió gènica provinents de microarrays i RNA-seq. Aquest mètode estima la variació de les vies moleculars a través d'una població de mostres i permet la integració de fonts heterogènies de dades biològiques amb mesures d'expressió a nivell de via molecular. Per il•lustrar les característiques de GSVA, l'hem aplicat a diversos casos usant diferents tipus de dades i adreçant qüestions biològiques. GSVA està disponible com a paquet de programari lliure per R dins el projecte Bioconductor. En segon lloc, hem desenvolupat una estratègia centrada en vies moleculars basada en el genoma per reposicionar fàrmacs per la diabetis tipus 2 (T2D). Aquesta estratègia consisteix en dues fases: primer es construeix una xarxa reguladora que s'utilitza per identificar mòduls de regulació gènica que condueixen a la malaltia; després, a partir d'aquests mòduls es busquen compostos que els podrien afectar. La nostra estratègia ve motivada per l'observació que els gens que provoquen una malaltia tendeixen a agrupar-se, formant mòduls patogènics, i pel fet que podria caldre una actuació simultània sobre múltiples gens per assolir un efecte en el fenotipus de la malaltia. Per trobar compostos potencials, hem usat dades genòmiques exposades a compostos dipositades en bases de dades públiques. Hem recollit unes 20.000 mostres que han estat exposades a uns 1.800 compostos. L'expressió gènica es pot interpretar com un fenotip intermedi que reflecteix les vies moleculars desregulades subjacents a una malaltia. Per tant, considerem que els gens d'un mòdul patològic que responen, a nivell transcripcional, d'una manera similar a l'exposició del medicament tenen potencialment un efecte terapèutic. Hem aplicat aquesta estratègia a dades d'expressió gènica en illots pancreàtics humans corresponents a individus sans i diabètics, i hem identificat quatre compostos potencials (methimazole, pantoprazole, extracte de taronja amarga i torcetrapib) que podrien tenir un efecte positiu sobre la secreció de la insulina. Aquest és el primer cop que una xarxa reguladora d'illots pancreàtics humans s'ha utilitzat per reposicionar compostos per a T2D. En conclusió, aquesta tesi aporta dos enfocaments diferents en termes de vies moleculars a problemes bioinformàtics importants, com ho son el contrast de la funció biològica i el reposicionament de fàrmacs "in silico". Aquestes contribucions demostren el paper central de les anàlisis basades en vies moleculars a l'hora d'interpretar dades genòmiques procedents d'instruments d'alt rendiment.
Kwon, Jungeun Sarah, Nicholas J. Everetts, Xia Wang, Weikang Wang, Croce Kimiko Della, Jianhua Xing, and Guang Yao. "Controlling Depth of Cellular Quiescence by an Rb-E2F Network Switch." CELL PRESS, 2017. http://hdl.handle.net/10150/625987.
Full textChetty, Vasu Nephi. "Necessary and Sufficient Informativity Conditions for Robust Network Reconstruction Using Dynamical Structure Functions." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3810.
Full textKramer, Frank [Verfasser], Tim [Akademischer Betreuer] Beißbarth, and Stephan [Akademischer Betreuer] Waack. "Integration of Pathway Data as Prior Knowledge into Methods for Network Reconstruction / Frank Kramer. Gutachter: Tim Beißbarth ; Stephan Waack. Betreuer: Tim Beißbarth." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2014. http://d-nb.info/105990764X/34.
Full textBayerlová, Michaela [Verfasser], Tim [Akademischer Betreuer] Beißbarth, and Burkhard [Akademischer Betreuer] Morgenstern. "Pathway and network analyses in context of Wnt signaling in breast cancer / Michaela Bayerlová. Betreuer: Tim Beißbarth. Gutachter: Tim Beißbarth ; Burkhard Morgenstern." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2016. http://d-nb.info/108560196X/34.
Full textRubanova, Natalia. "MasterPATH : network analysis of functional genomics screening data." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC109/document.
Full textIn this work we developed a new exploratory network analysis method, that works on an integrated network (the network consists of protein-protein, transcriptional, miRNA-mRNA, metabolic interactions) and aims at uncovering potential members of molecular pathways important for a given phenotype using hit list dataset from “omics” experiments. The method extracts subnetwork built from the shortest paths of 4 different types (with only protein-protein interactions, with at least one transcription interaction, with at least one miRNA-mRNA interaction, with at least one metabolic interaction) between hit genes and so called “final implementers” – biological components that are involved in molecular events responsible for final phenotypical realization (if known) or between hit genes (if “final implementers” are not known). The method calculates centrality score for each node and each path in the subnetwork as a number of the shortest paths found in the previous step that pass through the node and the path. Then, the statistical significance of each centrality score is assessed by comparing it with centrality scores in subnetworks built from the shortest paths for randomly sampled hit lists. It is hypothesized that the nodes and the paths with statistically significant centrality score can be considered as putative members of molecular pathways leading to the studied phenotype. In case experimental scores and p-values are available for a large number of nodes in the network, the method can also calculate paths’ experiment-based scores (as an average of the experimental scores of the nodes in the path) and experiment-based p-values (by aggregating p-values of the nodes in the path using Fisher’s combined probability test and permutation approach). The method is illustrated by analyzing the results of miRNA loss-of-function screening and transcriptomic profiling of terminal muscle differentiation and of ‘druggable’ loss-of-function screening of the DNA repair process. The Java source code is available on GitHub page https://github.com/daggoo/masterPATH
Zhang, Xiaoxiao. "Cell Fate Decisions in Early Embryonic Development." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10792.
Full textPais, Gomes Luís Catarina [Verfasser], and Georg [Akademischer Betreuer] Köhr. "Linking addiction-related behavior to synaptic efficacy and network activity in the prefrontal-accumbal pathway of behaving rats / Catarina Pais Gomes Luís ; Betreuer: Georg Köhr." Heidelberg : Universitätsbibliothek Heidelberg, 2019. http://d-nb.info/1182317995/34.
Full textBenedetti, Elisa [Verfasser], Fabian J. [Akademischer Betreuer] Theis, Fabian J. [Gutachter] Theis, and Dmitrij [Gutachter] Frishman. "Elucidating protein glycosylation mechanisms by combining network-based pathway analysis with prior knowledge / Elisa Benedetti ; Gutachter: Fabian J. Theis, Dmitrij Frishman ; Betreuer: Fabian J. Theis." München : Universitätsbibliothek der TU München, 2019. http://d-nb.info/1201819695/34.
Full textLuís, Catarina [Verfasser], and Georg [Akademischer Betreuer] Koehr. "Linking addiction-related behavior to synaptic efficacy and network activity in the prefrontal-accumbal pathway of behaving rats / Catarina Pais Gomes Luís ; Betreuer: Georg Köhr." Heidelberg : Universitätsbibliothek Heidelberg, 2019. http://nbn-resolving.de/urn:nbn:de:bsz:16-heidok-243554.
Full textAnderson, Robyn. "Developing a pathway out of poverty in the Global Coffee Production Network - a case study of employment creation for baristas in the speciality coffee industry." Master's thesis, University of Cape Town, 2017. http://hdl.handle.net/11427/25185.
Full textPatel, Gajendra. "Implementing and Evaluating MQLAIP: A Metabolism Query Language." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1289591644.
Full textDuncan, Andrew Paul. "The analysis and application of artificial neural networks for early warning systems in hydrology and the environment." Thesis, University of Exeter, 2014. http://hdl.handle.net/10871/17569.
Full textMORANDO, VERDIANA. "Evaluating the performance of policy networks: connecting theories to organizational praxis. A case study analysis in Lombardy Region to evaluate the performance of the integrated care network managing the patway of persons with Spinal Cord Injury." Doctoral thesis, Università Cattolica del Sacro Cuore, 2012. http://hdl.handle.net/10280/1512.
Full textExperimental case study design for the performance evaluation of health care public services. The thesis is broken down into two main parts: the first part deals with the performance framework construction wherein the international theoretical literature and experiences realized are retrieved and discussed. The second part deliveries an experimental case study design to validate the framework proposed. The case studies focuses on the integrated care pathway for persons whit spinal cord injury/dysfunction. The policy network sets out the Regional policy making and the unity of analysis is a Spinal Unit specialized centre. The framework proved to be consistent and adapted for evaluating policy network for integrated care.
Dall'Olio, Giovanni Marco 1983. "Applications of network theory to human population genetics : from pathways to genotype networks." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/133454.
Full textEn esta tesis hemos desarrollado dos métodos para estudiar los patrones de selección positiva y adaptación genética en el genoma humano. Ambos métodos se basan en aplicaciones de teoría de redes. En la primera aplicación hemos investigado cómo las señales de selección están distribuidas a lo largo de una ruta metabólica. Hemos utilizado una representación de la ruta de N-Glicosilación, para estudiar si determinadas posiciones tienen más probabilidades de estar implicadas en eventos de selección positiva. Hemos comparado la distribución de las señales de selección entre la primera parte de la ruta metabólica, que tiene una estructura muy lineal y está involucrada en un proceso conservado, y la segunda parte de la ruta, que tiene una estructura de redes compleja y está involucrada en adaptación al ambiente. En la segunda aplicación hemos aplicado el concepto de redes de genotipos (Genotype Networks) a datos de secuencia de nueva generación. El resultado es un análisis completo de cómo las poblaciones de 1000 Genomas han explorado el espacio de genotipo. Las redes de genotipos de regiones codificantes suelen estar más conectadas y más expandidas que las regiones no-codificantes. Además, por medio de simulaciones hemos observado los patrones esperados para eventos de selección positiva.
Dondelinger, Frank. "Machine learning approach to reconstructing signalling pathways and interaction networks in biology." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7850.
Full textMeggiato, Alberto <1987>. "Comparing metabolic networks at pathway level." Master's Degree Thesis, Università Ca' Foscari Venezia, 2016. http://hdl.handle.net/10579/8501.
Full textFaust, Karoline. "Development, assessment and application of bioinformatics tools for the extraction of pathways from metabolic networks." Doctoral thesis, Universite Libre de Bruxelles, 2010. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210054.
Full textIn large metabolic networks, there are numerous ways to connect the seed reactions. The main problem of the graph-based prediction approach is to differentiate biochemically valid connections from others. Metabolic networks contain hub compounds, which are involved in a large number of reactions, such as ATP, NADPH, H2O or CO2. When a graph algorithm traverses the metabolic network via these hub compounds, the resulting metabolic pathway is often biochemically invalid.
In the first step of the thesis, an already existing approach to predict pathways from two seeds was improved. In the previous approach, the metabolic network was weighted to penalize hub compounds and an extensive evaluation was performed, which showed that the weighted network yielded higher prediction accuracies than either a raw or filtered network (where hub compounds are removed). In the improved approach, hub compounds are avoided using reaction-specific side/main compound an- notations from KEGG RPAIR. As an evaluation showed, this approach in combination with weights increases prediction accuracy with respect to the weighted, filtered and raw network.
In the second step of the thesis, path finding between two seeds was extended to pathway prediction given multiple seeds. Several multiple-seed pathay prediction approaches were evaluated, namely three Steiner tree solving heuristics and a random-walk based algorithm called kWalks. The evaluation showed that a combination of kWalks with a Steiner tree heuristic applied to a weighted graph yielded the highest prediction accuracy.
Finally, the best perfoming algorithm was applied to a microarray data set, which measured gene expression in S. cerevisiae cells growing on 21 different compounds as sole nitrogen source. For 20 nitrogen sources, gene groups were obtained that were significantly over-expressed or suppressed with respect to urea as reference nitrogen source. For each of these 40 gene groups, a metabolic pathway was predicted that represents the part of metabolism up- or down-regulated in the presence of the investigated nitrogen source.
The graph-based prediction of pathways is not restricted to metabolic networks. It may be applied to any biological network and to any data set yielding groups of associated genes, enzymes or compounds. Thus, multiple-end pathway prediction can serve to interpret various high-throughput data sets.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Steinberg, Julia. "Functional genomics analyses of neuropsychiatric and neurodevelopmental disorders." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:e47d1ac2-de92-47d8-864b-dac0bf6669e8.
Full textNeumann, Fabian. "Prozessmanagement in der Computertomographie unter Anwendung der Netzplantechnik." Doctoral thesis, [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974140201.
Full textBucci, Francesca. "Information and communication technologies nella gestione integrata del diabete mellito: stato dell'arte, progetto Metabo come caso di studio." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amslaurea.unibo.it/9306/.
Full textHara, Mariko. "We'll meet again : music in dementia care." Thesis, University of Exeter, 2013. http://hdl.handle.net/10871/8861.
Full textAjjolli, Nagaraja Anamya. "Modelling of Metabolic Pathways for Biomolecule Production in Cell-Free Systems." Thesis, La Réunion, 2020. http://www.theses.fr/2020LARE0004.
Full textCell-free systems (CFS) are emerging as a powerful platform for biomanufacturing. The optimisation of the cell-free system is important to achieve maximum yield. The experimental optimisation is time-consuming and expensive. Different kinds of modelling emerged in the last decades, helping to optimise the pathway of interest in a shorter time at a low cost. In this study, we tested two approaches: systemic through the implementation of neural networks, and analytical through the use of differential equations. In the first step, an artificial neural network model was built to predict the flux through the pathway, and in the second step, a new methodology termed GC-ANN was developed to select optimum and cost-efficient enzyme balances for higher flux. This approach showed unexpected betterment of flux estimation, up to 63%. In the third step, a kinetic model was built and estimation of kinetic parameters for selected enzymes was achieved to replicate experimental conditions. Finally, linked to one of the most demanding chemicals, malate synthesis pathway was successfully modelled in the cell-free system. Even though many studies have been performed, biomanufacturing has not yet been possible for malate. The combination of the cell-free system and modelling could help achieve the biomanufacturing of malate. Overall, this thesis explores different mathematical modelling approaches, and their limits, for optimising metabolic pathways
Sachs, Karen Ph D. Massachusetts Institute of Technology. "Bayesian network models of biological signaling pathways." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/38865.
Full textIncludes bibliographical references (p. 153-165).
Cells communicate with other cells, and process cues from their environment, via signaling pathways, in which extracellular cues trigger a cascade of information flow, causing signaling molecules to become chemically, physically or locationally modified, gain new functional capabilities, and affect subsequent molecules in the cascade, culminating in a phenotypic cellular response. Mapping the influence connections among biomolecules in a signaling cascade aids in understanding of the underlying biological process and in development of therapeutics for diseases involving aberrant pathways, such as cancer and autoimmune disease. In this thesis, we present an approach for automatically reverse-engineering the structure of a signaling pathway, from high-throughput data. We apply Bayesian network structure inference to signaling protein measurements performed in thousands of single cells, using a machine called a flow cytorneter. Our de novo reconstruction of a T-cell signaling map was highly accurate, closely reproducing the known pathway structure, and accurately predicted novel pathway connections. The flow cytometry measurements include specific perturbations of signaling molecules, aiding in a causal interpretation of the Bayesian network graph structure.
(cont.) However, this machine can measure only -4-12 molecules per cell, too few for effective coverage of a signaling pathway. To address this problem, we employ a number of biologically motivated assumptions to extend our technique to scale up from the number of molecules measured to larger models, using measurements of overlapping variable subsets. We demonstrate this approach by scaling up to a model of 11 variables, using 15 overlapping 4-variable measurements.
by Karen Sachs.
Ph.D.