Relevant bibliographies by topics / Comparative genomics / Dissertations / Theses
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Dissertations / Theses on the topic 'Comparative genomics'

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Published: 4 June 2021
Last updated: 25 July 2025

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1

Loman, Nicholas James. "Comparative bacterial genomics." Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/2839/.

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For the most part, diagnostic clinical microbiology still relies on 19th century ideas and techniques, particularly microscopy and laboratory culture. In this thesis I investigate the utility of a new approach, whole-genome sequencing (WGS), to tackle current issues in infectious disease. I present four studies. The first demonstrates the utility of WGS in a hospital outbreak of Acinetobacter baumannii. The second study uses WGS to examine the evolution of drug resistance following antibiotic treatment. I then explore the use of WGS prospectively during an international outbreak of food-borne
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2

Axelsson, Erik. "Comparative Genomics in Birds." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7432.

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3

Eriksen, Niklas. "Combinatorial methods in comparative genomics." Doctoral thesis, KTH, Mathematics, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3508.

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4

Manee, Manee. "Comparative genomics of noncoding DNA." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html.

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High levels of primary sequence conservation are observed in many noncoding regions of eukaryotic genomes. These conserved noncoding elements (CNEs) have shown to be robust indicators of functionally constrained elements. Nevertheless, the function of only a small fraction of such CNEs is known and their role in genome biology remains largely a mystery. Comparative genomics analysis in model organisms can shed light on CNE function and evolution of noncoding DNA in general. Recently, it has been reported that short CNEs in the Drosophila genome are typically very AT-rich but have unusually hig
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5

Mikkelsen, Tarjei Sigurd 1978. "Mammalian comparative genomics and epigenomics." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/52808.

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Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Cataloged from student submitted PDF version of thesis.<br>Includes bibliographical references.<br>The human genome sequence can be thought of as an instruction manual for our species, written and rewritten over more than a billion of years of evolution. Taking a complete inventory of our genome, dissecting its genes and their functional components, and elucidating
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6

Ryder, Carol D. "Comparative genomics of Brassica oleracea." Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/51651/.

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The scientific case made by the AUTHOR’S comparative Brassica oleracea genomics work is presented through 5 peer reviewed research papers. In order to achieve a comprehensive understanding of the evolution of B. oleracea the identification of unique genome characteristics, established using comparative genomics, is required. The genome characteristics established within these papers deliver significant contributions to original knowledge. These include a detailed illustration of how macro scale synteny varies markedly between the B. oleracea and A. thaliana genomes; unambiguous integration of
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7

Dong, Xin. "Comparative genomics of rickettsia species." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5054/document.

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Le genre Rickettsia, sont des petites bactéries Gram-négatives et symbiotes intracellulaires obligatoires des eucaryotes. Les Rickettsia sont surtout connus pour leur pathogénicité et pour provoquer des maladies graves chez l'homme et les autres animaux. À ce jour, 26 espèces valides de Rickettsies ont été identifiées dans le monde entier, dont 20 sont des agents pathogènes éprouvées. Toutes les espèces de Rickettsies validées sont associées à des arthropodes. Les phylogénies basées sur divers marqueurs moléculaires ont présenté des topologies discordantes, avec seulement R. bellii et R. canad
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8

Sentausa, Erwin. "Intraspecies comparative genomics of Rickettsia." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5082/document.

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Le genre Rickettsia est composé de bactéries Gram-négatives, intracellulaires obligatoires qui causent un éventail de maladies humaines à travers le monde. Des nouvelles techniques ont permis de progresser dans l'identification et la classification des Rickettsia, y compris l'introduction de méthodes moléculaires comme la comparaison de séquences de gènes (ARNr 16S, ompA, ompB, gltA, sca4 …) et la création du statut de sous-espèce. La génomique et les techniques de séquençage de nouvelle génération ont permis d’accéder à une nouvelle façon d’en apprendre davantage sur la pathogenèse et l'évolu
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9

Benevides, Leandro. "Comparative Genomics of Faecalibacterium spp." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS129.

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Dans le côlon humain, le genre Faecalibacterium est le membre principal du groupe Clostridium leptum et comprend le deuxième genre représentatif le plus commun dans les échantillons fécaux, après Clostridium coccoides. Il a été reconnu comme une bactérie importante favorisant la santé intestinale et est aujourd'hui considéré comme un probiotique de prochaine génération. Jusqu'à récemment, on croyait qu'il n'y avait qu'une seule espèce dans ce genre, mais depuis 2012, certaines études ont commencé à suggérer l'existence de deux phylogroupes dans le genre. Cette nouvelle proposition de reclassif
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10

St, Jean Andrew Louis. "Haloarchaeal comparative genomics and the local context model of genomic evolution." Thesis, University of Ottawa (Canada), 1996. http://hdl.handle.net/10393/10308.

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Genomics is a rapidly expanding field of research that seeks to study the structure, function and evolution of an organism's genome. Genomic investigations were conducted on three species of haloarchaea, a monophyletic group of prokaryotes belonging to the kingdom Euryarchaeota of the domain Archaea that are adapted to high-salt environments. A physical and genetic map of the genome of Halobacterium salinarum GRB is described. This map and the previously published map of the genome of Haloferax volcanii DS2 were compared with the object of detecting any conservation in the order or spacing of
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11

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.

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12

Gaiarsa, S. "EVOLUTION, COMPARATIVE GENOMICS AND GENOMIC EPIDEMIOLOGY OF BACTERIA OF PUBLIC HEALTH IMPORTANCE." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/525881.

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La presente tesi è incentrata sull'epidemiologia genomica delle infezioni batteriche ospedaliere. L'ambiente ospedaliero è peculiare, in quanto al suo interno si concentrano un elevato numero di agenti batterici, pazienti con un sistema immunitario debole e un uso massiccio di sostanze antimicrobiche. Questa combinazione favorisce lo sviluppo e la selezione di ceppi resistenti agli antibiotici e la diffusione di infezioni opportunistiche: in generale il prosperare dei patogeni nosocomiali. Alcune tecniche all'avanguardia per lo studio di questo tipo di infezioni sono basate sull’uso della geno
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13

Dessimoz, Christophe. "Comparative genomics using pairwise evolutionary distances /." Zürich : ETH, 2009. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=18177.

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14

Ulrich, Luke. "Comparative Genomics of Microbial Signal Transduction." Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/7632.

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High-throughput genome processing, sophisticated protein sequence analysis, programming, and information management were used to achieve two major advances in the comparative genomics of microbial signal transduction. First, an integrated and flexible bioinformatics platform and the Microbial Signal Transduction database (MiST) were developed, which facilitated the genome-wide analysis of bacterial signal transduction. This platform was used successfully for the high-throughput identification and classification of signal transduction proteins in more than 300 archaeal and bacterial organisms.
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15

Golenetskaya, Natalia. "Adressing scaling challenges in comparative genomics." Phd thesis, Université Sciences et Technologies - Bordeaux I, 2013. http://tel.archives-ouvertes.fr/tel-00865840.

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La génomique comparée est essentiellement une forme de fouille de données dans des grandes collections de relations n-aires. La croissance du nombre de génomes sequencés créé un stress sur la génomique comparée qui croit, au pire géométriquement, avec la croissance en données de séquence. Aujourd'hui même des laboratoires de taille modeste obtient, de façon routine, plusieurs génomes à la fois - et comme des grands consortia attend de pouvoir réaliser des analyses tout-contre-tout dans le cadre de ses stratégies multi-génomes. Afin d'adresser les besoins à tous niveaux il est nécessaire de rep
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16

Buchan, Daniel William Alexander. "Protein domain evolution by comparative genomics." Thesis, University College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.407753.

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17

Kamvysselis, Manolis 1977. "Computational comparative genomics : genes, regulation, evolution." Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/7999.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.<br>Includes bibliographical references (p. 95-99).<br>Understanding the biological signals encoded in a genome is a key challenge of computational biology. These signals are encoded in the four-nucleotide alphabet of DNA and are responsible for all molecular processes in the cell. In particular, the genome contains the blueprint of all protein-coding genes and the regulatory motifs used to coordinate the expression of these genes. Comparative genome analysis of related species pr
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18

Coates-Brown, Rosanna. "Comparative genomics of the skin staphylococci." Thesis, University of Liverpool, 2015. http://livrepository.liverpool.ac.uk/2046659/.

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The human skin is a complex ecosystem which supports a diverse population of bacteria. Comparative genomic analyses are increasingly being used to explore the functional potential of this bacterial population . The ubiquity of Staphylococcus on human skin means this genus represents the most well-studied of the microbial skin residents, however most analysis has focussed on the significant clinical pathogenic species S. epidermidis and S. aureus. To investigate the biology of S. hominis, the second most frequent Staphylococcus species isolated from human skin after S. epidermidis, seven isolat
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19

Moore, Matthew Phillip. "Comparative genomics of Pseudomonas aeruginosa populations." Thesis, University of Liverpool, 2017. http://livrepository.liverpool.ac.uk/3021281/.

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Pseudomonas aeruginosa causes a wide range of infections, is often associated with antimicrobial resistance and is the primary cause of chronic lung infection in cystic fibrosis (CF) and the overall morbidity and mortality associated with the disease. As P. aeruginosa is an environmental bacterium that opportunistically infects CF patients most infecting lineages are distinct. The determination of common adaptive routes during infection is further complicated by within-lineage heterogeneity, multi-lineage infections and the emergence of transmissible strains. In order to better understand the
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20

Mularoni, Loris. "Comparative genomics of amino acid tandem repeats." Doctoral thesis, Universitat Pompeu Fabra, 2009. http://hdl.handle.net/10803/7187.

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Tandem amino acid repeats, also known as homopolimeric tract or homopeptides, are very common features of eukaryotic genomes and are present in nearly one-fifth of human encoded proteins. These structures have attracted much interest in the early 1990s when a number of neurological diseases associated with repeat expansion mutations were discovered in humans. Despite their abundance in coding proteins, little is known about their functional consequences. Two scenarios have been proposed. In one, tandem amino acid repeat is considered a neutral structure generated by slippage event and eventual
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21

Wuichet, Kristin. "Comparative Genomics of the Microbial Chemotaxis System." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/16193.

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This research project presents a comprehensive functional analysis of a complex prokaryotic signal transduction system and the mechanisms underlying its evolution. The chemotaxis system regulates motility in prokaryotes and is their most complex signal transduction system. The system has been extensively characterized experimentally, but recent studies have created new questions about the function and origin of this system. Comparative genomics analyses are well-suited for studying the chemotaxis system since it is present in taxonomically diverse organisms. The first aim of this project i
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22

Fuxelius, Hans-Henrik. "Methods and Applications in Comparative Bacterial Genomics." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8398.

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Comparative studies of bacterial genomes, now counting in the hundreds, generate massive amounts of information. In order to support a systematic and efficient approach to genomic analyses, a database driven system with graphic visualization of genomic properties was developed - GenComp. The software was applied to studies of obligate intracellular bacteria. In all studies, ORFs were extracted and grouped into ORF-families. Based on gene order synteny, orthologous clusters of core genes and variable spacer ORFs were identified and extracted for alignments and computation of substitution freque
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23

Garikipati, Dilip Kumar. "The comparative genomics and physiology of myostatin." Online access for everyone, 2007. http://www.dissertations.wsu.edu/Dissertations/Summer2007/D_Garikipati_070807.pdf.

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24

Mostowy, Serge. "Comparative genomics of the Mycobacterium tuberculosis complex." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=111834.

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The study of microbial evolution has been recently accelerated by the advent of comparative genomics, an approach enabling investigation of organisms at the whole-genome level. Tools of comparative genomics, including the DNA microarray, have been applied in bacterial genomes towards studying heterogeneity in DNA content, and to monitor global gene expression. When focused upon the study of microbial pathogens, genome analysis has provided unprecedented insight into their evolution, virulence, and host adaptation. Contributing towards this, I herein explore the evolutionary change affecting ge
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25

Li, Yang. "Understanding lineage-specific biology through comparative genomics." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:23398cc7-8bbe-4f5a-8cd9-1104591400cc.

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A major challenge in biology is to identify how different species arose and acquired distinct phenotypic traits. High-throughput sequencing is transforming our understanding of biology by allowing us to study genomes and cellular processes at genome-wide levels. Only a decade subsequent to the publication of the first human genome draft, genome assemblies of hundreds of organisms have been produced. Yet, genome analysis remains challenging and advances have lagged far behind our sequencing abilities and other technological advances. The next generation of comparative genomicists must therefore
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26

Park, Gyoungju Nah. "Comparative Genomics in Two Dicot Model Systems." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/194279.

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Comparative sequence analyses were performed with members of the Solanaceae and the Brassicaceae. These studies investigated genomic organization, determined levels of microcolinearity, identified orthologous genes and investigated the molecular basis of trait differences. The first analysis was performed by comparison of tomato (Solanum lycopersicum) genomic sequence (119 kb) containing the JOINTLESS1 (J1) locus with orthologous sequences from two potato species, a diploid, Solanum bulbocastanum (800-900 Mb, 2N=2X=24), and a hexaploid, Solanum demissum (2,700 Mb, 2N=6X=72). Gene colinearity w
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27

Syme, Robert Andrew. "Comparative Genomics of Parastagonospora and Pyrenophora species." Thesis, Curtin University, 2015. http://hdl.handle.net/20.500.11937/54044.

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The advancing technology and tools available for the important agricultural pathogens P. nodorum and P. avenaria pathosystems are leveraged here for intra-species comparison as well as comparisons to other related species. The comparisons have yielded insight into the evolutionary history of pathogen and host, insights into the mechanisms of genome evolution, and prediction of genes integral to fungal pathogenicity.
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28

Dang, Ha Xuan. "Mold Allergomics: Comparative and Machine Learning Approaches." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/64205.

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Fungi are one of the major organisms that cause allergic disease in human. A number of proteins from fungi have been found to be allergenic or possess immunostimulatory properties. Identifying and characterizing allergens from fungal genomes will help facilitate our understanding of the mechanism underlying host-pathogen interactions in allergic diseases. Currently, there is a lack of tools that allow us to rapidly and accurately predict allergens from whole genomes. In the context of whole genome annotation, allergens are rare compared to non-allergens and thus the data is considered highly s
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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.

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30

Kang, Lin. "Comparative Genomics Insights into Speciation and Evolution of Hawaiian Drosophila." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/85467.

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Speciation and adaptation have always been of great interest to biologists. The Hawaiian archipelago provides a natural arena for understanding adaptive radiation and speciation, and genomics and bioinformatics offer new approaches for studying these fundamental processes. The mode of speciation should have profound impacts on the genomic architecture and patterns of reproductive isolation of new species. The Hawaiian Drosophila are a spectacular example of sequential colonization, adaptive radiation, and speciation in the islands with nearly 1,000 estimated species, of which more than 500 hav
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31

Epamino, George Willian Condomitti. "Alinhamento múltiplo de genomas de eucariotos com montagens altamente fragmentadas." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-31102017-102826/.

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O advento do sequenciamento de nova geração (NGS - Next Generation Sequencing) nos últimos anos proporcionou um aumento expressivo no número de projetos genômicos. De maneira simplificada, as máquinas sequenciadoras geram como resultado fragmentos de DNA que são utilizados por programas montadores de genoma. Esses programas tentam juntar os fragmentos de DNA de modo a obter a representação completa da sequência genômica (por exemplo um cromossomo) da espécie sendo sequenciada. Em alguns casos o processo de montagem pode ser executado com maior facilidade para organismos com genomas de tamanhos
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32

Steward, Karen Frances. "Comparative genomics of Streptococcus equi and Streptococcus zooepidemicus." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708551.

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33

Migeon, Pierre. "Comparative genomics of repetitive elements between maize inbred lines B73 and Mo17." Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35377.

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Master of Science<br>Genetics Interdepartmental Program<br>Sanzhen Liu<br>The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17
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34

Åkerborg, Örjan. "Taking advantage of phylogenetic trees in comparative genomics." Doctoral thesis, KTH, Beräkningsbiologi, CB, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4757.

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Phylogenomics can be regarded as evolution and genomics in co-operation. Various kinds of evolutionary studies, gene family analysis among them, demand access to genome-scale datasets. But it is also clear that many genomics studies, such as assignment of gene function, are much improved by evolutionary analysis. The work leading to this thesis is a contribution to the phylogenomics field. We have used phylogenetic relationships between species in genome-scale searches for two intriguing genomic features, namely and A-to-I RNA editing. In the first case we used pairwise species comparisons, sp
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Åkerborg, Örjan. "Taking advantage of phylogenetic trees in comparative genomics /." Stockholm : School of Computer Science and Communication, Kungliga tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4757.

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36

Abbas, Ali Hadi. "Comparative structural genomics and phylogenomics of African trypanosomes." Thesis, University of Liverpool, 2018. http://livrepository.liverpool.ac.uk/3022845/.

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The pathogens responsible of the majority of African Animal trypanosomiasis (AAT) are Trypanosoma brucei, T. congolense and T. vivax. These three trypanosomes have very different biology both in the mammalian host and the insect vector. These differences are encoded in their genomes and whole genome sequence comparison of high quality genomic data should allow such comparisons to be performed. Whilst the T.b. brucei strain TREU927 genome assembly is currently aviable as a good quality draft, the current versions of T. congolense and T. vivax are highly fragmented and include large gaps that in
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Xia, Ai. "Comparative genomics of chromosomal rearrangements in malaria mosquitoes." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/37335.

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To better understand the evolutionary dynamics of chromosomal inversions, a physical map for an Asian malaria vector, Anopheles stephensi, was created and compared with the maps of the major African malaria vectors A. gambiae and A. funestus No interchromosomal transposition was observed between A. gambiae and A. stephensi. Several cases of euchromatin and heterochromatin transitions weridentified between A. gambiae and A. stephensi. The study of paracentric inversions between lineages in Anopheles mosquitoes demonstrated that X chromosome has the fastest rate of inversion fixations and highes
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Lyman, Cole Andrew. "Comparative Genomics Using the Colored de Bruijn Graph." BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/8441.

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Comparing genomes in a computationally efficient manner is a difficult problem. Methods that provide the highest resolution are too inefficient and methods that are efficient are too low resolution. In this thesis, we show that the Colored de Bruijn Graph (CdBG) is a suitable method for comparing genomes because it is efficient while maintaining a useful amount of resolution. To illustrate the usefulness of the CdBG, the phylogenetic tree for 12 species in the Drosophila genus is reconstructed using pseudo-homologous regions of the genome contained in the CdBG.
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Pryszcz, Leszek Piotr 1985. "Comparative genomics to unravel virulence mechanisms in fungal human pathogens." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/301437.

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Las Candidas forman uno de los grupos con mayor n´umero de hongos pat´ogenos en humanos. La relaci ´on que tienen desde un punto de vista filogen´etico demuestra que la capacidad de infectar humanos ha surgido varias veces de forma independiente en este clado. El complejo de Candida parapsilosis es ideal para investigar la aparici´on de virulencia puesto que contiene tres especies cercanas que muestran diferentes grados de virulencia y de importancia: C. parapsilosis, C. orthopsilosis y C. metapsilosis. En esta tesis presento la secuenciaci´on y posterior an´alisis de quince cepas de o
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Perrin, Amandine. "Tools for massive bacterial comparative genomics : Development and Applications." Electronic Thesis or Diss., Sorbonne université, 2022. https://theses.hal.science/tel-03789655.

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La génomique comparative bactérienne consiste à comparer les contenus en gène des différentes souches : leur pangenome. Avec le nombre croissant de séquençages, les logiciels existants au début de cette thèse arrivaient à leurs limites en termes de temps de calcul et de mémoire. L’enjeu était de passer à l’échelle de milliers de génomes dans un temps raisonnable, en gardant une précision correcte. De plus, à notre connaissance, aucun logiciel ne permettait d’effectuer toutes les étapes clés d’une étude de génomique comparative. C’est dans ce contexte que nous avons développé PanACoTA, un outil
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Bate, Rachael. "Mapping and gene identification within the Ids to Dmd region of the mouse X chromosome." Thesis, Oxford Brookes University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247810.

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42

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.

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43

Cheung, Hiu Tung (Tom). "Understanding mammalian transcriptional regulation using comparative and functional genomics." Diss., Connect to online resource, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3207751.

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Saski, Christopher A. "Chloroplast comparative genomics implications for phylogeny, evolution and biotechnology /." Connect to this title online, 2007. http://etd.lib.clemson.edu/documents/1193080368/.

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Wagner, Darlene Darlington. "Comparative genomics reveal ecophysiological adaptations of organohalide-respiring bacteria." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/45916.

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Organohalide-respiring Bacteria (OHRB) play key roles in the reductive dehalogenation of natural organohalides and anthropogenic chlorinated contaminants. Reductive dehalogenases (RDases) catalyze the cleavage of carbon-halogen bonds, enabling respiratory energy conservation and growth. Large numbers of RDase genes, a majority lacking experimental characterization of function, are found on the genomes of OHRB. In silico genomics tools were employed to identify shared sequence features among RDase genes and proteins, predict RDase functionality, and elucidate RDase evolutionary history. Th
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Ellegaard, Kirsten Maren, Lisa Klasson, Kristina Näslund, Kostas Bourtzis, and Siv G. E. Andersson. "Comparative Genomics of Wolbachia and the Bacterial Species Concept." Uppsala universitet, Molekylär evolution, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200821.

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The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double inf
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Nakjang, Sirintra. "Comparative genomics for studying the proteomes of mucosal microorganisms." Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1265.

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A tremendous number of microorganisms are known to interact with their animal hosts. The outcome of the interactions between microbes and their animal hosts range from modulating the maintenance of homeostasis to the establishment of processes leading to pathogenesis. Of the numerous species known to inhabit humans, the great majority live on mucosal surfaces which are highly defended. Despite their importance in human health, little is known about the molecular and cellular basis of most host-microbe interactions across the tremendous diversity of mucosal-adapted microorganisms. The ever-incr
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Muller, Carolin Anne. "Comparative genomics of chromosome replication in sensu stricto yeasts." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.603592.

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Precise, complete and timely replication of eukaryotic genomes is a prerequisite to cell division. Each chromosome replicates in a defined temporal order that is dictated by the variable activation timings and efficiencies of replication origins. However, so far the mechanisms regulating origin activity have remained elusive. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae. Powerful comparative genomic approaches are possible in budding yeasts due to the evolutionary range of sequenced genomes available and their tractability to genetic approaches. Previou
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Godinez, Ricardo. "Comparative Genomics of the Major Histocompatibility Complex in Amniotes." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10685.

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The major histocompatibility complex region (MHC) is a multi gene family present in all jawed vertebrates, with a fundamental role in vertebrate immunity. More than two decades of studies have resulted in the characterization of over a dozen MHC regions, and models of evolution explaining that the MHC has gradually increased in size and gene content since its origins without addressing their genomic context or the environmental selective forces. Furthermore, a compelling reconstruction of the evolutionary history of the MHC has been hampered due to phylogenetic gaps and the absence of comparat
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Edwards, Martin Tavis. "Comparative prokaryotic genomics : conservation of functional and spatial context." Thesis, Birkbeck (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428024.

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