Dissertations / Theses on the topic 'Genomic analysi'
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DI, CANITO ALESSANDRA. "Genomic and functional analysis of Rhodococcus strains to identify genes and degradative functions for soil quality evaluation." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2019. http://hdl.handle.net/10281/241307.
Full textSoil quality has been one of the major issues of the last decades, because of the increase of anthropogenic pollution. Soil contains organisms involved in vital functions (nutrient/hydrological cycles and degradation of toxic compounds). Under stress conditions, soil microorganisms undergo several alterations so molecular technologies use microbial communities as an ecological parameter in monitoring polluted sites. Bacteria belonging to Rhodococcus genus have an important role in recalcitrant compound degradations. It is a metabolically versatile genus, widely distributed in nature. Rhodococcus spp. can degrade a wide range of organic compounds (aliphatic/aromatic hydrocarbons, heterocyclic, nitriles, sulfuric, herbicides) and to survive in presence of toxic compounds, carbon starvation, UV irradiation and osmotic stress. In line with their catabolic diversity, they possess large and complex genomes, containing a multiplicity of catabolic genes, high genetic redundancy and a sophisticated regulatory network. The aim of this project is to obtain molecular tools to use as "marker" sequences for soil assessment, through analysis of metabolic pathways and catabolic gene clusters involved in the degradation of the most diffused environmental contaminants. In particular, this work focused the attention on three Rhodococcus strain genomes: R. opacus R7, R. aetherivorans BCP1 and R. erythropolis MI2. A Phenotype Microarray approach was used to evaluate R7 and BCP1 strains metabolic potential and their stress response. Also, the capability to utilize various contaminants (aliphatic hydrocarbons and cycloalkanes, aromatic compounds, polycyclic aromatic compounds, naphthenic acids and other carboxylic acids) and to persist under stress conditions (high osmolarity, pH stress, toxic compounds, antibiotics) was tested. A genome-based approach was used to relate their abilities to genetic determinants involved in the analysed metabolisms (naphthalene, o-xylene, n-alkanes, naphthenic acids, phenols, phthalate) and in their environmental persistence. In particular, o-xylene and naphthenic acids degradations were investigated in R. opacus R7. Computational and molecular analyses revealed the putative involvement of several genes in these degradation pathways. R7 can degrade o-xylene by the induction of the akb genes (deoxygenation) producing the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for monooxygenases/hydroxylases (prmA and pheA1A2A3), supports the involvement of other genes that induce the formation of phenols, converging to the phenol oxidation path. The activation of converging oxygenase systems represents a strategy in Rhodococcus genus to degrade recalcitrant compounds and to persist in contaminated environments. NAs degradation pathway is not fully clear but two main routes have been proposed: i) aromatization of the cyclohexane ring ii) activation as CoA thioester. RT and RT-qPCR results showed that R. opacus R7 degrade cyclohexanecarboxylic acid (CHCA) molecule (used as a model) by a cyclohexane carboxylate CoA ligase (aliA). An application of this work was demonstrated by a microcosm approach, simulating a bioaugmentation process with R7 strain. Autochthone bacteria and R7 capabilities to degrade CHCA were evaluated and compared; results indicated that R7 can degrade the contaminant faster than the microbial community and that its contribute increased CHCA degradation rate. The degradation rate was followed by RT and RT-qPCR, monitoring the expression of the aliA gene. Moreover, a biotechnological application was investigated in R. erythropolis MI2, studying the disulfide 4,4-dithiodibutyric acid (DTDB) degradation pathway. DTDB is a promising substrate for polythioester (PTE) synthesis; indeed, its degradation produces the PTE building block 4-mercaptobutyric acid. The aim was pursued generating R. erythropolis MI2 marker-free deletion mutants for genes involved in the final steps of the pathway.
Wong, Chi-fat, and 黃志發. "Genome sequencing and comparative genomic analysis of Pseudomonas mendocina DLHK." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hdl.handle.net/10722/197162.
Full textpublished_or_final_version
Biological Sciences
Master
Master of Philosophy
Bertoldi, Loris. "Bioinformatics for personal genomics: development and application of bioinformatic procedures for the analysis of genomic data." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421950.
Full textNell’ultimo decennio, l’enorme diminuzione del costo del sequenziamento dovuto allo sviluppo di tecnologie ad alto rendimento ha completamente rivoluzionato il modo di approcciare i problemi genetici. In particolare, il sequenziamento dell’intero esoma e dell’intero genoma stanno contribuendo ad un progresso straordinario nello studio delle varianti genetiche umane, aprendo nuove prospettive nella medicina personalizzata. Essendo un campo relativamente nuovo e in rapido sviluppo, strumenti appropriati e conoscenze specializzate sono richieste per un’efficiente produzione e analisi dei dati. Per rimanere al passo con i tempi, nel 2014, l’Università degli Studi di Padova ha finanziato il progetto strategico BioInfoGen con l’obiettivo di sviluppare tecnologie e competenze nella bioinformatica e nella biologia molecolare applicate alla genomica personalizzata. Lo scopo del mio dottorato è stato quello di contribuire a questa sfida, implementando una serie di strumenti innovativi, al fine di applicarli per investigare e possibilmente risolvere i casi studio inclusi all’interno del progetto. Inizialmente ho sviluppato una pipeline per analizzare i dati Illumina, capace di eseguire in sequenza tutti i processi necessari per passare dai dati grezzi alla scoperta delle varianti sia germinali che somatiche. Le prestazioni del sistema sono state testate mediante controlli interni e tramite la sua applicazione su un gruppo di pazienti affetti da tumore gastrico, ottenendo risultati interessanti. Dopo essere state chiamate, le varianti devono essere annotate al fine di definire alcune loro proprietà come la posizione a livello del trascritto e della proteina, l’impatto sulla sequenza proteica, la patogenicità, ecc. Poiché la maggior parte degli annotatori disponibili presentavano errori sistematici che causavano una bassa coerenza nell’annotazione finale, ho implementato VarPred, un nuovo strumento per l’annotazione delle varianti, che garantisce la migliore accuratezza (>99%) comparato con lo stato dell’arte, mostrando allo stesso tempo buoni tempi di esecuzione. Per facilitare l’utilizzo di VarPred, ho sviluppato un’interfaccia web molto intuitiva, che permette non solo la visualizzazione grafica dei risultati, ma anche una semplice strategia di filtraggio. Inoltre, per un’efficace prioritizzazione mediata dall’utente delle varianti umane, ho sviluppato QueryOR, una piattaforma web adatta alla ricerca all’interno dei geni causativi, ma utile anche per trovare nuove associazioni gene-malattia. QueryOR combina svariate caratteristiche innovative che lo rendono comprensivo, flessibile e facile da usare. La prioritizzazione è raggiunta tramite un processo di selezione positiva che fa emergere le varianti maggiormente significative, piuttosto che filtrare quelle che non soddisfano i criteri imposti. QueryOR è stato usato per analizzare i due casi studio inclusi all’interno del progetto BioInfoGen. In particolare, ha permesso di scoprire le varianti causative dei pazienti affetti da malattie da accumulo lisosomiale, evidenziando inoltre l’efficacia del pannello di sequenziamento sviluppato. Dall’altro lato invece QueryOR ha semplificato l’individuazione del gene LRP2 come possibile candidato per spiegare i soggetti con un fenotipo simile alla malattia di Dent, ma senza alcuna mutazione nei due geni precedentemente descritti come causativi, CLCN5 e OCRL. Come corollario finale, è stata effettuata un’analisi estensiva su varianti esomiche ricorrenti, mostrando come la loro origine possa essere principalmente spiegata da imprecisioni nel genoma di riferimento, tra cui regioni mal assemblate e basi non corrette, piuttosto che da errori piattaforma-specifici.
Mungall, Christopher. "Next-generation information systems for genomics." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5020.
Full textChen, Yuansha. "Comparative genomic analysis of Vibrio cholerae O31 capsule, O-antigen, pathogenesis and genome /." College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/4112.
Full textThesis research directed by: Marine-Estuarine-Environmental Sciences. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
Danks, Jacob R. "Algorithm Optimizations in Genomic Analysis Using Entropic Dissection." Thesis, University of North Texas, 2015. https://digital.library.unt.edu/ark:/67531/metadc804921/.
Full textSinha, Amit U. "Discovery and analysis of genomic patterns applications to transcription factor binding and genome rearrangement /." Cincinnati, Ohio : University of Cincinnati, 2008. http://www.ohiolink.edu/etd/view.cgi?1204227723.
Full textAdvisor: Raj Bhatnagar. Title from electronic thesis title page (viewed April 24, 2008). Keywords: computational biology; bioinformatics; transcription factor; genome rearrangement. Includes abstract. Includes bibliographical references.
Morlot, Jean-Baptiste. "Annotation of the human genome through the unsupervised analysis of high-dimensional genomic data." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066641/document.
Full textThe human body has more than 200 different cell types each containing an identical copy of the genome but expressing a different set of genes. The control of gene expression is ensured by a set of regulatory mechanisms acting at different scales of time and space. Several diseases are caused by a disturbance of this system, notably some cancers, and many therapeutic applications, such as regenerative medicine, rely on understanding the mechanisms of gene regulation. This thesis proposes, in a first part, an annotation algorithm (GABI) to identify recurrent patterns in the high-throughput sequencing data. The particularity of this algorithm is to take into account the variability observed in experimental replicates by optimizing the rate of false positive and false negative, increasing significantly the annotation reliability compared to the state of the art. The annotation provides simplified and robust information from a large dataset. Applied to a database of regulators activity in hematopoiesis, we propose original results, in agreement with previous studies. The second part of this work focuses on the 3D organization of the genome, intimately linked to gene expression. This structure is now accessible thanks to 3D reconstruction algorithm from contact data between chromosomes. We offer improvements to the currently most efficient algorithm of the domain, ShRec3D, allowing to adjust the reconstruction according to the user needs
SINHA, AMIT U. "Discovery and Analysis of Genomic Patterns: Applications to Transcription Factor Binding and Genome Rearrangement." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1204227723.
Full textSchiavo, Giuseppina <1986>. "Analysis of the pig genome for the identification of genomic regions affecting production traits." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6919/1/Schiavo_Giuseppina_Tesi_Dottorato_XVII_ciclo.pdf.
Full textSchiavo, Giuseppina <1986>. "Analysis of the pig genome for the identification of genomic regions affecting production traits." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6919/.
Full textOlivares, Chauvet Pedro. "Multi-scale analysis of chromosome and nuclear architecture." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/multiscale-analysis-of-chromosome-and-nuclear-architecture(32a7b634-035b-4c6b-83f9-735f83bc73fb).html.
Full textNg, Esther. "Integration of genetic data and genomic annotation in the analysis of genome wide association studies." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:fd0d2dab-d52c-4d8c-9321-5e88628bf528.
Full textSantos-Silva, Alan Roger 1981. "Analise das caracteristicas clinico-patologicas e da ploidia do DNA em pacientes jovens com carcinoma espinocelular de lingua : um estudo colaborativo internacional." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/287850.
Full textTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba
Made available in DSpace on 2018-08-15T17:55:17Z (GMT). No. of bitstreams: 1 Santos-Silva_AlanRoger_D.pdf: 1071923 bytes, checksum: 996d56a5e4895653ebcd0b9e1636e7e2 (MD5) Previous issue date: 2010
Resumo: Predominantemente, o carcinoma espinocelular (CEC) de boca afeta pacientes idosos e com frequência se desenvolve em associação com o consumo de fumo e álcool. Todavia, evidências científicas têm sugerido o aumento da incidência desta malignidade em pacientes com menos de 40 anos de idade e não expostos aos tradicionais fatores de risco. Informações disponíveis referentes ao câncer de boca em pacientes jovens são escassas e controversas, dificultando a compreensão da patogênese, do comportamento biológico e do prognóstico destes tumores. Como consequência, seu tratamento tem sido baseado principalmente na experiência profissional de cada centro médico. Este trabalho teve como objetivos estudar as características demográficas, os fatores de risco e os aspectos clínicos no momento do diagnóstico, além do perfil biológico de CECs de língua em pacientes com até 40 anos. Foi realizada uma análise retrospectiva multiinstitucional a fim de se investigar gênero, cor da pele, consumo de tabaco e álcool, tamanho dos tumores, metástase regional e à distância, diferenciação histológica e ploidia do DNA dos tumores por meio de citometria por imagem. Os resultados mostraram que tumores em pacientes jovens foram frequentemente detectados em mulheres e pacientes não fumantes e não etilistas, enquanto em pacientes idosos foram detectados, predominantemente, em homens fumantes e etilistas. Além disso, constatou-se que CECs de língua em jovens não se distinguem quanto ao tamanho, a metástases regionais ou à distância e nem quanto ao grau de diferenciação histológica quando comparados com idosos. Ressalta-se, entretanto, que tumores em jovens apresentaram maiores incidências de aneuploidia, tetraploidia e de outros parâmetros de anormalidades da ploidia do DNA. Concluindo, pacientes jovens com CEC de língua apresentaram perfil clínico e biológico peculiares, favorecendo a hipótese de que pacientes jovens com CEC de boca possuem instabilidade genômica aumentada e indicando uma possível natureza genética diferente entre os CECs de língua de jovens e de idosos
Abstract: Oral squamous cell carcinoma (SCC) predominately affects elderly patients and frequently develops in association with tobacco and alcohol consumption. However, an increasing of this malignant disease has been observed in patients younger than 40 years of age, who are not exposed to the traditional risk factors. Data regarding oral cancer in young patients are scarce and controversial, making the determination of the pathogenesis, biological behaviour and prognosis of these tumours difficult. As a consequence, treatment has been mainly based on the professional experience of each medical centre. The aims of this work were to study demographic features, risk factors and clinical aspects at the moment of diagnosis as well as the biologic profile of patients of less than 40 years of age with tongue SCC. A multi-centre retrospective analysis was performed to investigate gender, race, tobacco consumption and alcohol intake, size of the tumour, regional and distant metastasis, histological differentiation and DNA ploidy of tumours through image cytometry. Tumours in young patients were frequently detected in females and nonsmoking and non-drinking patients while older patients were predominantly smoking and drinking males. In addition, tongue SCC in young patients did not differ in size, regional and distant metastasis or tumour grade of differentiation when compared to those in older patients. This study highlighted that tumours from young patients presented higher incidences of aneuploidy, tetraploidy and other parameters related to DNA ploidy abnormalities. In conclusion, young patients with tongue SCC presented a distinct clinical and biological profile, favouring the hypothesis that young patients with oral SCC may have an increased genomic instability and indicating the possibility of underlying genetic differences between TSCC in young and older patients
Doutorado
Patologia
Doutor em Estomatopatologia
Jiang, Sheng. "Application of nested PCR, whole genome amplification and comparative genomic hybridisation for single cell genetic analysis." Thesis, University of Glasgow, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366140.
Full textGlen, McGillivary. "Comparative Genomic Analysis Between the Haemophilus influenzae biogroup aegyptius Brazilian Purpuric Fever Invasive Strain F3031 and the Haemophilus influenzae biogroup aegyptius Non-invasive Strain F1947." Miami University / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=miami1088607238.
Full textKittler, Ralf. "Functional genomic analysis of cell cycle progression in human tissue culture cells." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2006. http://nbn-resolving.de/urn:nbn:de:swb:14-1161253856455-48321.
Full textSelman, Mohammed. "Genomic Analysis of Encephalitozoon Species." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30314.
Full textTam, Mandy Chi-Mun. "Genomic analysis of mouse tumorigenesis." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37454.
Full textIncludes bibliographical references.
The availability of the human and mouse genome sequences has spurred a growing interest in analyzing mouse models of human cancer using genomic techniques. Comparative genomic studies on mouse and human tumors can be valuable in two major ways: in validating mouse models and in identifying genes that are common to mouse and human tumorigenesis. Many analytic tools have emerged in recent years for human genome mining. Some of these tools have been translated to the murine versions. The work in this thesis described the application of two new whole-genome analytic techniques to study mouse tumorigensis: Representational Oligonucleotide Microarray Analysis (ROMA) for tumor DNA copy number asessment and single nucleotide polymorphism (SNP) genotyping using the SNaPshotM system (Applied Biosystems) to detect loss of heterozygosity (LOH) in mouse tumors. The murine version of ROMA was tested on DNA from early-stage KrasGJ2D-derived lung cancers and metastatic retinoblastoma in mice with retinal-specific Rb and p130 deletions. We were interested in identifying the additional genetic lesions that got positively selected during tumorigenesis of these mice.
(cont.) Several recurrent chromosomal copy number gains and losses were observed in the DNA of KrasGJ2D-derived lung tumors. In addition, a focal amplification of the murine N-Myc locus was detected in the metastatic retinoblastomas, demonstrating the capability of ROMA to detect copy number changes at a single-gene resolution. For genome-wide allelotyping, a panel of 147 mouse SNPs were individually validated in 129S4/SvJae vs. C57BL/6J strains and were chosen as markers in the genotyping panel. We worked out a multiplex protocol to genotype the SNPs in an efficient manner. Through this protocol, we generated low-density global LOH maps of lung tumors from mice expressing KrasG12D. LOH that spanned entire chromosomes was seen in a subset of the tumors. A loss of the wild-type p53 allele was also observed in some cases.
by Mandy Chi-Mun Tam.
Ph.D.
Revilla, Sánchez Manuel. "Genomic and functional genomic analysis of fatty acid composition in swine." Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/405710.
Full textPork is one of the main sources of human-consumed meat and consumer’s preference towards high quality meat is increasing. Hence, understanding the molecular mechanisms affecting meat production and quality would help in the selection of these traits. Meat quality is determined largely by its fatty acid (FA) composition and understanding the underlying molecular processes of FA composition is the general objective of this thesis. We analyzed quantitative trait loci (QTL) on porcine chromosome 8 (SCC8) for FA composition in backfat, identifying two trait-associated SNP regions at 93 Mb and 119 Mb. The strongest statistical signals for both regions were observed for palmitoleic acid and, C18:0/C16:0 and C18:1(n-7)/C16:1(n-7) elongation ratios. MAML3 and SETD7 genes were analyzed as positional candidate genes in the 93 Mb region. The two novel microsatellites analyzed in the MAML3 gene, and the SETD7:c.700G>T SNP in the SETD7 gene did not show the strongest signal in this region, discarding these polymorphisms as the causal mutations. Furthermore, in the 119 Mb region, the ELOVL6:c.-533C>T SNP showed a strong association with the percentage of palmitic and palmitoleic acids and elongation ratios in backfat. These results for ELOVL6 gene, support the hypothesis that it has a pleiotropic effect in backfat and muscle for the 119 Mb QTL, and reinforce this gene as a strong candidate for the SSC8 QTL for FA composition. Moreover, whole genome sequence (WGS) data from Iberian and Landrace pigs were used to identify 1,279 copy number variations (CNVs), merging into 540 swine CNV regions (CNVRs). The impact of four of them in growth and FA composition in intramuscular fat and backfat was studied. Association with carcass length and FA composition in backfat and intramuscular fat was showed for the CNVR112, containing the GPAT2 gene which catalyse the biosynthesis of triglycerides and glycerophospholipids. These results underline the importance of CNVRs affecting economically important traits in pigs. Finally, the adipose tissue mRNA expression of 44 candidate genes related with lipid metabolism was analyzed in 115 animals. The expression genome-wide association (eGWAS) identified 193 eSNPs located in 19 expression QTLs (eQTLs). Three out of 19 eQTLs corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs had trans-regulatory effects. These findings and the polymorphisms evaluated for some of these genes provide new data to further understand the functional mechanisms implicated in the variation of meat quality traits in pigs.
Lorentzen, Marc. "Diversity and genomic characteristics of Oenococcus oeni." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0428.
Full textOenococcus oeni is a lactic acid bacteria species adapted to the inhospitable environment of fermenting wine, where it shows a remarkable degree of specialization to the stress of low pH and high ethanol that allows it to proliferate where most bacteria fail to survive. The bacteria is supremely important in wine production, because it carries out malolactic fermentation, a process that occurs after alcoholic fermentation, where malic acid is metabolised into lactic acid and the pH of the wine is raised. The species has only a small genome and accumulates mutations several orders of magnitude faster than other lactic acid bacteria due to a loss of DNA mismatch repair genes. This has likely sped up the process of domestication to wine. The degree of specialization has been demonstrated by finding specific populations adapted to red or white wines in the same region. In this study, we used high throughput sequencing and genomics approaches to elucidate the diversity of O. oeni strains, to identify their genomic characteristics and measure their dispersion in different environments as well as their dynamics during fermentation. Because of its importance to wine-making, several hundred strains have been isolated and sequenced. In this work, we have expanded upon the collection of genomes by sequencing strains from cider and kombucha and performing phylogenetic analyses to clarify the population structure of the species. By calculating a species-wide pangenome, we performed comparative genomics to explore gene clusters that were specific to one or more sub-populations. With next generation sequencing, we produced fully circularized genomes from the major sub-populations and analysed their genomic arrangements. These new genomes were annotated with new, automatic pipelines and manual curation for the first time since the publication of the reference genome PSU-1. The evolution of bacterial communities over the course of fermentation, from grape must to finished wine, was examined with 16S amplicon sequencing in four Bordeaux wineries. Using a universal and a specific primer-set, we compared the biodiversity in wines resulting from organic or conventional farming practices. In addition, with the newly defined phylogenetic groups, we developed a qPCR experiment to detail the composition of O. oeni in the fermentations and cemented the dispersal of even rarely isolated strain sub-populations in grape must. This new method was also used to analyse the diversity of O. oeni strains in the base wines of Cognac and during the production of cider, two products that are distinguished from traditional wine production by not using sulfite. The two other species in the Oenococcus genus, kitaharae and alcoholitolerans, are also found in the environments of fermenting beverages. O. kitaharae does not have a functional malolactic gene, but the more recently discovered O. alcoholitolerans was thought capable of performing the malolactic reaction. We characterized this, as well as the species tolerance for the stressors of the wine environment. Finding it unable to survive in wine, we produced a fully circularized genome of O. alcoholitolerans and performed a comparative genomics analysis to identify the O. oeni genes that enable it to tolerate the pH and ethanol, which O. alcoholitolerans and O. kitaharae lacks. In conclusion, we have used the new technologies of next generation sequencing to produce high-quality genomes and performed extensive, species-wide comparative analyses that allowed us to identify patterns in gene presence that provide likely explanations for environmental adaptation
Roberts, Nicola Diane. "Patterns of somatic genome rearrangement in human cancer." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275454.
Full textPolke, James. "Functional genomics in the stroke-prone spontaneously hypertensive rat genome wide and candidate gene analysis /." Connect to e-thesis, 2008. http://theses.gla.ac.uk/258/.
Full textPh.D. thesis submitted to the Faculty of Medicine, Division of Cardiovascular and Medical Sciences, University of Glasgow, 2008. Includes bibliographical references. Print version also available.
Polke, James M. "Functional genomics in the stroke-prone spontaneously hypertensive rat : genome wide and candidate gene analysis." Thesis, University of Glasgow, 2008. http://theses.gla.ac.uk/258/.
Full textTennant, Peter Andrew. "Genome editing using site-specific nucleases : targeting highly expressed genomic regions for robust transgene expression and genetic analysis." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/22857.
Full textShaw, Daniel 1993. "Streamlining minimal bacterial genomes : Analysis of the pan bacterial essential genome, and a novel strategy for random genome deletions in Mycoplasma pneumoniae." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/668244.
Full textDiscernir cuales son los componentes que podrían constituir una célula mínima es un desafío clave para la Biología Sintética. En esta tesis, se presentan dos nuevas herramientas para facilitar esta tarea. (i) Una nueva metodología para minimizar el genoma de Mycoplasma pneumoniae mediante la deleción aleatoria de material genético. Esta técnica combina el sistema Cre/lox con la mutagénesis aleatoria mediada por transposones para generar poblaciones bacterianas en las que los sitios lox están distribuidos de manera aleatoria a lo largo de su genoma. Esto permite la generación de poblaciones bacterianas en las que el tamaño de las deleciones efectuadas varia desde 50 pb hasta 25 kb. (ii) El primer análisis a gran escala de la esencialidad genética en múltiples especies bacterianas, y cómo la composición y función del grupo de genes esenciales de una bacteria cambia en función de la complejidad de su genoma.
Stranneheim, Henrik. "Enabling massive genomic and transcriptomic analysis." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45957.
Full textQC 20111115
Ao, Sio-iong. "Data mining algorithms for genomic analysis." Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/hkuto/record/B38319822.
Full textAo, Sio-iong, and 區小勇. "Data mining algorithms for genomic analysis." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B38319822.
Full textWilliamson, Daniel. "Genomic and expression analysis of Rhabdomysarcoma." Thesis, Institute of Cancer Research (University Of London), 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406321.
Full textRaab, R. Michael. "Genomic analysis of hepatic insulin resistance." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33762.
Full textIncludes bibliographical references (leaves 159-191).
Type II Diabetes mellitus is a genetically complex disease characterized by insulin resistance in peripheral tissues, which results in simultaneous hyperglycemia and hyperinsulinemia. Because of the prevalence of type II diabetes, many researchers are investigating the genetics of glucose homeostasis, however, traditional mapping techniques have not been successful in determining all of the genes that regulate glycemia. To complement these efforts, we used DNA microarrays to find differentially expressed genes and combinatorial siRNA screening to investigate the effects of hepatic gene transcription during periods of high and low glucose production. This strategy provides a new approach to studying the molecular mechanisms of disease pathogenesis. Our investigations focused on discovering new genes that influence hepatic metabolism and glucose production. Hepatocytes help maintain whole body glycemia by providing glucose and other substrates during non-feeding periods. DNA microarrays containing 17,000 unique gene probes were used to study hepatic gene transcription during normal, insulin resistant, and fasting states in C57/BL/6J mice. We analyzed this data set using a combination of statistical and multivariate techniques to determine 41 different, genes that are differentially expressed and highly discriminatory of the treatment groups.
(cont.) Hepatocytes perform many physiological roles, thus to investigate which genes from the microarray analysis affected hepatic metabolism, we developed combinatorial RNA-interference (RNAi) based gene silencing techniques. Using combinatorial siRNA screening, we silenced genes that were over-expressed within the microarray data set to study loss of function effects on hepatic metabolism, which was quantified by measuring intracellular metabolite concentrations in relevant metabolic pathways. Based upon the metabolite dependent clustering of experimental and control samples using Fisher Discriminant Analysis, four of the silenced genes had a significant effect on key metabolites involved in hepatic glucose output. Of these four genes, three were shown to influence hepatic glucose output in our primary cell model.
by R. Michael Raab.
Ph.D.
Alqahtani, Khaled Mubarek A. "Survival analysis based on genomic profiles." Thesis, University of Leeds, 2016. http://etheses.whiterose.ac.uk/16471/.
Full textPratas, Diogo. "Compression and analysis of genomic data." Doctoral thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/16286.
Full textGenomic sequences are large codi ed messages describing most of the structure of all known living organisms. Since the presentation of the rst genomic sequence, a huge amount of genomics data have been generated, with diversi ed characteristics, rendering the data deluge phenomenon a serious problem in most genomics centers. As such, most of the data are discarded (when possible), while other are compressed using general purpose algorithms, often attaining modest data reduction results. Several speci c algorithms have been proposed for the compression of genomic data, but unfortunately only a few of them have been made available as usable and reliable compression tools. From those, most have been developed to some speci c purpose. In this thesis, we propose a compressor for genomic sequences of multiple natures, able to function in a reference or reference-free mode. Besides, it is very exible and can cope with diverse hardware speci cations. It uses a mixture of nite-context models (FCMs) and eXtended FCMs. The results show improvements over state-of-the-art compressors. Since the compressor can be seen as a unsupervised alignment-free method to estimate algorithmic complexity of genomic sequences, it is the ideal candidate to perform analysis of and between sequences. Accordingly, we de ne a way to approximate directly the Normalized Information Distance, aiming to identify evolutionary similarities in intra- and inter-species. Moreover, we introduce a new concept, the Normalized Relative Compression, that is able to quantify and infer new characteristics of the data, previously undetected by other methods. We also investigate local measures, being able to locate speci c events, using complexity pro les. Furthermore, we present and explore a method based on complexity pro les to detect and visualize genomic rearrangements between sequences, identifying several insights of the genomic evolution of humans. Finally, we introduce the concept of relative uniqueness and apply it to the Ebolavirus, identifying three regions that appear in all the virus sequences outbreak but nowhere in the human genome. In fact, we show that these sequences are su cient to classify di erent sub-species. Also, we identify regions in human chromosomes that are absent from close primates DNA, specifying novel traits in human uniqueness.
As sequências genómicas podem ser vistas como grandes mensagens codificadas, descrevendo a maior parte da estrutura de todos os organismos vivos. Desde a apresentação da primeira sequência, um enorme número de dados genómicos tem sido gerado, com diversas características, originando um sério problema de excesso de dados nos principais centros de genómica. Por esta razão, a maioria dos dados é descartada (quando possível), enquanto outros são comprimidos usando algoritmos genéricos, quase sempre obtendo resultados de compressão modestos. Têm também sido propostos alguns algoritmos de compressão para sequências genómicas, mas infelizmente apenas alguns estão disponíveis como ferramentas eficientes e prontas para utilização. Destes, a maioria tem sido utilizada para propósitos específicos. Nesta tese, propomos um compressor para sequências genómicas de natureza múltipla, capaz de funcionar em modo referencial ou sem referência. Além disso, é bastante flexível e pode lidar com diversas especificações de hardware. O compressor usa uma mistura de modelos de contexto-finito (FCMs) e FCMs estendidos. Os resultados mostram melhorias relativamente a compressores estado-dearte. Uma vez que o compressor pode ser visto como um método não supervisionado, que não utiliza alinhamentos para estimar a complexidade algortímica das sequências genómicas, ele é o candidato ideal para realizar análise de e entre sequências. Em conformidade, definimos uma maneira de aproximar directamente a distância de informação normalizada (NID), visando a identificação evolucionária de similaridades em intra e interespécies. Além disso, introduzimos um novo conceito, a compressão relativa normalizada (NRC), que é capaz de quantificar e inferir novas características nos dados, anteriormente indetectados por outros métodos. Investigamos também medidas locais, localizando eventos específicos, usando perfis de complexidade. Propomos e exploramos um novo método baseado em perfis de complexidade para detectar e visualizar rearranjos genómicos entre sequências, identificando algumas características da evolução genómica humana. Por último, introduzimos um novo conceito de singularidade relativa e aplicamo-lo ao Ebolavirus, identificando três regiões presentes em todas as sequências do surto viral, mas ausentes do genoma humano. De facto, mostramos que as três sequências são suficientes para classificar diferentes sub-espécies. Também identificamos regiões nos cromossomas humanos que estão ausentes do ADN de primatas próximos, especificando novas características da singularidade humana.
Wang, Yehong. "Analysis of heterochromatin-associated genomic instability." Diss., [Riverside, Calif.] : University of California, Riverside, 2009. http://proquest.umi.com/pqdweb?index=0&did=1957340941&SrchMode=2&sid=1&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1268763263&clientId=48051.
Full textIncludes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed March 16, 2010). Includes bibliographical references. Also issued in print.
Adhikari, Bishwo. "Genomic Analysis of Nematode-Environment Interaction." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2578.
Full textSambo, Francesco. "Advanced Algorithms for Genomic Data Analysis." Doctoral thesis, Università degli studi di Padova, 2010. http://hdl.handle.net/11577/3426964.
Full textObiettivo del presente lavoro di tesi è lo sviluppo di tecniche algoritmiche innovative per l’identificazione di relazioni causali fra i geni di un organismo a partire da esperimenti di DNA microarray. Le relazioni causa-effetto fra i geni possono essere apprese a partire dai dati di microarray (Reverse Engineering) e riassunte in una Rete di Regolazione Genica, un grafo i cui nodi rappresentano i geni e i cui archi rappresentano le relazioni causali fra i geni: questa tesi presenta tre algoritmi innovativi di Reverse Engineering, progettati per elaborare diversi tipi di esperimenti di microarray e con diversi livelli di dettaglio nella descrizione dei sistemi biologici, e due studi sulla difficoltà nell'inferire le Reti di Regolazione Genica. Il primo contributo originale della tesi è l'applicazione del Ragionamento Qualitativo all’elaborazione di misurazioni in stato stazionario di esperimenti di perturbazione sistematica dei geni, vale a dire esperimenti nei quali l’espressione di ogni gene a turno viene alterata e un solo campione dell’espressione genica viene misurato ogni volta che il sistema raggiunge lo stato stazionario. Il secondo algoritmo proposto, CNET, è basato su una funzione euristica progettata per identificare relazioni causali a partire da serie temporali di espressione genica, cioè osservazioni ripetute dello stesso sistema biologico in istanti temporali consecutivi. L'algoritmo è costruito in modo tale da riconoscere le relazioni causali anche in presenza di rumore e di ritardi variabili nella regolazione. Successivamente vengono presentati due studi approfonditi, il primo sulle relazioni fra la performance di due algoritmi di Reverse Engineering e le proprietà strutturali e topologiche della Rete di Regolazione Genica da inferire e il secondo sul panorama di fitness attorno alla configurazione ottima dei parametri di una particolare classe di sistemi dinamici non lineari, le Reti Neurali Dinamiche Ricorsive, che descriva un insieme di serie temporali di espressione genica. Entrambi gli studi hanno consentito di ottenere informazioni utili e originali sulla difficoltà nell'inferire Reti di Regolazione Genica a partire da dati di DNA microarray. Infine, viene presentato un algoritmo innovativo di ottimizzazione mista (continua e discreta) per il fit di sistemi di equazioni differenziali non lineari a esperimenti contenenti serie temporali di espressione genica su piccola scala, composto di due moduli interagenti: una procedura di ricerca locale per esplorare lo spazio discreto delle strutture di rete e una procedura di ottimizzazione continua per l’idenficazione dei parametri ottimi del sistema. La performance dei tre algoritmi proposti viene analizzata sia su dati simulati sia, in certi casi, su dati reali di DNA microarray: i metodi si dimostrano competitivi con lo stato dell’arte degli algoritmi di Reverse Engineering.
Schlueter, Shannon Dwayne. "Plant genome informatics evaluation and analysis of genomic DNA features involved in the transcriptional processing of protein coding genes /." [Ames, Iowa : Iowa State University], 2006.
Find full textJi, Boyang. "Comparative and Functional Genome Analysis of Magnetotactic Bacteria." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM4065.
Full textMagnetotactic bacteria (MTB) are a diverse group of aquatic prokaryotes, which synthesize membrane-Enclosed magnetic crystals known as magnetosomes. In this thesis, the genome sequences of two marine MTB strains, Magnetospira sp. QH-2 and magneto-Ovoid strain MO-1 were analyzed. The magnetosome gene cluster synteny and mam gene correlation indicate that the insertion of the magnetosome island into QH-2 chromosome occurred after divergence between freshwater and marine magnetospirilla. Comparative genomic analysis revealed three distinct groups of sequenced MTB strains: Group I with Magnetospirillum spp. strains and Magnetospira strain, Group II with MO-1 strain and M. marinus MC-1, and Group III including Desulfovibrio magneticus RS-1. In addition, it shows an adaptive evolution of two marine MTB strains to marine sediments in comparison with closely related freshwater species. Moreover, comparative metabolic network analysis reveals high level of intra-Group similarity and inter-Group variety in MTB. With anoxic network enzymes, potential “MTB” strains are predicted, and are consistent with recently isolated MTB strains. It suggested that the anoxic metabolic network might be one restricted constraint for MTB distribution in bacterial lineages. Interestingly, analyses from ribosomal proteins to the whole MTB genome strongly support a taxonomic chimeric nature of MO-1 and MC-1 genes, and may represent a novel Proteobacteria lineage. Additionally, I also participate to genome analyses of piezophilic Desulfovibrio and Phaeospirillum molischianum strains as well as genome-Wide analysis of bacterial tyrosine kinases
Håfström, Therese. "Genome closure and bioinformatic analysis of the parallel sequenced bacterium Brachyspira intermedia PWS/AT." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-164335.
Full textFeng, Yuanjian. "Detection and Characterization of Multilevel Genomic Patterns." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/38577.
Full textPh. D.
Eversley, Chevonne D. Threadgill David W. "Integrative genomic analysis of sporadic colorectal cancer." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2874.
Full textTitle from electronic title page (viewed Jun. 4, 2010). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Curriculum in Genetics and Molecular Biology." Discipline: Genetics and Molecular Biology; Department/School: Medicine.
Koerner, Henrike. "Analysis of genomic alterations in malignant melanoma." Diss., lmu, 2007. http://nbn-resolving.de/urn:nbn:de:bvb:19-77810.
Full textSantani, Avni Bhawan. "Genomic analysis of the horse Y chromosome." Texas A&M University, 2004. http://hdl.handle.net/1969.1/1494.
Full textClifford, Raphael. "Indexed strings for large scale genomic analysis." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.268368.
Full textDuangsonk, Kwanjit. "Genomic and genetic analysis of Burkholderia pseudomallei." Thesis, University of Liverpool, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437528.
Full textFrampton, Garrett M. "Genomic analysis of control of cell type." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/62777.
Full textCataloged from PDF version of thesis.
Includes bibliographical references.
In mammalian development, a single fertilized egg grows into a complex organism, comprised of organs and tissues made up of hundreds of different specialized cell types. All of these cells contain the same genome, but express distinct sets of genes and proteins, which give the cells their specialized functions. Understanding how this process occurs is one of the fundamental goals of biology. Research using new technology for high-resolution genome-wide location analysis and gene expression profiling has allowed characterization of the transcriptional regulatory circuitry of cells in unprecedented detail. From this research emerges an improved understanding of how these cells work, how they malfunction in disease, and several general principles. This thesis describes several studies designed to understand the transcriptional regulatory circuitry of three different medically important cell types; embryonic stem cells, regulatory T cells and MLL leukemia cells.
by Garrett M. Frampton.
Ph.D.
Pengelly, Reuben. "Genomic data analysis : populations, patients & pipelines." Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/397102/.
Full textLiu, Yiding. "Technologies for Proteomic and Genomic Biomarker Analysis." Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1229461302.
Full textTennant, Richard Kenneth. "Genomic analysis of microfossils in lake sediments." Thesis, University of Exeter, 2015. http://hdl.handle.net/10871/20649.
Full textManser, Paul. "Methods for Integrative Analysis of Genomic Data." VCU Scholars Compass, 2014. http://scholarscompass.vcu.edu/etd/3638.
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