Дисертації з теми "Genomics analyses"
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Seibert, Sara Rose. "Host-parasite interactions: comparative analyses of population genomics, disease-associated genomic regions, and host use." Wright State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=wright1590585260282244.
Повний текст джерелаSteinberg, 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.
Повний текст джерелаBeghini, Francesco. "Integrative computational microbial genomics for large-scale metagenomic analyses." Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/296396.
Повний текст джерелаShultz, Randall William. "Genomic and Molecular Analyses of the Core DNA Replication Machinery in Plants." NCSU, 2007. http://www.lib.ncsu.edu/theses/available/etd-03132007-124000/.
Повний текст джерелаHerzog, Rebecca [Verfasser]. "Global change genomics - comparative genomic analyses on environmental associated speciation and adaptation processes in Odonata / Rebecca Herzog." Hannover : Gottfried Wilhelm Leibniz Universität, 2021. http://d-nb.info/1238221785/34.
Повний текст джерелаSoares, Siomar de Castro. "Pan-genomic analyses of Corynebacterium pseudotuberculosis and characterization of the biovars ovis and equi through comparative genomics." Universidade Federal de Minas Gerais, 2013. http://hdl.handle.net/1843/BUOS-9B8JTZ.
Повний текст джерелаItou, Junji. "Functional and comparative genomics analyses of pmp22 in medaka fish." Kyoto University, 2009. http://hdl.handle.net/2433/126464.
Повний текст джерелаDumitriu, Alexandra. "Genome-wide expression and genomic data integration analyses in sporadic Parkinson disease." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31542.
Повний текст джерелаParkinson disease (PD) is the second most common neurodegenerative disorder, affecting an estimated 2% of the population above 65 years of age. Although familial forms of PD have been linked to specific mutations responsible for the onset of the disease, the majority of PD cases is still of unknown etiology. PD has been traditionally studied using individual genetic methods, such as linkage analysis, genome-wide association (GWAS), or microarray expression studies. Nevertheless, the intrinsic disease genetic variability, and the unilateral analysis approach of available datasets made the detection of robust gene or pathway signals difficult. Studies of PD that combine a range of systems genetics approaches, and integrate complementary disease-relevant genetic datasets, represent a promising approach for accommodating prior inconsistent, as well as diverse results. To investigate the genetics of idiopathic PD, I performed the largest genome-wide expression study in brain tissue to date. The study was carried out on the 1-color Agilent 60-mer Whole Human Genome Microarray, and included 26 neurologically healthy control and 27 PD samples from the frontal cortex Brodmann 9 area (BA9). The selected brain samples were of high quality (high pH and RNA integrity, no significant signs of Alzheimer disease pathology), and had rich documentation of neuropathological and clinical information available. I analyzed the microarray expression results in combination with genotyping data for PD-associated single nucleotide polymorphisms obtained for the microarray brain samples, and detected a pathway of interest for PD involving the FOXO1 (Forkhead box protein O1) gene. This result was verified in additional publically available expression datasets. I then performed a network-based canonical pathway analysis of PD, combining results from available GWAS, microarray expression, and animal model expression studies. The used analysis framework was a human functional-linkage network (FLN), consisting of genes as nodes, and weighted links indicating the confidence of gene-pair involvement in similar biological processes. I demonstrated the relevance of the used FLN for studying PD. Additionally, I ranked genes and pathways based on the available disease datasets. The frontal cortex BA9 study, and an additional non-PD microarray study were used as the positive and negative controls, respectively, for the obtained results.
Dumitriu, Alexandra. "Genome-wide expression and genomic data integration analyses in sporadic Parkinson Disease." Thesis, Boston University, 2010. https://hdl.handle.net/2144/31542.
Повний текст джерелаPLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
Parkinson disease (PD) is the second most common neurodegenerative disorder, affecting an estimated 2% of the population above 65 years of age. Although familial forms of PD have been linked to specific mutations responsible for the onset of the disease, the majority of PD cases is still of unknown etiology. PD has been traditionally studied using individual genetic methods, such as linkage analysis, genome-wide association (GWAS), or microarray expression studies. Nevertheless, the intrinsic disease genetic variability, and the unilateral analysis approach of available datasets made the detection of robust gene or pathway signals difficult. Studies of PD that combine a range of systems genetics approaches, and integrate complementary disease-relevant genetic datasets, represent a promising approach for accommodating prior inconsistent, as well as diverse results. To investigate the genetics of idiopathic PD, I performed the largest genome-wide expression study in brain tissue to date. The study was carried out on the 1-color Agilent 60-mer Whole Human Genome Microarray, and included 26 neurologically healthy control and 27 PD samples from the frontal cortex Brodmann 9 area (BA9). The selected brain samples were of high quality (high pH and RNA integrity, no significant signs of Alzheimer disease pathology), and had rich documentation of neuropathological and clinical information available. I analyzed the microarray expression results in combination with genotyping data for PD-associated single nucleotide polymorphisms obtained for the microarray brain samples, and detected a pathway of interest for PD involving the FOXO1 (Forkhead box protein O1) gene. This result was verified in additional publically available expression datasets. I then performed a network-based canonical pathway analysis of PD, combining results from available GWAS, microarray expression, and animal model expression studies. The used analysis framework was a human functional-linkage network (FLN), consisting of genes as nodes, and weighted links indicating the confidence of gene-pair involvement in similar biological processes. I demonstrated the relevance of the used FLN for studying PD. Additionally, I ranked genes and pathways based on the available disease datasets. The frontal cortex BA9 study, and an additional non-PD microarray study were used as the positive and negative controls, respectively, for the obtained results.
2031-01-01
Dunning, Mark J. "Genome-wide analyses using bead-based microarrays." Thesis, University of Cambridge, 2008. https://www.repository.cam.ac.uk/handle/1810/218542.
Повний текст джерелаAnastasi, Elisa. "Comparative genomics and emerging antibiotic resistance in Rhodococcus equi." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/25887.
Повний текст джерелаKamps-Hughes, Nicholas. "Massively Parallel Sequencing-Based Analyses of Genome and Protein Function." Thesis, University of Oregon, 2015. http://hdl.handle.net/1794/19234.
Повний текст джерелаEndo, Yoshinori. "Comparative study of mammalian evolution by genomic analyses and pluripotent stem cell technology." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263514.
Повний текст джерелаYang, Bo. "Analyses bioinformatiques et classements consensus pour les données biologiques à haut débit." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112250/document.
Повний текст джерелаIt is thought to be more and more important to solve biological questions using Bioinformatics approaches in the post-genomic era. This thesis focuses on two problems related to high troughput data: bioinformatics analysis at a large scale, and development of algorithms of consensus ranking. In molecular biology and genetics, RNA splicing is a modification of the nascent pre-messenger RNA (pre-mRNA) transcript in which introns are removed and exons are joined. The U2AF heterodimer has been well studied for its role in defining functional 3’ splice sites in pre-mRNA splicing, but multiple critical problems are still outstanding, including the functional impact of their cancer-associated mutations. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to define ~88% of functional 3’ splice sites in the human genome. Numerous U2AF binding events also occur in other genomic locations, and metagene and minigene analysis suggests that upstream intronic binding events interfere with the immediate downstream 3’ splice site associated with either the alternative exon to cause exon skipping or competing constitutive exon to induce inclusion of the alternative exon. We further build up a U2AF65 scoring scheme for predicting its target sites based on the high throughput sequencing data using a Maximum Entropy machine learning method, and the scores on the up and down regulated cases are consistent with our regulation model. These findings reveal the genomic function and regulatory mechanism of U2AF, which facilitates us understanding those associated diseases.Ranking biological data is a crucial need. Instead of developing new ranking methods, Cohen-Boulakia and her colleagues proposed to generate a consensus ranking to highlight the common points of a set of rankings while minimizing their disagreements to combat the noise and error for biological data. However, it is a NP-hard questioneven for only four rankings based on the Kendall-tau distance. In this thesis, we propose a new variant of pivot algorithms named as Consistent-Pivot. It uses a new strategy of pivot selection and other elements assignment, which performs better both on computation time and accuracy than previous pivot algorithms
Rana, Shivani [Verfasser], Michael [Gutachter] Bonkowski, Ludwig [Gutachter] Eichinger, Becker [Gutachter] Burkhard, and Raimund [Gutachter] Wegener. "Genomics analyses in kelp species / Shivani Rana ; Gutachter: Michael Bonkowski, Ludwig Eichinger, Becker Burkhard, Raimund Wegener." Köln : Universitäts- und Stadtbibliothek Köln, 2020. http://d-nb.info/122853442X/34.
Повний текст джерелаDhladhla, Busisiwe I. R. "Enumeration of insect viruses using microscopic and molecular analyses: South African isolate of cryotophlebia leucotreta granulovirus as a case study." Thesis, Nelson Mandela Metropolitan University, 2012. http://hdl.handle.net/10948/d1008395.
Повний текст джерелаRands, Chris M. D. "Analyses of functional sequence in mammalian and avian genomes." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:27e0ac20-eb27-423c-9493-a8a1c6cc57b8.
Повний текст джерелаAnani, Hussein. "La génomique bactérienne : un outil puissant pour la taxonomie et les analyses évolutives." Thesis, Aix-Marseille, 2020. http://theses.univ-amu.fr.lama.univ-amu.fr/200702_ANANI_94nya773wjmhky699k81cng_TH.pdf.
Повний текст джерелаThe birth of genomics has revolutionized the classification of bacterial taxa. Currently, thanks to the high number of available bacterial genomes (> 250,000) and genome-based taxonomic tools, inferring accurate phylogenomic analyses of human pathogenic bacteria is achievable. During our thesis, we have first highlighted the usefulness of pangenomic analyses in clinical microbiology. In addition, since the taxonomy of Bartonella species, the agents of several human infectious diseases, is poorly understood, we have studied 148 genomes from all Bartonella species in order to determine their genetic relatedness by using several taxonomic tools and generated their first pangenome. Hence, we have defined specific genome-based thresholds for the classification of isolates at the genus and species levels. Furthermore, using the culturomics strategy, we used the taxono-genomics approach to describe 25 new bacterial taxa isolated from a wide spectrum of samples from different countries. Therefore, our results confirm that, in 2020, genomics enables updating the traditional bacterial taxonomy and help to better understand bacterial evolution
Hammesfahr, Björn [Verfasser], Martin [Akademischer Betreuer] Kollmar, Burkhard [Akademischer Betreuer] Morgenstern, and Dirk [Akademischer Betreuer] Fasshauer. "Genomics and Phylogeny of Cytoskeletal Proteins: Tools and Analyses / Björn Hammesfahr. Gutachter: Burkhard Morgenstern ; Dirk Fasshauer. Betreuer: Martin Kollmar." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2013. http://d-nb.info/104405185X/34.
Повний текст джерелаXu, Ke. "Comparative genomic and epigenomic analyses of human and non-human primate evolution." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/52935.
Повний текст джерелаSidhu, Yaadwinder Singh. "Molecular tools for functional genomic analyses of the stealth pathogenesis of wheat by Zymoseptoria tritici." Thesis, University of Exeter, 2015. http://hdl.handle.net/10871/20219.
Повний текст джерелаSeshadri, Chitra. "Genome wide epigenetic analyses of Araptus attenuatus, a bark beetle." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4167.
Повний текст джерелаGustafsson, Susanne. "Population genetic analyses in the orchid genus Gymnadenia : a conservation genetic perspective." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3305.
Повний текст джерелаFerrer, Obiol Joan. "The evolutionary history of shearwaters: genomic analyses to resolve a radiation of pelagic seabrids." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/673437.
Повний текст джерелаUna de les preguntes fundacionals del camp de la biologia evolutiva és com es diferencien les poblacions i esdevenen noves espècies, i té importants implicacions en l’establiment dels patrons locals i globals de biodiversitat específica. Ernst Mayr va subratllar la importància de l’aïllament geogràfic com a mecanisme promotor d’especiació: “les poblacions en localitats aïllades comencen un procés de diferenciació i, quan aquesta diferenciació és suficient, les poblacions esdevenen dues espècies”. En l’ambient marí, la manca de barreres físiques evidents suggereix que la panmixi (en espècies amb gran capacitat de moviment) i l’aïllament per distància (en espècies de mobilitat reduïda) són els patrons prevalents. En canvi, s’ha detectat diferenciació a petita escala entre diferents poblacions i diferents espècies en un elevat nombre d’organismes marins mòbils, un fenomen que es coneix com la “paradoxa de les espècies marines”. Els ocells marins de l’ordre dels Procellariiformes representen un dels exemples més extrems d’aquesta paradoxa. Per una banda, els Procellariiformes són ocells marins amb gran capacitat de moviment i alta capacitat dispersiva que duen a terme algunes de les migracions més llargues del planeta. Per altra banda, són espècies molt fidels a les seves zones de cria, fenomen que probablement limiti el flux gènic i reforci la diferenciació genètica. Aquesta tesi té com a objectiu caracteritzar els patrons i processos que contribueixen a la diversificació genètica i fenotípica, a l’especiació i a la dispersió a diferents escales evolutives. Per assolir aquest objectiu, m’he focalitzat en les baldrigues (Calonectris, Puffinus i Ardenna), un grup amenaçat de Procellariiformes distribuït per tot el planeta. Mitjançant una aproximació que combina dos tipus de marcadors filogenòmics que evolucionen amb diferents taxes de substitució nucleotídica, i anàlisis filogenètiques i de detecció d’introgressió infereixo una filogènia ben resolta. Aquesta aproximació ha permès descobrir que la majoria del conflicte filogenètic en les baldrigues és producte dels alts nivells de sorteig incomplet de llinatges (incomplete lineage sorting) degut a esdeveniments ràpids d’especiació. L’anàlisi dels temps de divergència ha demostrat un gran impacte de l’extinció de megafauna marina del Pliocè en les baldrigues, probablement a causa de la sobtada reducció en la disponibilitat d’hàbitats costaners. Posteriorment, el Pliocè tardà i el principi del Pleistocè van ser períodes de molta i ràpida especiació i dispersió, probablement a causa dels canvis climàtics del Pleistocè. Les anàlisis biogeogràfiques han demostrat que els corrents marins promouen la dispersió i que l’efecte fundador és un mecanisme important d’especiació en les baldrigues. Les nostres anàlisis, combinant dades genòmiques amb evidència morfològica i ecològica, no han donat suport a les classificacions taxonòmiques actuals del grup de les baldrigues del gènere Puffinus del nord de l’Atlàntic i del Mediterrani i, per tant, proposo una classificació taxonòmica més adequada pel grup. A més a més, la detecció d’estructura genètica a petita escala en les espècies d’aquest grup de baldrigues destaca la necessitat de gestió d’unitats evolutives significatives per sota del nivell d’espècie. Les anàlisis de genòmica de poblacions han identificat la deriva genètica com a principal promotor de divergència en el genoma. Per concloure, el conjunt de les investigacions d’aquesta tesi identifiquen la prevalença del sorteig incomplet de llinatges al llarg de diferents escales evolutives, destaquen l’important paper dels esdeveniments paleoceanogràfics com a promotors de diversificació i indiquen la importància de l’evolució neutra com a causa de diferenciació poblacional en ocells marins pelàgics. Globalment, aquesta tesi demostra la utilitat de diferents aproximacions genòmiques, mitjançant anàlisis filogenètiques i de genètica de poblacions en diferents escales evolutives per proporcionar nou coneixement sobre la història evolutiva de les baldrigues.
Gholami, Behjat. "Functional analyses of candidate genes for osteoporosis : RUNX2 and LRP5 interplay during differentiation of the hFOB human osteoblast cell line." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/471516.
Повний текст джерелаL'osteoporosi es caracteritza per una baixa massa òssia i un deteriorament de la microarquitectura del teixit ossi. LRP5 és un membre de la superfamília de receptors de lipoproteïnes de baixa densitat, que actua com a co-receptor de la via de Wnt. LRP5 té una gran influència en la densitat mineral òssia. Runx2 és un membre de la família de factors de transcripció Runt amb un paper essencial en el control de la determinació i la diferenciació dels osteoblasts. La seva expressió és necessària per a la regulació dels gens de l'esquelet. Fins fa poc, Runx2 i LRP5 no havien estat connectats directament. Estudis recents han revelat la presència de cinc llocs d'unió de Runx2 en una regió de 2,9 kb upstream de LRP5 i s’ha documentat la unió de Runx2 a aquests llocs in vitro. Per explorar aquesta relació in vivo, en aquesta tesi es va emprar un protocol de diferenciació d’osteoblasts utilitzant la línia cel·lular hFOB. Es van avaluar els nivells de transcripció de RUNX2 i LRP5, juntament amb els de OCN, SOST i ALP al llarg de 21 dies de diferenciació. També es va avaluar les proteïnes Runx2 i LRP5. Per provar la ocupació de Runx2 als 5 llocs d'unió del promotor de LRP5, es van realitzar assaigs d'immunoprecipitació de cromatina durant la diferenciació de les cèl·lules hFOB, (dies 0, 7 i 21). Només es va observar unió en tots els cinc llocs en el dia 7, i no en els dies 0 i 21. La unió de Runx2 al promotor de LRP5 es descriu per primera vegada en aquesta tesi.
Pickett, Brandon D. "Applications of and Algorithms for Genome Assembly and Genomic Analyses with an Emphasis on Marine Teleosts." BYU ScholarsArchive, 2021. https://scholarsarchive.byu.edu/etd/8997.
Повний текст джерелаHolzapfel, Marion. "De l’épidémiologie moléculaire aux analyses fonctionnelles de Brucella chez les ruminants, une approche intégrée pour l’identification et l’étude de la diversité phénotypique d’un genre génétiquement homogène." Thesis, Paris Est, 2018. http://www.theses.fr/2018PESC1141.
Повний текст джерелаBrucellosis is a zoonotic disease caused by the bacterial genus Brucella (B.), whose global incidence is estimated at 500,000 human cases per year. The reservoir is animal, affecting mainly livestock. The most important species for humans are B. melitensis, B. abortus and B. suis, which share more than 90% sequence identity. Although highly genetically related, Brucella spp. exhibit a variety of phenotypic characteristics, host preference and pathogenicity. The genetic homogeneity of these species may appear as an asset for the development of robust universal diagnostic tools. On the other hand, it is a challenge to distinguish them, making it difficult to precisely characterize isolates from the same outbreak. As part of this thesis, a real-time PCR molecular diagnostic tool targeting the genus Brucella was developed and optimized. The method has been evaluated on ruminant milk samples; these samples may be an important source of Brucella and may be useful for herd-scale disease screening. Based on the detection of the IS711 insertion element, a sequence present in several copies within the genome, this method displays sensitivity and specificity values that make it interesting for a global scheme to fight against brucellosis. On the other hand, in order to improve the understanding of the genetic stability of B. melitensis, an original panel of strains isolated in an outbreak and involving four different host species was compared. Thus, using different complementary approaches, their genomic sequences, phenotypic characteristics and their behavior in an in vitro model were compared. Our results did not highlight markers that would suggest that mutations in the genome are essential to adapt to a new host
Doan, Quoc Khanh. "Genetic and genomic variation of resistance to viral nervous necrosis in wild populations of european seabass (Dicentrachus labrax)." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT094/document.
Повний текст джерелаEuropean seabass is one of the most economic species in aquaculture in Mediterranean areas. Viral nervous necrosis (VNN), a disease affecting at least 70 aquatic species, has become the most serious threat to seabass cultured industry. While numerous studies have been performed in order to control this disease, no simple and effective procedures are available. In this thesis, we question genetic variability and the potential of selective breeding as an opportunity to address thwart this threat.After a general introduction (first chapter) and a deep literature review of nodavirus in aquaculture (second chapter), we explore in the third chapter the genetic variability of resistance of different wild populations of European seabass, namely Northern Atlantic (NAT), Western Mediterranean (WEM), Northern-East Mediterranean (NEM) and Southern-East Mediterranean (SEM). To address this question, 2011 fish derived from a full-factorial mating scheme, where 9 WEM dams were crossed with 60 sires originated from NAT, WEM, NEM and SEM (15 sires per population), were reared in “common garden”. At 202 days, 1472 were challenged by nodavirus intraperitoneal injection at a mean body weight of 15.8 g. The rest of fish were kept in a single tank in order to collect performance traits. Strikingly, after pedigree recovery, we reveal a very strong and significant differentiation in VNN resistance among sires’ origin (ranging from 53 to 90%), offspring from East Mediterranean sires being the most resistant (83-90% of survival), offspring from WEM sires being intermediate (62% of survival) and offspring from NAT sires being the most sensitive (53% of survival only). A moderate liability heritability for VNN resistance (0.26±0.11) was estimated and negative correlations between resistance and production traits were shown.In the fourth chapter, a search of Quantitative Trait Loci (QTL) linked to the resistance was performed using a medium linkage map as examined. Therefore, 1717 individuals belonging 397 full-sib families and their parents were genotyped for 2722 SNP markers spotted on a SNPChip. From 1274 significant loci, a 24 linkage groups medium-density linkage map was constructed, as well as sex-specific and Origin-specific linkage maps. From these results, we show a 1.25-fold sex-biased heterochiasmy in favor to female recombination rate. Finally, genome scans for QTLs were performed in different methods, and while no QTLs were identified for both “time to death” or survival, we discuss the effect of the experimental design used.In the fifth chapter, a two-step unweighted then weighted Genome-Wide Association Study (GWAS & wGWAS) was carried out based on linear mixed models using the same SNPs as for QTL mapping. The aim was to determine whether we can detect significant individual SNPs linked to resistance against VNN. After SNPs weight calculation, the wGWAS detected one significant SNP explaining 3.11% of the resistance belonging to LG9. Finally, the potential for genomics prediction for VNN resistance using the different genomic models was performed and extensively presented. However, no significant differences were observed between genomic-based estimated breeding values and pedigree-based estimated breeding values.In conclusion, this study depicts a large genetic variation for VNN resistance in wild seabass populations but with negative genetic correlations with production traits. These latter results are valuable to help to define strategies for genetic improvement of resistance against VNN of European seabass. Moreover, the first assumptions on the location of potential QTLs claim for a fine QTL mapping and an expectable add-value of the use of genomic information in potential marker-assisted selection to VNN resistance in European seabass
Meakin, Nicholas G. "Metagenomic analyses of marine new production under elevated CO2 conditions." Thesis, University of Stirling, 2009. http://hdl.handle.net/1893/1555.
Повний текст джерелаBatut, Bérénice. "Étude de l'évolution réductive des génomes bactériens par expériences d'évolution in silico et analyses bioinformatiques." Thesis, Lyon, INSA, 2014. http://www.theses.fr/2014ISAL0108/document.
Повний текст джерелаGiven a popular view, evolution is an incremental process based on an increase of molecular complexity of organisms. However, some organisms have undergo massive genome reduction like the endosymbionts. In this case the reduction can be explained by the Muller’s ratchet due to the endosymbiont lifestyle with small population and lack of recombination. However, in some marine bacteria, like Prochlorococcus et Pelagibacter, lineage have undergo up to 30% of genome reduction. Their lifestyle is almost the opposite to the one of the endosymbionts and reductive genome evolution can not be easily explicable by the Muller’s ratchet. Some other hypothesis has been proposed but none can explain all the observed genomic characteristics. In the thesis, I am interested in the reductive evolution of Prochlorococcus. I used two approaches: a theoretical one using simulation where different scenarios are tested and an analysis of Prochlorococcus genomes in a phylogenetic framework to determine the causes and characteristics of genome reduction. The combination of these two approaches allows to propose an hypothetical evolutive history for the reductive genome evolution of Prochlorococcus
Leconte, Jade. "Analyses de variations génomiques liées à la biogéographie des picoalgues Mamiellales Survey of the green picoalga Bathycoccus genomes in the global ocean Genome Resolved Biogeography of Mamiellales Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans." Thesis, université Paris-Saclay, 2020. https://www.biblio.univ-evry.fr/theses/2020/interne/2020UPASE013.pdf.
Повний текст джерелаMamiellales are an order of unicellular cosmopolitan green algae with ecologically important species such as Bathycoccus, Micromonas or Ostreococcus, major contributors to the primary production. This thesis uses this phytoplankton group with known reference genomes as a study model in order to better analyze the impact of the environment on plankton using samples from the Tara Oceans expedition.To do this, different analyses were carried out to define their biogeography and ecological preferences, first in temperate waters then in the cold, nutrient-rich waters of the Arctic Ocean. In both cases, temperature was shown to be the main factor distinguishing the environment in which the different genomes were found. We then carried out a more detailed study in particular on Bathycoccus prasinos, a species abundant in these two distinct environments, in order to establish its population structure, which proved to be clearly separated into three groups: southern , arctic and temperate samples, again showing an impact of temperature but not only in view of the genomic distance between the first two basins.Finally, our study was extended with various collaborations, allowing us to observe a group of heterotrophic protists, the stramenopiles, and to perform analyses at the much larger scale of communities. All of these results conclude once again, among other things, on the strong impact of temperature, leading us to contribute to the question about the current context of climate change and its impact on plankton
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/.
Повний текст джерелаKittler, 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.
Повний текст джерелаMungall, Christopher. "Next-generation information systems for genomics." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5020.
Повний текст джерелаRubanova, Natalia. "MasterPATH : network analysis of functional genomics screening data." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC109/document.
Повний текст джерелаIn 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
Liu, Yuan. "Mixed anova model analysis of microarray experiments with locally polled error /." Electronic version (PDF), 2004. http://dl.uncw.edu/etd/2004/liuy/yuanliu.pdf.
Повний текст джерелаTchitchek, Nicolas. "Novel statistical and geometrical methods for integrative genomics." Paris 7, 2011. http://www.theses.fr/2011PA077207.
Повний текст джерелаDuring the three years of my Ph. D. Project, I developed several complementary methods and frameworks for the analysis of -omics data, such as: (i) a framework for integrative genomics in which every kind of information that can be obtained about the genomic processes and features are modeled in a common probabilistic manner, allowing then to analyze the correlations among the heterogeneous genome-wide information, (ii) a fold-change based statistical test for the identification of differentially and similarly expressed genes between two biological conditions, allowing also the determination of confidence intervals of specific confidence levels for the fold-change. (iii) novel dimensionality reduction methods that outperform other related existing methods and provide more interpretable geometrical representations in the context of large dataset of-omics data. These methods have been applied to several biological analyses and studies as part of different scientific collaborations: (i) to identify functional Glucocorticoid Response Elements in the promoter regions of specific candidate genes involved in Type 1 Pseudohypoaldosteronism. (ii) to uncover the host transcriptional responses underlying differences between low- and high- pathogenic pulmonary viruses based on a compendium of host transcription responses of infected cells from mouse lungs. (iii) to study the progression of the hepatitis C virus in infected patients who underwent orthotopic liver transplantation, based on a cohort of transcriptome profiles for liver biopsy specimens, (iv) to analyze an Expression Sequence Tag library obtained from PBMC of African green monkeys infected or not by the SIV
Prakash, Amol. "Algorithms for comparative sequence analysis and comparative proteomics /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/6904.
Повний текст джерелаBenevides, Leandro. "Comparative Genomics of Faecalibacterium spp." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS129.
Повний текст джерелаWithin the human colon, the genus Faecalibacterium is the main member of the Clostridium leptum cluster and comprises the second-most common representative genus in fecal samples, after Clostridium coccoides. It has been recognized as an important bacterium promoting the intestinal health and today is considered as a potential next generation probiotic. Until recently, it was believed that there was only one species in this genus, but since 2012, some studies have begun to suggest the existence of two phylogroups into the genus. This new proposition of reclassification into this genus increases the importance of new studies, with all strains, to better understand the diversity, the interactions with the host and the safety aspects in its use as probiotic. Briefly, in this work we introduce the comparative genomics analyzes to the genus Faecalibacterium performing a deep phylogenetic study and evaluating the safety aspects for its use as a probiotic. The phylogenetic analyzes included not only the classical use of 16S rRNA gene, but also the utilization of 17 complete genomes and techniques like whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome. Also, this is the first work to combine an analysis of pangenome development with ANI analysis in order to corroborate the assignment of strains to new species. The phylogenetic analyzes confirmed the existence of more than one species into the genus Faecalibacterium. Moreover, the safety assessment involved the (1) prediction of horizontally acquired regions (Antibiotic resistance islands, Metabolic islands and phage regions), (2) prediction of metabolic pathways, (3) search of genes related to antibiotic resistance and (4) search of bacteriocins. These analyzes identified genomic islands in all genomes, but none of than are exclusive to one strain or genospecies. Also, were identified 8 genes related to antibiotic resistance mechanisms distributed among the genomes. 126 metabolic pathways were predicted and among than some were highlighted: Bisphenol A degradation, Butanoate metabolism and Streptomycin biosynthesis. In addition, we studied the genomic context of one protein (Microbial Anti-inflammatory Molecule - MAM) first described by our group. This investigation shows that MAM appears close to genes related to sporulation process and, in some strains, close to an ABC-transporter
Pethick, Florence Elizabeth. "Comparative genomic analyses of Corynebacterium pseudotuberculosis." Thesis, University of Glasgow, 2013. http://theses.gla.ac.uk/4287/.
Повний текст джерелаWilson, Ian. "Comparative genomic analyses of Entamoeba species." Thesis, University of Liverpool, 2014. http://livrepository.liverpool.ac.uk/2007270/.
Повний текст джерелаSelman, Mohammed. "Genomic Analysis of Encephalitozoon Species." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30314.
Повний текст джерелаTam, Mandy Chi-Mun. "Genomic analysis of mouse tumorigenesis." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37454.
Повний текст джерелаIncludes 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.
Collinet, Claudio. "System Survey of Endocytosis by Functional Genomics and Quantitative Multi-Parametric Image Analysis." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-38278.
Повний текст джерелаLorentzen, Marc. "Diversity and genomic characteristics of Oenococcus oeni." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0428.
Повний текст джерелаOenococcus 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
Karanam, Suresh Kumar. "Automation of comparative genomic promoter analysis of DNA microarray datasets." Thesis, Available online, Georgia Institute of Technology, 2004:, 2003. http://etd.gatech.edu/theses/available/etd-04062004-164658/unrestricted/karanam%5Fsuresh%5Fk%5F200312%5Fms.pdf.
Повний текст джерелаSchroeder, Michael Philipp 1986. "Analysis and visualization of multidimensional cancer genomics data." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/301436.
Повний текст джерелаEl cancer és una malaltia complexa causada per alteracions somàtiques del genoma i epigenoma de les cèl•lules tumorals. Un augment d’inversions i l'accés a tecnologies de baix cost ha provocat un increment important en la generació de dades genòmiques de càncer. La disponibilitat d’aquestes dades ofereix noves possibilitats per entendre millor les propietats moleculars del càncer. En aquest àmbit, presento dos mètodes que aprofiten aquesta gran disponibilitat de dades genòmiques de càncer: OncodriveROLE, un procediment per a classificar gens “drivers” del càncer segons si el seu mode d’acció ésl'activació o la pèrdua de funció del producte gènic; i MutEx, un estadístic per a mesurar la tendència de les mutacions somàtiques a l’exclusió mútua. Tanmateix, la manca de precedents d’aquesta gran dimensió de dades fa sorgir nous problemes en quant a la seva accessibilitat i exploració, els quals intentem solventar amb noves eines de visualització: i) Heatmaps interactius de Gitools amb dades genòmiques de càncer a gran escala, a punt per ser explorades, ii) jHeatmap, un heatmap interactiu per la web capaç de mostrar dades genòmiques de cancer multidimensionals i dissenyat per la seva inclusió a portals web; i iii) SVGMap, un servidor web per traslladar dades en figures SVG customitzades, útil per a la transl•lació de mesures experimentals en un model visual.
Landfors, Mattias. "Normalization and analysis of high-dimensional genomics data." Doctoral thesis, Umeå universitet, Institutionen för matematik och matematisk statistik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-53486.
Повний текст джерелаRevilla, 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.
Повний текст джерелаPork 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.
Ming, Jingsi. "Statistical methods for integrative analysis of genomic data." HKBU Institutional Repository, 2018. https://repository.hkbu.edu.hk/etd_oa/545.
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