Дисертації з теми "Genomics study"
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Pang, See-Tong. "A functional genomics approach to study prostate disorders /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-640-5/.
Повний текст джерелаShebe, Khadija Ahmed. "Genomics study of anti-tuberculosis drug-induced hypersensitivity reactions." Master's thesis, University of Cape Town, 2015. http://hdl.handle.net/11427/15679.
Повний текст джерелаNorman-Marzella, Nancy L. "Evidence-Based Practice Self-Study Education Program for Staff Nurses on Genomics." ScholarWorks, 2019. https://scholarworks.waldenu.edu/dissertations/7416.
Повний текст джерелаWeirather, Jason Lee. "Computational approaches to the study of human trypanosomatid infections." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/4976.
Повний текст джерелаCurreem, Oi-ting Shirly. "The study of environmental adaptability of laribacter hongkongensis by genomic and proteomic approach." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43931686.
Повний текст джерелаHerniou, Elisabeth Anne. "Use of comparative genomics and phylogenetics to study the evolution of the Baculoviridae." Thesis, Imperial College London, 2003. http://hdl.handle.net/10044/1/7698.
Повний текст джерелаMartinez-Hernandez, Francisco. "The power of one: Study of the marine virosphere using single-virus genomics." Doctoral thesis, Universidad de Alicante, 2019. http://hdl.handle.net/10045/118218.
Повний текст джерелаLa presente tesis ha sido financiada por el Ministerio de Economía y competitividad español (refs. CGL2013-40564-R and SAF2013-49267-EXP), por la Generalitat Valenciana (ref. ACOM/2015/133 and ACIF/2015/332), y por la Gordon and Betty Moore Foundation (ref. 5334).
Lee, Yiu-fai. "Analysis for segmental sharing and linkage disequilibrium a genomewide association study on myopia /." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43912217.
Повний текст джерелаHeeger, Felix [Verfasser]. "Genomics Approaches to the Study of Diversity and Function of Aquatic Fungi / Felix Heeger." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1176634666/34.
Повний текст джерелаRhode, Clint. "Signatures of selection in natural and cultured Abalone (Haliotis midae) : a population genomics study." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/79895.
Повний текст джерелаENGLISH ABSTRACT: The South African abalone, Haliotis midae, commonly known as perlemoen, is an economically important gastropod mollusc. Historically, this species maintained a lucrative fisheries sector; however with increasingly lower landings there has now been a shift to aquaculture. Efforts to conserve natural populations and to improve abalone aquaculture production are thus running in parallel. Previous studies reported significant disparities in parental contributions in aquaculture populations that could explain the rapid divergence of commercial stocks from wild populations. Furthermore, subtle, but significant, population differentiation has also been reported for wild populations on the west-, south-, and east coast of the South African coastline. This study therefore aimed to investigate the evolutionary forces, in particularly selection, facilitating population divergence in wild and cultured H. midae populations using a population genomics approach. By using both microsatellite- and single nucleotide polymorphism (SNP) markers it was found that approximately 10% to 27% of the H. midae genome may be influenced by selection. When incorporating these loci into analyses of population differentiation (e.g. AMOVA, factorial correspondence analysis and estimates of genetic distance) there was a marked increase in genetic divergence between wild and cultured populations (especially when using microsatellite loci) and amongst populations from different geographic regions (particularly supported by the SNP loci). The differences in population clustering as highlighted by microsatellite- and SNP markers can most likely be attributed to the genomic distribution of the respective loci: The SNP markers were developed from EST sequences and therefore mostly represents protein structural variation; whereas the microsatellite markers, found to be putatively under selection, were mainly located in regulatory motifs. The results of this study therefore confirmed previous observations of divergence amongst wild- and cultured populations, but more importantly demonstrated that selection is an important factor driving this divergence. In wild populations selection probably facilitates adaptation to local environmental conditions, whilst amongst aquaculture population adaptation to captivity, husbandry practices and artificial selection may be important determinants. There is evidence for population bottlenecks in wild- and cultured populations; nonetheless long-term effective population sizes seem to be large. Amongst the wild populations, however, short-term population sizes appear to be small most likely due to differential spawning rates amongst reproductively active animals leading to temporal fluctuation in genetic diversity. The results indicate that contact between wild and cultured abalone should be minimised to prevent any adverse effects due to outbreeding depression. With regards to conservation, an emphasis on maintaining adaptive diversity of the wild stocks might be warranted. Continued genetic monitoring is advisable for both wild and cultured abalone populations as to optimally manage the abalone resource for both conservation and commercial viability and sustainability.
AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is 'n ekonomies belangrike buikpotige weekdier. Histories het hierdie spesie 'n winsgewende vissery gehandhaaf, maar met steeds dalende vangste is daar nou 'n verskuiwing na akwakultuur. Pogings om natuurlike populasies te bewaar en perlemoen te verbeter vir verhoogde akwakultuur produksie loop dus in parallel. Vorige studies het bevind dat beduidende verskille in ouerlike bydraes tot die nageslag, in akwakultuur populasies, kan verduidelik hoekom die populasies so vinnig divergeer van die wilde voorouers. Verder, is subtiele, maar betekenisvolle genetiese differensiasie tussen wilde populasies aan die wes-, suid-en ooskus van die land gevind. Hierdie studie is dus daarop gemik om ondersoek in te stel na die mate waartoe verskeie evolusionêre prosesse, in besonder seleksie, die populasie divergensie in beide wilde en gekweekte H. midae teweegbring deur gebruik te maak van ‘n populasie genomika benadering. Deur gebruik te maak van beide mikrosatelliet- en enkel nukleotied polimorfisme (ENP) merkers is dit bevind dat ongeveer 10% tot 27% van die H. midae genoom moontlik beïnvloed word deur seleksie. Met die gebruik van loki onder seleksie tydens die ontleding van populasie differensiasie (bv. AMOVA, faktoriaal korrespondensie analise en genetiese afstand ramings) was daar 'n merkbare toename in genetiese divergensie tussen wilde- en gekweekte populasies (veral wanneer mikrosatelliet loki gebruik is) en onder die populasies vanuit verskillende geografiese gebiede (veral ondersteun deur die ENP loki). Die verskille in die populasie groeperings soos uitgelig deur die mikrosatelliet- en ENP-merkers kan waarskynlik toegeskryf word aan die genomiese verspreiding van die onderskeie loki: Die ENP-merkers is ontwikkel vanaf uitgedrukte volgorde merker (UVM) volgordes en daarom verteenwoordig dit meestal proteïen strukturele veranderinge, terwyl mikrosatelliet merkers eerder in regulatoriese motiewe geleë is. Die resultate van hierdie studie steun dus vorige waarnemings, maar meer belangrik, het dit getoon dat seleksie ‘n betekenisvolle faktor in populasie divergensie in beide wilde en gekweekte populasies is. In wilde populasies fasiliteer seleksie waarskynlik die aanpassing tot plaaslike omgewingstoestande terwyl seleksie onder die gekweekte populasies teweeggebring kan word as gevolg van aanpassing tot aanhouding, boerdery praktyke en kunsmatige seleksie. Daar is bewyse vir populasie bottelnekke in wilde- en gekweekte populasies; tog blyk langtermyn effektiewe populasiegroottes om redelik groot te wees. Onder die wilde populasies is egter gevind dat kort-termyn populasiegroottes klein kan wees, waarskynlik as gevolg van differensiële broeikoerse onder reproduktiewe diere. Dit het tot gevolg dat daar beduidende fluktuasies is in temporale genetiese diversiteit. Die resultate dui daarop dat kontak tussen wilde en gekweekte perlemoen tot 'n minimum beperk moet word om enige nadelige effekte weens uitteling depressie te voorkom. Verder, met betrekking tot bewaring, is ‘n klem op die handhawing van aangepaste genetiese diversitiet dalk geregverdig. Voortgesette genetiese monitering word aanbeveel vir beide wilde- en gekweekte perlemoen populasies ter wille van die optimale bestuur van die perlemoen hulpbron vir beide bewaring en kommersiële lewensvatbaarheid en volhoubaarheid.
International Foundation for Science
National Research Foundation of South Africa
Stellenbosch University
Thomas, Samantha Marie. "Induced pluripotent stem cells as a model to study individual variation and comparative genomics." Thesis, The University of Chicago, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10195620.
Повний текст джерелаThe past decade of genetics research has been defined by the discovery of the profound effects non-coding genetic variation can have on the phenotypes that distinguish humans from each other and from our close evolutionary relatives. The full implications of this new understanding are largely unexplored, however, as modern ethics restricts experimentation in humans and most primates, rendering data from dynamic processes almost non-existent. The study of regulatory molecular dynamics has been changed entirely by the availability of protocols to generate iPSCs and differentiate them into adult cell types. The molecular basis of disease mechanisms, drug response, and developmental processes can now be studied in the relevant tissue, presenting an overwhelming spectrum of possible applications. Of particular interest to comparative biologists, long-standing questions about the relative conservation of early developmental states can now, for the first time, be ethically explored in closely related primates. In this dissertation, we first discuss evidence that iPSCs can faithfully model genetic variation, even when sourced from highly dysregulated cells. We then use an iPSC-based model to study the temporal profile of conservation between humans and chimpanzees during early endoderm development and identify patterns of divergence over developmental stages.
Zhuang, Jiali. "Structural Variation Discovery and Genotyping from Whole Genome Sequencing: Methodology and Applications: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/875.
Повний текст джерелаZhuang, Jiali. "Structural Variation Discovery and Genotyping from Whole Genome Sequencing: Methodology and Applications: A Dissertation." eScholarship@UMMS, 2009. http://escholarship.umassmed.edu/gsbs_diss/875.
Повний текст джерелаSaunders, Gary Ian. "Comparative genomics of nematodes : Caenorhabditis elegans as a tool to study the Haemonchus contortus genome." Thesis, University of Glasgow, 2010. http://theses.gla.ac.uk/1607/.
Повний текст джерелаCurreem, Oi-ting Shirly, and 嘉藹庭. "The study of environmental adaptability of laribacter hongkongensis bygenomic and proteomic approach." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43931686.
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 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 джерелаLogotheti, Marianthi. "Integration of functional genomics and data mining methodologies in the study of bipolar disorder and schizophrenia." Doctoral thesis, Örebro universitet, Institutionen för medicinska vetenskaper, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-52644.
Повний текст джерелаMunung, Nchangwi Syntia. "African researchers' perceptions and expectations of the benefits of genomics research in Africa : a qualitative study." Master's thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20960.
Повний текст джерелаKeays, Maria C. "The desaturase gene family : an evolutionary study of putative speciation genes in 12 species of Drosophila." Thesis, University of St Andrews, 2011. http://hdl.handle.net/10023/2478.
Повний текст джерелаAlegria, Marcos Castanheira. "Identificação de interações proteína-proteína envolvendo os produtos dos Loci hrp, vir e rpf do fitopatógeno Xanthomonas axonopodis pv. citri." Universidade de São Paulo, 2004. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-22082016-162740/.
Повний текст джерелаCitrus Canker, caused by the bacterial plant pathogen Xanthomonas axonopodis pv. citri (Xac) presents one of the most serious problems to Brazilian citriculture. We have initiated a project to identify protein-protein interactions involved in pathogenicity of Xac. Using a yeast two-hybrid system based on GAL4 DNA-binding and activation domains, we have focused on identifying interactions involving subunits, regulators and substrates of: Type Three Secretion System (TTSS), Type Four Secretion System (TFSS) and Quorum Sensing/Rpf System. Components of these systems were used as baits to screening a random Xac genomic library. The TTSS is coded by the hrp (hypersensitive response and pathogenicity), hrc (hrp conserved) and hpa (hrp associated) genes in the chromosomal hrp locus. This secretion system can translocate efector proteins from the bacterial cytoplasm into the host cells. We have identified several previously uncharacterized interactions involving: 1) HrpG, a two-component system response regulator responsible for the expression of Xac hrp operons, and XAC0095, a previously uncharacterized protein encountered only in Xanthomonas spp; 2) HpaA, a protein secreted by the TTSS, HpaB and the C-terminal domain HrcV; 3) HrpB1, HrpD6 and HrpW; 4) HrpB2 and HrcU; 5) Homotropic interactions were also identified for the ATPase HrcN. Xac contains two virB gene clusters, one on the chromosome and one on the pXAC64 plasmid, each of which codes for a unique and previously uncharacterized TFSS. Components of the TFSS of pXAC64, which is most similar to conjugation systems, showed interactions involving proteins coded by the same locus: 1) Homotropic interactions of TrwA; 2) XACb0032 and XACb0033; 3) XAC0035 homotropic interactions; 4) VirB1 and VirB9; 5) XACb0042 and VirB6; 6) XACb0043 and XACb0021 b. Components of the chromosomal TFSS exhibited interactions involving: 1) VirD4 and a group of 12 uncharacterized proteins with a common C-terminal domain motif, include XAC2609 whose gene resides within the vir locus; 2) XAC2609 and XAC261 O; 3) Homotropic interactions of VirB11; 4) XAC2622 and VirB9. Analysis of Quorum Sensing/Rpf System components revealed interactions between the principal Rpf proteins which control Xanthomonas quorum sensing: 1) RpfC and RpfF; 2) RpfC and RpfG; 3) RpfF homotropic interactions; 4) RpfC and CmfA, a protein that presents similarity with Cmf (conditioned medium factor) of Dictyostelium discoideum, which contrais quorum sensing in this organism. The protein-protein interactions that we have detected reveal insights into the composition, organization and regulation of these important mechanisms involved in Xanthomonas pathogenicity.
Marwaha, Shruti. "A Genomics and Mathematical Modeling Approach for the Study of Helicobacter Pylori associated Gastritis and Gastric Cancer." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439308645.
Повний текст джерелаKumwenda, Benjamin. "Comparative genomics study of completely sequenced Thermus sp. strains to enhance and facilitate their application in biotechnology." Thesis, University of Pretoria, 2013. http://hdl.handle.net/2263/40247.
Повний текст джерелаThesis (PhD)--University of Pretoria, 2013.
gm2014
Biochemistry
unrestricted
Dunbar, Ellyn. "Genetic and Environmental Influences of Bullying Involvement: A Longitudinal Twin Study." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5311.
Повний текст джерелаJain, Sourabh. "Comparative genomic study for identifying gene acquisitions in Megavirales." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0184/document.
Повний текст джерелаDiscovery of giant viruses with giant genome size and surprising genomic features raises different question about their origin and evolution. Many phylogenetic studies have pointed out decisive role of HGTs and genetic exchanges on evolution of MVs, but, majority of them are based on closely related MV families. To investigate HGT events, we have determined gene distributions and gene phylogenies for the 86 complete MV ORFomes classified in 6 defined and 4 putative families, in context of their homologs from other domains of life. Using an automated phylogenetic workflow MimiLook, 4577 OGs were detected, out of which, 91% of OGs were found to be family specific, whereas, 9% are represented by proteins from 2 or more MV families. 414 OGs were detected as HGT event. We applied a similar procedure to the 7,898 non-orthologous proteins to detect transfer events and identified 259 HGTs from non-orthologous proteins. Instances of HGT were found to be depicting donor specificity, as viruses of vertebrates/invertebrates acquired genes from donors like Euteleostomii, Eutheria, Baculoviridae and proteobacteria; algal viruses and protozoan viruses were found to be acquiring genes from donors like Dictyostellium, Mammeillales, Firmicutes, Clostridiales. In conclusion, clear distinction can be seen in the genome mosaicism of distantly related Megavirale families, where they evolved via genome specificity and family specific gene acquisitions from their respective ecological niche. Our systematic search for HGT events of non-megavirale origin provides the first estimate of the total contribution of HGT in family specific genome mosaicism of distantly related Megavirales
Mentzer, Alexander. "Identification and characterisation of the genetic determinants of variable response to antigens from infectious agents." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:702692ee-6971-4bc1-be8e-f6082a10cc92.
Повний текст джерелаMignogna, Kristin. "Genome-Wide Systems Genetics of Alcohol Consumption and Dependence." VCU Scholars Compass, 2019. https://scholarscompass.vcu.edu/etd/5946.
Повний текст джерелаRutschmann, Sereina [Verfasser]. "Evolutionary processes in mayflies (Ephemeroptera) : genomics approaches to the study of ancient origins and recent diversification / Sereina Rutschmann." Berlin : Freie Universität Berlin, 2015. http://d-nb.info/1068504730/34.
Повний текст джерелаHuang, Yun [Verfasser]. "Combining genomics and transcriptomics to study adaptation to lake and river habitats in three-spined sticklebacks / Yun Huang." Kiel : Universitätsbibliothek Kiel, 2018. http://d-nb.info/1152264176/34.
Повний текст джерелаCavani, Ligia. "Genetic study of Babesia bovis infection level and the association with tick resistance in Hereford and Braford cattle /." Jaboticabal, 2019. http://hdl.handle.net/11449/181344.
Повний текст джерелаCoorientador: Rodrigo Giglioti
Coorientador: Fernando Flores Cardoso
Banca: Danísio Prado Munari
Banca: Ricardo da Fonseca
Banca: Guilherme Jordão de Magalhães Rosa
Banca: Maria Eugênia Zerlotti Mercadante
Resumo: Babesiose bovina é uma doença transmitida pelo carrapato, sendo que a Babesia bovis é considerada a espécie mais patogênica. Ambos são considerados como um entrave na melhoria da produtividade da bovinocultura de corte nos trópicos, especialmente para animais de raças taurinas e suas cruzas. Esse estudo analisou uma população de bovinos Hereford e Braford e foi composto por quatro capítulos com os seguintes objetivos: Capítulo 1) Revisão de literatura; Capítulo 2) Estimação de parâmetros genéticos para contagem de carrapatos (TC) e B. bovis usando modelos lineares e modelos lineares generalizados; Capítulo 3) Avaliar a habilidade de predição e a possibilidade de aplicação da seleção genômica e conduzir estudos de associação genômica ampla (GWAS) para nível de infecção de B. bovis (IB); Capítulo 4) Procurar por estruturas causais entre TC, IB, ganho de peso do nascimento a desmama (WG) e ganho de peso da desmama ao sobreano (YG) usando a abordagem do modelo de equação estrutural (SEM). Os carrapatos foram contados manualmente em um lado do animal. A quantificação de B. bovis foi feita por meio de ensaios de qPCR. No Capítulo 2, os dados de contagem de carrapato e B. bovis estavam em escala logaritímica para as análises usando modelos lineares. O modelo de Poisson foi aplicado para contagem de carrapato sem tranformação logarítimica e para os modelos probit o fenótipo foi considerado como ausência (0) ou presença (1) de B. bovis baseado em três diferentes limiares (BBt1: IB usa... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Bovine babesiosis is a tick-borne disease, and the Babesia bovis is considered the most pathogenic species. Both parasites constitute major drawbacks for improvement of beef cattle productivity in the tropics, especially when purebred and crossbred taurine animals are used. This study analyzed a population of Hereford and Braford cattle and it was composed of four chapters with the following objectives: Chapter 1) Literature review; Chapter 2) Estimate genetic parameters for tick count (TC) and B. bovis using linear and generalized linear models; Chapter 3) Evaluate predictive ability and application of genomic selection and performed genome wide association studies (GWAS) for B. bovis infection level (IB) using single step GBLUP model; Chapter 4) Search for causal structures to investigate potential functional relationships among TC, IB, weight gain from birth to weaning (WG), and weight gain from weaning to yearling (YG) using structural equation modeling (SEM). Tick counts were performed by manually counting adult female ticks on one side of each animal. The B. bovis quantification was performed using a qPCR assay. In the Chapter 2, the tick count and B. bovis records were in log scale for analysis using linear model. A Poisson model was applied for tick count without log transformation and for probit model the phenotype was assessed by absence or presence of B. bovis based on three different thresholds (BBt1: IB using the threshold observed; BBt2: BB using threshold as a ... (Complete abstract click electronic access below)
Doutor
Tzika, Athanasia. "Small steps and grand leaps: a study of micro- and macroevolutionary processes." Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210546.
Повний текст джерелаPopulation genetics, conservation, and phylogeny inference. The Jamaican boa (Epicrates subflavus) is an endemic species, whose natural populations greatly and constantly declined since the late 19th century, mainly due to predation by introduced species, human persecution, and habitat destruction. Using species-specific nuclear microsatellite loci and mitochondrial sequences, we investigated the population structure of this endangered reptile. All analyses pinpointed to an Eastern versus (Western+Central) pattern of differentiation in agreement with geological data and patterns of differentiation uncovered in other vertebrate and invertebrate Jamaican species. The same molecular markers were employed on 80 Jamaican boas of the European captive breeding program. This approach allowed us to (i) clarify all ambiguities in the studbook, (ii) correct parental allocation errors and (iii) assess the genetic diversity and the level of inbreeding of the current captive population. These results provide important insights for guiding the development of proper ex-situ and in-situ species survival and habitat management plans for this vulnerable snake. In the same framework of classical evolutionary genetics, we performed preliminary analyses of cytochrome b-like sequences in representatives of all cetacean families (but one), and revealed the presence of at least four nuclear mitochondrial pseudogenes that were independently inserted into the nuclear genome.
Evo-Devo. The emergence of Evolutionary Developmental biology has caused a partial shift in the criteria for the selection of model species. Thus far, the main criterion was the relevance of a species for understanding human biology, whereas in the frame of the new discipline, it is the understanding of the generative mechanisms underlying biological diversity that is put forward. We discussed a few criteria and limitations of major relevance to the choice of model species for Evo-Devo studies, and applied a pragmatic approach to identify possible model species within Amniotes.
Moreover, we developed MANTiS, an application pipeline that aims at integrating genomic, functional and expression data with evolutionary concepts, thus constituting the missing link between multi-species genome comparisons and functional analyses. Using MANTiS, we proceeded in the analysis of 35 metazoan full genomes for identifying all lineage-specific gene gains and losses. These results were combined with functional and expression analyses, and we demonstrated the much higher performance of MANTiS against popular databases of ortholog clusters (InParanoid, OrthoMCL, RoundUp).
Finally, preliminary results of our attempt to adapt the new revolutionary technology of DNA sequencing in microfabricated high-density picoliter reactors (developed by 454/Roche) to the ultra-fast sequencing of brain full transcriptomes in multiple reptilian species are highly promising. As an example, the Crocodylus sample generated more than 72 Mbases (per run), which were successfully assembled in approximately 31,000 contigs. One third of the latter could be matched to known sequences in the transcriptome of related species. After fine-tuning of the in silico analyses, and incorporation of genomic sequence data, we expect our approach to provide important insights not only in the evolution of central nervous system novelties in vertebrates, but in transcriptomes in general as the brain transcriptome is one of the most complex among all organs.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Häkkinen, Suvi T. "A functional genomics approach to the study of alkaloid biosynthesis and metabolism in Nicotiana tabacum and Hyoscyamus muticus cell cultures /." [Espoo, Finland] : VTT, 2008. http://www.vtt.fi/inf/pdf/publications/2008/P696.pdf.
Повний текст джерелаMelo, Thaise Pinto de [UNESP]. "Genome-wide association study of reproduction traits in Nelore cattle, including additional phenotypic information from non-genotyped animals." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/123734.
Повний текст джерелаEsta dissertação foi dividida em três capítulos, o primeiro é uma revisão de literatura sobre o assunto que será discutido nos capítulos seguintes. No segundo capítulo, foi realizado um estudo de associação genômica ampla para a característica idade ao primeiro parto (IPP) em gado Nelore, que objetivou: 1) avaliar se a informação fenotípica adicional dos animais não genotipados afeta o mapeamento de QTLs da IPP; avaliar, por simulação, se esta informação fenotípica adicional contribui para detectar QTLs mais precisamente para uma característica complexa, com poucos genótipos disponíveis. O terceiro capítulo apresenta um estudo de associação para a característica reconcepção de primíparas (RP) em gado Nelore, cujo objetivo foi detectar importantes regiões genômicas (QTLs) associadas com esta característica. No capítulo dois, estudos de associação foram realizados utilizando as metodologias Bayes C e Weighted single step GBLUP (WssGBLUP) e as 10 janelas de marcadores (de 1Mb) que explicaram a maior proporção da variância para IPP foram identificadas e exploradas. Dois cenários foram investigados, um incluindo todas as fêmeas com informação fenotípica disponível (cenário SI - 43.482 fêmeas), e outro incluindo apenas as fêmeas com genótipo disponível (cenário SII - 1.813 fêmeas). Três iterações foram realizadas no método WssGBLUP, sendo recomputados os efeitos dos animais e dos SNPs a cada iteração. Foi simulada uma população com parâmetros e estrutura similares aos dos dados reais, com dois diferentes níveis de desequilíbrio de ligação (alto e baixo) entre os marcadores adjacentes. No capítulo três, os dados consistiram de 142.878 registros fenotípicos de RP e 2.923 genótipos. Os estudos de associação foram realizados com o método WssGBLUP usando três diferentes pesos (iterações) para os efeitos dos SNPs. Para cada iteração subsequente a variância genética ...
This dissertation was divided in three chapters, the first one is a literature review about the subject that will be discussed in subsequent chapters. In the second chapter, a genome wide association study (GWAS) for age at first calving (AFC) in Nelore cattle was performed, using real and simulated data, aiming to 1) assess if additional phenotypic information from non-genotyped animals affect QTL mapping of AFC; 2) evaluate, by simulation, if this additional phenotypic information contributes to detect QTLs more precisely for a low heritable complex trait, and with few available genotypes. The third chapter presents a GWAS for heifer rebreeding (HR) in Nelore cattle. In chapter two, GWA studies were performed using Bayes C and weighted single step GBLUP (WssGBLUP) methods and the top 10 marker windows (1Mb) that explained the larger proportion of variance for AFC were identified and further explored. Two scenarios were investigated, one including all females with available phenotypic information (SI scenario, with 43,482 females), and the other including just the females with available genotype (SII scenario, with 1,813 females). Three iterations were performed in WssGBLUP, recomputing the animals and SNPs effect in each subsequent iteration. It was simulated a population mimicking the parameters and the structure of the real dataset. Two different disequilibrium linkage levels (low and high) between adjacent markers were simulated. In chapter three, the data consisted of 142,878 HR phenotypic records and 2,923 genotypes. The GWAS was performed with WssGBLUP method using three different weightings (iterations) for the SNP effects. Total genetic variances were calculated for the top 10 1Mb SNP-windows, detected by each iteration. On each subsequent iteration, the genetic variance was distributed for a smaller number of SNPs, and the SNP effects were recomputed. Genes possibly associated with HR were searched to reinforce the suggestive ...
Melo, Thaise Pinto de. "Genome-wide association study of reproduction traits in Nelore cattle, including additional phenotypic information from non-genotyped animals /." Jaboticabal, 2015. http://hdl.handle.net/11449/123734.
Повний текст джерелаCoorientador: Lucia Galvão de Albuquerque
Banca: Henrique Nunes de Oliveira
Banca: Idalmo Garcia Pereira
Resumo: Esta dissertação foi dividida em três capítulos, o primeiro é uma revisão de literatura sobre o assunto que será discutido nos capítulos seguintes. No segundo capítulo, foi realizado um estudo de associação genômica ampla para a característica idade ao primeiro parto (IPP) em gado Nelore, que objetivou: 1) avaliar se a informação fenotípica adicional dos animais não genotipados afeta o mapeamento de QTLs da IPP; avaliar, por simulação, se esta informação fenotípica adicional contribui para detectar QTLs mais precisamente para uma característica complexa, com poucos genótipos disponíveis. O terceiro capítulo apresenta um estudo de associação para a característica reconcepção de primíparas (RP) em gado Nelore, cujo objetivo foi detectar importantes regiões genômicas (QTLs) associadas com esta característica. No capítulo dois, estudos de associação foram realizados utilizando as metodologias Bayes C e "Weighted single step GBLUP" (WssGBLUP) e as 10 janelas de marcadores (de 1Mb) que explicaram a maior proporção da variância para IPP foram identificadas e exploradas. Dois cenários foram investigados, um incluindo todas as fêmeas com informação fenotípica disponível (cenário SI - 43.482 fêmeas), e outro incluindo apenas as fêmeas com genótipo disponível (cenário SII - 1.813 fêmeas). Três iterações foram realizadas no método WssGBLUP, sendo recomputados os efeitos dos animais e dos SNPs a cada iteração. Foi simulada uma população com parâmetros e estrutura similares aos dos dados reais, com dois diferentes níveis de desequilíbrio de ligação (alto e baixo) entre os marcadores adjacentes. No capítulo três, os dados consistiram de 142.878 registros fenotípicos de RP e 2.923 genótipos. Os estudos de associação foram realizados com o método WssGBLUP usando três diferentes pesos (iterações) para os efeitos dos SNPs. Para cada iteração subsequente a variância genética...
Abstract: This dissertation was divided in three chapters, the first one is a literature review about the subject that will be discussed in subsequent chapters. In the second chapter, a genome wide association study (GWAS) for age at first calving (AFC) in Nelore cattle was performed, using real and simulated data, aiming to 1) assess if additional phenotypic information from non-genotyped animals affect QTL mapping of AFC; 2) evaluate, by simulation, if this additional phenotypic information contributes to detect QTLs more precisely for a low heritable complex trait, and with few available genotypes. The third chapter presents a GWAS for heifer rebreeding (HR) in Nelore cattle. In chapter two, GWA studies were performed using Bayes C and weighted single step GBLUP (WssGBLUP) methods and the top 10 marker windows (1Mb) that explained the larger proportion of variance for AFC were identified and further explored. Two scenarios were investigated, one including all females with available phenotypic information (SI scenario, with 43,482 females), and the other including just the females with available genotype (SII scenario, with 1,813 females). Three iterations were performed in WssGBLUP, recomputing the animals and SNPs effect in each subsequent iteration. It was simulated a population mimicking the parameters and the structure of the real dataset. Two different disequilibrium linkage levels (low and high) between adjacent markers were simulated. In chapter three, the data consisted of 142,878 HR phenotypic records and 2,923 genotypes. The GWAS was performed with WssGBLUP method using three different weightings (iterations) for the SNP effects. Total genetic variances were calculated for the top 10 1Mb SNP-windows, detected by each iteration. On each subsequent iteration, the genetic variance was distributed for a smaller number of SNPs, and the SNP effects were recomputed. Genes possibly associated with HR were searched to reinforce the suggestive ...
Mestre
Li, Xingang. "Heritability enrichment of immunoglobulin G N-glycosylation relevant genes in specific tissues." Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2020. https://ro.ecu.edu.au/theses/2386.
Повний текст джерелаLee, Yiu-fai, and 李耀暉. "Analysis for segmental sharing and linkage disequilibrium: a genomewide association study on myopia." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43912217.
Повний текст джерелаLee, Bo-Hyung. "High thoughput study of biofilm and virulence in Listeria monocytogenes using innovative approaches." Thesis, Université Clermont Auvergne (2017-2020), 2019. http://www.theses.fr/2019CLFAC017.
Повний текст джерелаConditions and proliferation in a wide range of environments from soil to mammalian host cells. The genetic heterogeneity in L. monocytogenes is reflected on its diversified clonal structure which correlates, to some extent, with phenotypic traits such as virulence or stress resistance. The thesis investigated two most prominent phenotypes, biofilm formation and virulence potential, from various perspectives using state-of-the art technologies. Throughout the studies, large panels of isolates were used to represent the intraspecific diversity. Unfavourable stimuli such as cold shock and nutrient deprivation induced bacterial adhesion step. Addition of NaCl to growth cultures stimulated biofilm production and, surprisingly, it significantly intensified biofilm maturation of nutrient-deprived cells. High degree of variation in relative biofilm productivity was observed among serotypes, genotypes, as well as isolates across culture conditions, however, certain genotype (clonal complex 26) revealed distinctively higher biofilm production under cold temperature (10°C) suggesting an association of genotype with biofilm phenotype. Pan-GWAS identified a number of genes among which those implicated in functions such as ‘transformation/competence’, ‘phage-related genes’, and ‘metabolism of phosphate’ will need further investigations for their roles in biofilm formation. RNA sequencing analysis revealed high intraspecific heterogeneity in basal transcriptome profiles that featured the role of regulatory network including certain transcriptional factors with key roles in virulence such as σB, PrfA, and CodY. The transcriptomic plasticity between lineage I and II as well as hyper- and hypovirulent genotypes supported the evolutionary and epidemiological characteristics of L. monocytogenes. Moreover, the central metabolic pathway was implicated in the infection in Galleria mellonella model system. Conclusively, the thesis explored intraspecific diversity in L. monocytogenes and resulted in ample phenotypic, genomic, and transcriptomic findings. With the integrative omics approach in listeriology, the present work will contribute to unveiling the physiology and pathogenesis of the bacterium
Jian, Xueqiu. "A Family-Based Association Study of Conduct Disorder." Digital Commons @ East Tennessee State University, 2010. https://dc.etsu.edu/etd/1697.
Повний текст джерелаMancia, Annalaura <1976>. "Functional Genomics and Cell Biology of the Dolphin (Tursiops runcatus): Establishment of Novel Molecular Tools to Study Marine Mammals in Changing Environments." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2010. http://amsdottorato.unibo.it/2462/.
Повний текст джерелаSomavilla, Adriana Luiza [UNESP]. "Prediction of genomic-enabled breeding values and genome-wide association study for feedlot average daily weight gain in Nelore cattle." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/128158.
Повний текст джерелаA seleção para taxa de crescimento utilizando o número de dias para atingir determinado peso ou ganho de peso médio resultaria em menores ciclos de produção. Manter o aumento da produtividade exige, entre outros fatores, a utilização de animais melhorados, tanto nos sistemas de pastagem quanto de confinamento. Além disso, as informações genômicas podem ser usadas para predizer os valores genéticos genômicos (GEBVs) mais cedo na vida dos animais, o que reduziria os intervalos de geração e aumentaria os ganhos de produtividade. Inúmeros trabalhos tem sido conduzidos para identificar metodologias apropriadas à determinadas raças e características, o que irá resultar em GEBVs mais acurados. Os objetivos deste estudo foram comparar a acurácia de predição dos GEBVs e a habilidade de identificar regiões genômicas e genes relacionados ao ganho de peso médio diário em bovinos da raça Nelore, pela aplicação de diferentes modelos de regressão e densidades genotípicas. Informações genômica e fenotípica de 804 novilhos nascidos em três safras, filhos de 34 touros, foram utilizadas para predizer GEBVs por meio de três modelos (Bayesian GBLUP, BayesA e BayesC ), quatro densidades genotípicas (Illumina BovineHD BeadChip, TagSNPs, GeneSeek indicus de alta (HDi) e baixa (LDi) densidades) e dois fenótipos ajustados. A estrutura de família foi considerada por meio da análise de componentes principais. Os animais foram distribuídos em subconjunto de treinamento (safras 1 e 2) ou validação (safra 3) para realização da análise de validação cruzada. Estimativas de correlação de Pearson, coeficientes de regressão e erro quadrado médio foram usados para avaliar acurácia, inflação e viés dos GEBVs estimados, respectivamente. O estudo de associação ampla do genoma (GWAS) também foi realizado nos mesmos conjuntos de dados, entretanto, os resultados foram comparados com...
Selection for fast growth rates using number of days to achieve specific weights or average weight gain would result in shorter production periods. Maintaining the rate of productivity increasing will demand, among other factors, genetically improved animals in both pasture and feedlot systems. Besides, genomic information could be used to predict genomic-enabled breeding values (GEBVs) earlier in animals' life, which would reduce generation intervals and increase productivity gains. Numerous studies have been conducted in order to identify appropriate methodologies to specific breeds and traits, which will result in more accurate GEBVs. The aim of this study was to compare the prediction accuracy of GEBVs and the ability to identify genomic regions and genes related to average weight daily gain in Nelore cattle, by applying different regression models and genotypes densities datasets. Genomic and phenotypic information of 804 steers born in three season, offspring of 34 bulls, were used to predict GEBVs through three models (Bayesian GBLUP, BayesA and BayesC ), four genotypic densities (Illumina BovineHD BeadChip, TagSNPs, GeneSeek Genomic Profiler High (HDi) and Low (LDi) density indicus) and two adjusted phenotypes. Family structure was accounted by using principal component analysis. Animals were assigned either to training (seasons 1 and 2) or testing (season 3) subsets to perform the cross-validation analysis. Estimates of Pearson correlation, regression coefficients and mean squared errors were used to access accuracy, inflation and bias of the estimated GEBVs, respectively. Genome-wide association study (GWAS) was also performed on above datasets, however, results were compared based on ...
Somavilla, Adriana Luiza. "Prediction of genomic-enabled breeding values and genome-wide association study for feedlot average daily weight gain in Nelore cattle /." Jaboticabal, 2015. http://hdl.handle.net/11449/128158.
Повний текст джерелаCoorientador: Luciana Correia de Almeida Regitano
Coorientador: Fabiana Barichello Mokry
Banca: Luiz Lehmann Coutinho
Banca: Rogério Abdallah Curi
Banca: Marcos Vinicius Gualberto Barbosa da Silva
Banca: Nedenia Bonvino Stafuzza
Resumo: A seleção para taxa de crescimento utilizando o número de dias para atingir determinado peso ou ganho de peso médio resultaria em menores ciclos de produção. Manter o aumento da produtividade exige, entre outros fatores, a utilização de animais melhorados, tanto nos sistemas de pastagem quanto de confinamento. Além disso, as informações genômicas podem ser usadas para predizer os valores genéticos genômicos (GEBVs) mais cedo na vida dos animais, o que reduziria os intervalos de geração e aumentaria os ganhos de produtividade. Inúmeros trabalhos tem sido conduzidos para identificar metodologias apropriadas à determinadas raças e características, o que irá resultar em GEBVs mais acurados. Os objetivos deste estudo foram comparar a acurácia de predição dos GEBVs e a habilidade de identificar regiões genômicas e genes relacionados ao ganho de peso médio diário em bovinos da raça Nelore, pela aplicação de diferentes modelos de regressão e densidades genotípicas. Informações genômica e fenotípica de 804 novilhos nascidos em três safras, filhos de 34 touros, foram utilizadas para predizer GEBVs por meio de três modelos (Bayesian GBLUP, BayesA e BayesC ), quatro densidades genotípicas (Illumina BovineHD BeadChip, TagSNPs, GeneSeek indicus de alta (HDi) e baixa (LDi) densidades) e dois fenótipos ajustados. A estrutura de família foi considerada por meio da análise de componentes principais. Os animais foram distribuídos em subconjunto de treinamento (safras 1 e 2) ou validação (safra 3) para realização da análise de validação cruzada. Estimativas de correlação de Pearson, coeficientes de regressão e erro quadrado médio foram usados para avaliar acurácia, inflação e viés dos GEBVs estimados, respectivamente. O estudo de associação ampla do genoma (GWAS) também foi realizado nos mesmos conjuntos de dados, entretanto, os resultados foram comparados com...
Abstract: Selection for fast growth rates using number of days to achieve specific weights or average weight gain would result in shorter production periods. Maintaining the rate of productivity increasing will demand, among other factors, genetically improved animals in both pasture and feedlot systems. Besides, genomic information could be used to predict genomic-enabled breeding values (GEBVs) earlier in animals' life, which would reduce generation intervals and increase productivity gains. Numerous studies have been conducted in order to identify appropriate methodologies to specific breeds and traits, which will result in more accurate GEBVs. The aim of this study was to compare the prediction accuracy of GEBVs and the ability to identify genomic regions and genes related to average weight daily gain in Nelore cattle, by applying different regression models and genotypes densities datasets. Genomic and phenotypic information of 804 steers born in three season, offspring of 34 bulls, were used to predict GEBVs through three models (Bayesian GBLUP, BayesA and BayesC ), four genotypic densities (Illumina BovineHD BeadChip, TagSNPs, GeneSeek Genomic Profiler High (HDi) and Low (LDi) density indicus) and two adjusted phenotypes. Family structure was accounted by using principal component analysis. Animals were assigned either to training (seasons 1 and 2) or testing (season 3) subsets to perform the cross-validation analysis. Estimates of Pearson correlation, regression coefficients and mean squared errors were used to access accuracy, inflation and bias of the estimated GEBVs, respectively. Genome-wide association study (GWAS) was also performed on above datasets, however, results were compared based on ...
Doutor
Harshfield, Eric Leigh. "Genomics of lipid metabolism : identification of genetic determinants of lipid metabolites and the effect of perturbations of lipid levels on coronary heart disease risk factors." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/277818.
Повний текст джерелаChen, Hui-Min. "A More Accessible Drosophila Genome to Study Fly CNS Development: A Dissertation." eScholarship@UMMS, 2015. http://escholarship.umassmed.edu/gsbs_diss/758.
Повний текст джерелаPlummer, Dylan. "Facilitating the Study of Chromatin Organization with Deep Learning." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1589203000193806.
Повний текст джерелаLuo, Chengwei. "Development of algorithms for metagenomics and applications to the study of evolutionary processes that maintain microbial biodiversity." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/47730.
Повний текст джерелаTurón, Rodrigo Gemma. "A genome editing based approach to study tumor cell heterogeneity." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/667524.
Повний текст джерелаEls tumors colorectals no són una entitat homogènia sinó que estan formats per una barreja de cèl·lules de fenotips variats, reminiscents dels tipus cel·lulars de l’epiteli intestinal sa. Estudis recents suggereixen que el creixement del càncer colorectal (CCR), igual que el de l’intestí normal, està mediat per una jerarquia amb origen en cèl·lules mare. Les cèl·lules mare del càncer, identificades per l’expressió del gen LGR5, es troben a l’àpex de la jerarquia i impulsen l’expansió del CCR i la metàstasis. Aquesta tesi se centra en caracteritzar la dinàmica d’expansió dels diferents compartiments tumorals i en identificar les cèl·lules que en mantenen el creixement. També hem intentat elucidar quina és la cèl·lula d’origen de la metàstasi. Per a realitzar aquest projecte primer hem desenvolupat nous models per estudiar la malaltia humana, combinant el cultiu d’organoids derivats de pacients i l’edició genòmica mitjançant CRISPR/Cas9. Això ens ha permès visualitzar diferents tipus cel·lulars tumorals in vivo usant LGR5, KRT20 i EMP1 com a marcadors de cèl·lula mare, cèl·lula diferenciada i cèl·lula invasiva, respectivament. Addicionalment, també hem establert un sistema per seguir la progènie de les poblacions mencionades. Hem descobert que tant el compartiment de cèl·lules mare com el diferenciat són capaços de donar lloc a una progènie que persisteix en el temps, suggerint que ambdós tipus cel·lulars contribueixen al creixement tumoral. A més a més, hem observat plasticitat entre els dos compartiments, cosa que indica que la jerarquia cel·lular es perd durant el desenvolupament del tumor. Finalment, mitjançant l’ús d’EMP1 com a marcador de cèl·lules invasives hem identificat un subgrup de cèl·lules diferenciades amb propietats migratòries i amb potencial per reclutar cèl·lules mieloides. La nostra hipòtesi és que la població EMP1+ és la que dissemina del tumor primari i inicia la metàstasi. En resum , les nostres dades suposen una nova visió en l’estudi del mode de creixement del càncer de colon d’estadis avançats en humà, i suggereixen que els trets de cèl·lula mare no són necessaris per creixement tumoral ni la disseminació metastàtica, contràriament al que es pensava inicialment, degut als estudis realitzats en adenoma de ratolí.
Lin, Ling. "Genetic Approaches to Study Transcriptional Activation and Tumor Suppression: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/610.
Повний текст джерелаJones, Donald Thomas. "A study of Hardy-Weinberg equilibrium, linkage equilibrium, and population structure in Hispanics using seven genetic markers." CSUSB ScholarWorks, 1997. https://scholarworks.lib.csusb.edu/etd-project/1478.
Повний текст джерелаYan, Shuangchun. "Using the Bacterial Plant Pathogen Pseudomonas syringae pv. tomato as a Model to Study the Evolution and Mechanisms of Host Range and Virulence." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/77293.
Повний текст джерелаPh. D.
Singh, Babita 1986. "Large-scale study of RNA processing alterations in multiple cancers." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/572859.
Повний текст джерелаEl procesamiento del ARN y sus alteraciones son determinantes para entender el fenotipo de las células en condiciones normales y de enfermedad. En particular, alteraciones en el procesamiento de ARN de determinados genes se han vinculado a características distintivas del cáncer ampliamente aceptadas. Con la disponibilidad de datos genómicos y transcriptómicos a gran escala paramúltiples tipos de cáncer, es posible abordar cuestiones ambiciosas como la obtención de una visión global de las alteraciones en el procesamiento de ARN que son específicas para cada tipo de cáncer, así como de aquellas las comunes a varios tipos. El primer objetivo de esta tesis es obtener una visión global de las alteraciones del procesamiento de ARN en diferentes tipos de tumores, así como de las alteraciones en las proteínas de unión a ARN (componente trans), y si dichas alteraciones resultan en un procesamiento diferencial del RNA. Utilizando datos de más de 4000 pacientes para 11 tipos de tumores, establecemos la relación entre las alteraciones de las proteínas de unión a ARN y cambios de splicing en múltiples tipos de tumores. El segundo objetivo va un paso más allá y explora en detalle las alteraciones del procesamiento de ARN con respecto a mutaciones en las secuencias reguladoras del ARN (componente cis). Utilizando datos de genomas completos para más de 1000 pacientes, estudiamos a fondo la secuencia de genes para identificar regiones cortas significativamente mutadas en partes codificantes y no codificantes por proteína, y que además están enriquecidas en posibles sitios reguladores del ARN, incluyendo regiones intrónicas profundas. La recurrencia de las mutaciones en algunas regiones no codificantes es comparable a la de algunos genes drivers de cáncer conocidos. Además, analizamos el impacto de estas mutaciones a nivel del ARN mediante el uso de datos de secuenciación de ARN de las mismas muestras. Este trabajo propone una estrategia novedosa y potente para estudiar las mutaciones en cáncer con el fin de identificar nuevos mecanismos oncogénicos. Además, compartimos la inmensa cantidad de datos generados en estos análisis para que otros investigadores los puedan estudiar en detalle y validarlos experimentalmente.