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Loman, Nicholas James. "Comparative bacterial genomics". Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/2839/.
Pełny tekst źródłaAxelsson, Erik. "Comparative Genomics in Birds". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7432.
Pełny tekst źródłaEriksen, Niklas. "Combinatorial methods in comparative genomics". Doctoral thesis, KTH, Mathematics, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3508.
Pełny tekst źródłaManee, 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.
Pełny tekst źródłaMikkelsen, Tarjei Sigurd 1978. "Mammalian comparative genomics and epigenomics". Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/52808.
Pełny tekst źródłaThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references.
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 how these genes are selectively used to establish and maintain cell types with markedly different behaviors, are key challenges of modern biology. In this thesis we present contributions to our understanding of the structure, function and evolution of the human genome. We rely on two complementary approaches. First, we study signatures of evolutionary processes that have acted on the genome using comparative sequence analysis. We generate high quality draft genome sequences of the chimpanzee, the dog and the opossum. These species share a last common ancestor with humans approximately 6 million, 80 million and 140 million years ago, respectively, and therefore provide distinct perspectives on our evolutionary history. We apply computational methods to explore the functional organization of the genome and to identify genes that contribute to shared and species-specific traits. Second, we study how the genome is bound by proteins and packaged into chromatin in distinct cell types. We develop new methods to map protein-DNA interactions and DNA methylation using single-molecule based sequencing technology. We apply these methods to identify new functional sequence elements based on characteristic chromatin signatures, and to explore the relationship between DNA sequence, chromatin and cellular state.
by Tarjei Sigurd Mikkelsen.
Ph.D.
Ryder, Carol D. "Comparative genomics of Brassica oleracea". Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/51651/.
Pełny tekst źródłaDong, Xin. "Comparative genomics of rickettsia species". Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5054/document.
Pełny tekst źródłaThe Rickettsia genus is composed of small, Gram-negative, bacteria that are obligate intracellular eukaryotic symbionts. Members of the genus Rickettsia are best known for infecting and causing severe diseases in humans and other animals. To date, 26 valid Rickettsia species have been identified worldwide, including 20 that are proven pathogens. All validated Rickettsia species are associated to arthropods that act as vectors and/or reservoirs. The phylogenies based on various molecular markers have resulted in discrepant topologies, with R. bellii and R. canadensis being classified neither among spotted fever nor typhus group rickettsiae. In this thesis, using the advanced whole genomic sequencing methods, we have and analyzed the genomic sequences from four Rickettsia species, including R. helvetica, R. honei, R. australis and R. japonica. Phylogenomics constitute a new strategy to better understand their evolution. These microorganisms underwent a reductive genomic evolution during their specialization to their intracellular lifestyle. Several evolutive characteristics, such as gene rearrangement, reduction, horizontal gene transfer and aquisition of selfish DNA, have shaped Rickettsia genomes. These processes may play an important role in free-living bacteria for balancing the size of genome in order to adapt the intracellular life style. In addition, in contrast with the concept of bacteria becoming pathogens by acquisition of virulence factors, rickettsial pathogenecity may be linked to genomic reduction of metabolism and regulation pathways
Sentausa, Erwin. "Intraspecies comparative genomics of Rickettsia". Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5082/document.
Pełny tekst źródłaThe Rickettsia genus is composed of Gram-negative, obligate intracellular bacteria that cause a range of human diseases around the world. New techniques have led to progress in the identification and classification of Rickettsia, including the introduction of molecular methods like sequence comparison (16S rRNA, ompA, ompB, gltA, sca4 …) and the creation of the subspecies status. Genomics and next-generation sequencing have opened a new way to learn more about the pathogenesis and evolution of Rickettsia. The first part of this thesis is a review on the advantages and limitations of genomics in prokaryotic taxonomy, while the second part consists of the genomic analyses of five Rickettsia subspecies and a new Rickettsia species. Using high-throughput sequencing methods, we obtained the draft genomes of R. sibirica sibirica, R. sibirica mongolitimonae, R. conorii indica, R. conorii caspia, R. conorii israelensis, and R. gravesii. This work can be a basis of further studies to increase the understanding on the disease-causing mechanisms, evolutionary relationships, and taxonomy of rickettsiae
Benevides, Leandro. "Comparative Genomics of Faecalibacterium spp". Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS129.
Pełny tekst źródłaWithin 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
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.
Pełny tekst źródłaPrakash, Amol. "Algorithms for comparative sequence analysis and comparative proteomics /". Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/6904.
Pełny tekst źródłaGaiarsa, 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.
Pełny tekst źródłaThe present thesis is focused on genomic epidemiology of bacterial hospital infections. The hospital environment is unique, as it concentrates a high number of bacterial agents, frequent antibiotic use, and patients with weak immune systems. This combination favours the development and selection of antibiotic resistant strains and the spread of opportunistic infections: in general the thriving of nosocomial pathogens. Genomics and evolutionary approaches have emerged as the cutting edge tools for studying this kind of infections, allowing to study the genomic features of bacterial strains and their evolution. Thanks to the possibility to sequence DNA at a constantly cheaper price, research projects are supported by a growing number of genomes and a considerable amount of genomic data is available in the databases, expanding the amount of possible investigations that can be performed. The first work presented here describes the evolution of the Clonal Complex 258 (CC258) of Klebsiella pneumoniae. Single nucleotide polymorphisms (SNPs) allowed to reconstruct the global phylogeny of the entire species and to collocate the CC258 in its evolutionary context. Furthermore, it was possible to detect the presence of a 1.3 Mb recombination in the genomes of the clade in analysis. A molecular clock approach allowed to date this and other previously discovered recombination events. These findings were used to complete the picture of the evolutionary history of CC258, which is characterized by frequent macro-recombination events. A quick evolutive strategy characterized by exchange of high amount of information is a common feature to other nosocomial pathogens, which develop “superbug” phenotypes. Although common, the macro-recombination evolution model is not shared by all nosocomial infection bacteria. One exception is the SMAL strain of Acinetobacter baumannii, presented in another subproject of this thesis. In this work, the genomes of Sequence Type (ST) 78 of A. baumannii were analyzed. Phylogeny and comparative genomics revealed the presence of two different clades within the ST, presenting different evolutive “lifestyles”. One group (containing the SMAL genomes) was characterized by a lower gene content variability and by the presence of a higher copy number of insertion sequences (ISs). One IS interrupts the comEC/rec2 gene in all the SMAL genomes. This gene codes for a protein involved in the exogenous DNA importation, thus its inactivation limits the gene exchange, suggesting an explanation for the low genomic plasticity. In another work presented in this document, genomic epidemiology was applied to reconstruct the spreading routes of a K. pneumoniae epidemic event in an hospital intensive care unit. At first, a phylogenetic approach was used to separate the isolates that belonged to the outbreak from the sporadic ones. Then the isolation dates and genomic SNPs allowed to build a genomic network, which modelled the chain of infection events in the ward. The reconstruction suggested a star-like diffusion of the pathogen from patient zero to the other infected ones, thus revealing a systematic error in the biosafety procedures of the hospital. This almost-forensic application of genomic epidemiology was also used in two other works presented, both of them concerning the reconstruction of food-borne infections. In one of the works, focused on Salmonella enterica, only synonymous SNPs were used as input to a phylogenetic based investigation, in order to filter out pathoadaptative mutations. In the other article, epidemiological data, molecular typing and SNP-based phylogeny were used to investigate the infection of nine Listeria monocytogenes isolates, which were believed to be part of the same outbreak and in the end proved to be genomically unrelated. Lastly, a review paper on genomic epidemiology is also presented. The article is focused on the latest high impact publications analyzing the genome evolution of bacterial pathogens as well as the propagation dynamics of epidemic outbreaks in very short periods of time. The article also describes the latest historical epidemiological studies, which are possible thanks to modern DNA isolation and sequencing technologies.
Dessimoz, Christophe. "Comparative genomics using pairwise evolutionary distances /". Zürich : ETH, 2009. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=18177.
Pełny tekst źródłaUlrich, Luke. "Comparative Genomics of Microbial Signal Transduction". Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/7632.
Pełny tekst źródłaGolenetskaya, Natalia. "Adressing scaling challenges in comparative genomics". Phd thesis, Université Sciences et Technologies - Bordeaux I, 2013. http://tel.archives-ouvertes.fr/tel-00865840.
Pełny tekst źródłaBuchan, 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.
Pełny tekst źródłaKamvysselis, Manolis 1977. "Computational comparative genomics : genes, regulation, evolution". Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/7999.
Pełny tekst źródłaIncludes bibliographical references (p. 95-99).
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 provides a general approach for identifying these functional elements, by virtue of their stronger conservation across evolutionary time. In this thesis we address key issues in the comparative analysis of multiple species. We present novel computational methods in four areas (1) the automatic comparative annotation of multiple species and the determination of orthologous genes and intergenic regions (2) the validation of computationally predicted protein-coding genes (3) the systematic de-novo identification of regulatory motifs (4) the determination of combinatorial interactions between regulatory motifs. We applied these methods to the comparative analysis of four yeast genomes, including the best-studied eukaryote, Saccharomyces cerevisiae or baker's yeast. Our results show that nearly a tenth of currently annotated yeast genes are not real, and have refined the structure of hundreds of genes. Additionally, we have automatically discovered a dictionary of regulatory motifs without any previous biological knowledge. These include most previously known regulatory motifs, and a number of novel motifs. We have automatically assigned candidate functions to the majority of motifs discovered, and defined biologically meaningful combinatorial interactions between them. Finally, we defined the regions and mechanisms of rapid evolution, with important biological implications.
(cont.) Our results demonstrate the central role of computational tools in modem biology. The analyses presented in this thesis have revealed biological findings that could not have been discovered by traditional genetic methods, regardless of the time or effort spent. The methods presented are general and may present a new paradigm for understanding the genome of any single species. They are currently being applied to a kingdom-wide exploration of fungal genomes, and the comparative analysis of the human genome with that of the mouse and other mammals.
by Manolis (Kellis) Kamvysselis.
Ph.D.
Coates-Brown, Rosanna. "Comparative genomics of the skin staphylococci". Thesis, University of Liverpool, 2015. http://livrepository.liverpool.ac.uk/2046659/.
Pełny tekst źródłaMoore, Matthew Phillip. "Comparative genomics of Pseudomonas aeruginosa populations". Thesis, University of Liverpool, 2017. http://livrepository.liverpool.ac.uk/3021281/.
Pełny tekst źródłaMularoni, Loris. "Comparative genomics of amino acid tandem repeats". Doctoral thesis, Universitat Pompeu Fabra, 2009. http://hdl.handle.net/10803/7187.
Pełny tekst źródłaWuichet, Kristin. "Comparative Genomics of the Microbial Chemotaxis System". Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/16193.
Pełny tekst źródłaFuxelius, 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.
Pełny tekst źródłaGarikipati, 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.
Pełny tekst źródłaMostowy, 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.
Pełny tekst źródłaWith the availability of whole-genome sequence data and tools of comparative genomics, our publications have advanced the recognition that large sequence polymorphisms (LSPs) deleted from Mycobacterium tuberculosis, the causative agent of TB in humans, serve as accurate markers for molecular epidemiologic assessment and phylogenetic analysis. These LSPs have proven informative both for the types of genes that vary between strains, and for the molecular signatures that characterize different MTC members. Genomic analysis of atypical MTC has revealed their diversity and adaptability, illuminating previously unexpected directions of MTC evolution. As demonstrated from parallel analysis of BCG vaccines, a phylogenetic stratification of genotypes offers a predictive framework upon which to base future genetic and phenotypic studies of the MTC. Overall, the work presented in this thesis has provided unique insights and lessons having direct clinical relevance towards understanding TB pathogenesis and BCG vaccination.
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.
Pełny tekst źródłaPark, Gyoungju Nah. "Comparative Genomics in Two Dicot Model Systems". Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/194279.
Pełny tekst źródłaSyme, Robert Andrew. "Comparative Genomics of Parastagonospora and Pyrenophora species". Thesis, Curtin University, 2015. http://hdl.handle.net/20.500.11937/54044.
Pełny tekst źródłaDang, Ha Xuan. "Mold Allergomics: Comparative and Machine Learning Approaches". Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/64205.
Pełny tekst źródłaPh. D.
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.
Pełny tekst źródłaKang, Lin. "Comparative Genomics Insights into Speciation and Evolution of Hawaiian Drosophila". Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/85467.
Pełny tekst źródłaPh. D.
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/.
Pełny tekst źródłaThe advent of Next Generation Sequencing (NGS) in recent years has led to an expressive increase in the number of genomic projects. In a simplified way, sequencing machines generate DNA fragments that are used by genome assembler software. These programs try to merge the DNA fragments to obtain the complete representation of the genomic sequence (for example a chromosome) of the species being sequenced. In some cases the assembling process can be performed more easily for organisms with small-sized genomes (e.g. bacteria with a genome length of approximately 5Mpb) through pipelines that automate most of the task. A trickier scenario arises when the species has a very large genome (above 1Gbp) and complex elements, as in the case of some eukaryotes. In those cases the result of the assembly is usually composed of thousands of fragments (called contigs), an order of magnitude much higher than the number of chromosomes estimated for an organism (usually in the order two digits), giving rise to a highly fragmented assembly. A common activity in these projects is the comparison of the assembly with that of another genome as a form of validation and also to identify common elements between organisms. Although the problem of pairwise alignment of large genomes is well circumvented by existing approaches, multiple alignment of large genomes with highly fragmented assemblies remains a difficult task due to its time and computational requirements. This work consists of a methodology for doing multiple alignment of large eukaryotic genomes with highly fragmented assemblies, a problem that few solutions are able to cope with. Our star alignment-based implementation, was able to accomplish a MSA of groups of assemblies with different levels of fragmentation. The largest of them, a set of 5 reptilian genomes where the B. jararaca assembly (800,000 contigs, N50 of 3.1Kbp) was used as anchor, took 14 hours of execution time to provide a map of conserved regions among the participating species. The algorithm was implemented in a software named FROG (FRagment Overlap multiple Genome alignment), available under the General Public License v3 (GPLv3) terms.
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.
Pełny tekst źródłaMigeon, Pierre. "Comparative genomics of repetitive elements between maize inbred lines B73 and Mo17". Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35377.
Pełny tekst źródłaGenetics Interdepartmental Program
Sanzhen Liu
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 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, revealing differences in organization of highly repetitive sequences between the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
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.
Pełny tekst źródłaQC 20100923
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.
Pełny tekst źródłaAbbas, Ali Hadi. "Comparative structural genomics and phylogenomics of African trypanosomes". Thesis, University of Liverpool, 2018. http://livrepository.liverpool.ac.uk/3022845/.
Pełny tekst źródłaXia, Ai. "Comparative genomics of chromosomal rearrangements in malaria mosquitoes". Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/37335.
Pełny tekst źródłaPh. D.
Lyman, Cole Andrew. "Comparative Genomics Using the Colored de Bruijn Graph". BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/8441.
Pełny tekst źródłaPryszcz, 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.
Pełny tekst źródłaCandida species constitute one of the most prevalent groups of fungal pathogens. From their phylogenetic relationships it is clear that virulence to humans has emerged in this clade several, independent times. The Candida parapsilosis complex is particularly suitable to investigate the emergence of virulence, with three closely-related species of varying degree of pathogenicity and of growing relevance: C. parapsilosis, C. orthopsilosis and C. metapsilosis. In this thesis I present the genome sequencing and analysis of fifteen strains from this clade, sampled from clinical and environmental sources. Notably, genomes of C. orthopsilosis Type 1 and C. metapsilosis were sequenced for the first time. Our results show for the first time the genomic evidence for the existence of recombination, mating and hybridization in this clade, previously considered asexual. We propose the independent emergence of clinical isolates from environmental lineages and a possible role of hybridization in the acquisition of relevant traits for pathogenesis. Finally, in order to gain insight into the emergence of virulence in this clade, we have compared the genomes of all three species of C. parapsilosis complex. We have found expansions in gene families known to be involved in virulence, like adhesins, membrane transporters and extracellular enzymes, as well as expansions in gene families not implicated in virulence so far. Altogether, our findings provide the grounds for numerous hypotheses about the emergence of virulence in Candida spp. and for their future experimental testing. 1
Perrin, Amandine. "Tools for massive bacterial comparative genomics : Development and Applications". Electronic Thesis or Diss., Sorbonne université, 2022. https://theses.hal.science/tel-03789655.
Pełny tekst źródłaBacterial comparative genomics consists in comparing the gene contents of different strains: their pangenome. With the increasing number of strains sequenced, the tools available when I started this PhD were reaching their limits in terms of computation time and space. The aim was to develop a method able to handle thousands of genomes, accurately and in a reasonable amount of time. Besides, to our knowledge, no tool was able to do all key steps of any comparative genomics study. This spurred the development of PanACoTA, a tool to standardize and automatize the process to build the key collections of data needed for these studies. This includes all steps from downloading genomes with a quality control until the inference of a phylogenetic tree based on the core genome (genes shared by all strains). In order to be able to adapt to specific needs (exploration of parameters, additional steps), we implemented it in a modular way. For the “pangenome” module, we developed a new method, based on recent tools of genome comparison and clustering. Robust to changes in sampling size, this method can infer a pangenome of 4000 strains in 30 minutes. During its development, we applied PanACoTA to different kinds of studies. We showed its usefulness for short-term studies (find specificity of a pathogenic strain of E. anophelis), long-term (genomic diversity of E. coli species), or to identify different species in an little-known genus (Morganella)
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.
Pełny tekst źródłaKaranam, 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.
Pełny tekst źródłaCheung, 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.
Pełny tekst źródłaSaski, Christopher A. "Chloroplast comparative genomics implications for phylogeny, evolution and biotechnology /". Connect to this title online, 2007. http://etd.lib.clemson.edu/documents/1193080368/.
Pełny tekst źródłaWagner, Darlene Darlington. "Comparative genomics reveal ecophysiological adaptations of organohalide-respiring bacteria". Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/45916.
Pełny tekst źródłaEllegaard, Kirsten Maren, Lisa Klasson, Kristina Näslund, Kostas Bourtzis i 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.
Pełny tekst źródłaNakjang, Sirintra. "Comparative genomics for studying the proteomes of mucosal microorganisms". Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1265.
Pełny tekst źródłaMuller, 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.
Pełny tekst źródłaGodinez, Ricardo. "Comparative Genomics of the Major Histocompatibility Complex in Amniotes". Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10685.
Pełny tekst źródłaEdwards, 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.
Pełny tekst źródła