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Mousset, Sylvain. "Sélection et neutralité dans le polymorphisme de séquence d'un échantillon populationnel africain de Drosophila melanogaster". Paris 6, 2002. http://www.theses.fr/2002PA066267.
Pełny tekst źródłaVerdier, Yann. "Sélection, identification et caractérisation partielle d'antigènes du spermatozoïde du renard (Vulpes vulpes) en vue de leur utilisation dans un vaccin contraceptif". Nancy 1, 2002. http://docnum.univ-lorraine.fr/public/SCD_T_2002_0307_VERDIER.pdf.
Pełny tekst źródłaClotault, Jérémy. "Impact de la sélection sur l'expression et la variabilité de séquence de gènes de la voie de biosynthèse des carotenoïdes chez la carotte cultivée". Angers, 2009. http://www.theses.fr/2009ANGE0060.
Pełny tekst źródłaCarrot domestication and breeding have led to a diversity of cultivated carrot types exhibiting a high variability for carotenoid content in the root. Carotenoid biosynthesis genes are probably involved in carotenoid level differences, and could have been a selection target for plant breeding. The objectives of this thesis were to investigate the role of transcriptional variations for carotenoid biosynthesis genes on carotenoid accumulation during root development in variously coloured carrots, and to characterise the impact of selection and demographic history, particularly genetic structure, on carotenoid biosynthesis gene sequence variability in cultivated carrots. . . .
Ayel, Elodie. "Reconnaissance spécifique de l'ADN en double-brin par des oligonucléotides : sélection in vitro en présence de ligand". Paris 6, 2009. http://www.theses.fr/2009PA066329.
Pełny tekst źródłaAlibert, Christine. "A propos des snRNPs U2 et U5, et de la sélection des sites de branchement et 3' au cours de l'épissage des ARNs prémessagers". Montpellier 2, 1990. http://www.theses.fr/1990MON20056.
Pełny tekst źródłaDesprés, Laurence. "Histoire évolutive des schistosomes : Phylogénies moléculaires : coévolution et capture d'hôtes : modèle de fixation de la gonochorie". Montpellier 2, 1991. http://www.theses.fr/1991MON20275.
Pełny tekst źródłaMacalou, Sira. "Le transporteur ABCG2 de multiples drogues : rôle d’une séquence spécifique et recherche d’inhibiteurs sélectifs". Thesis, Lyon 1, 2009. http://www.theses.fr/2009LYO10301.
Pełny tekst źródłaDuring chemotherapy, cancer cells frequently succeed to escape the toxic effects of drugs by developing mechanisms of chemoresistance which often result from the presence of an efflux system of these drugs. Such a chemoresistance is correlated to the MDR (MultiDrug Resistance) phenotype and associated to overexpression of membrane ATPases belonging to the ABC (ATP-Binding Cassette) transporters. The ABCG2 transporter belongs to this large family of proteins. Sequence alignment allowed the identification of a specific (LSGGE) sequence in ABCG2, which is quite similar to the canonical sequence signature (VSGGE) of all ABC transporters. Point mutation of these residues into alanine produced a loss of function in L352A and S353A mutants, as observed in transport and on ATPase activity. Structure-activity relationships drawn from some compounds among the family of flavonoids allowed the identification of MBLI 97, boeravinone G, MHT and ABI as potent and ABCG2-specific inhibitors, able to revert multidrug resistance and chemosensitize cell growth. The study of specific sequences and use of specific inhibitors of these transporters constitute strategies to abolish cancer cell chemoresistance and to increase the efficiency of chemotherapeutic treatments
Bourguignon, Pierre Yves Vincent. "Parcimonie dans les modèles Markoviens et application à l'analyse des séquences biologiques". Thesis, Evry-Val d'Essonne, 2008. http://www.theses.fr/2008EVRY0042.
Pełny tekst źródłaMarkov chains, as a universal model accounting for finite memory, discrete valued processes, are omnipresent in applied statistics. Their applications range from text compression to the analysis of biological sequences. Their practical use with finite samples, however, systematically require to draw a compromise between the memory length of the model used, which conditions the complexity of the interactions the model may capture, and the amount of information carried by the data, whose limitation negatively impacts the quality of estimation. Context trees, as an extension of the model class of Markov chains, provide the modeller with a finer granularity in this model selection process, by allowing the memory length to vary across contexts. Several popular modelling methods are based on this class of models, in fields such as text indexation of text compression (Context Tree Maximization and Context Tree Weighting). We propose an extension of the models class of context trees, the Parcimonious context trees, which further allow the fusion of sibling nodes in the context tree. They provide the modeller with a yet finer granularity to perform the model selection task, at the cost of an increased computational cost for performing it. Thanks to a bayesian approach of this problem borrowed from compression techniques, we succeeded at desiging an algorithm that exactly optimizes the bayesian criterion, while it benefits from a dynamic programming scheme ensuring the minimisation of the computational complexity of the model selection task. This algorithm is able to perform in reasonable space and time on alphabets up to size 10, and has been applied on diverse datasets to establish the good performances achieved by this approach
Meslin, Camille. "Analyse de l'évolution de gènes impliqués dans la reproduction". Thesis, Tours, 2011. http://www.theses.fr/2011TOUR4030.
Pełny tekst źródłaGenes involved in reproduction evolve rapidly and are often under positive selection. The objective of this work was to study the evolution of some of these genes, potentially involved in speciation, through their involvement in prezygotic barriers.Our results show that for the SAL1 gene, involved in pheromonal recognition in pig, three amino acids under positive selection participate in the specific binding of the pig pheromone. We also perform an evolutionary analysis of genes experimentally shown to be involved in the sperm-oocyte interaction during fertilization. Each of the nineteen species studied exhibit a particular pattern of evolution, characterized by gene gains and losses, as well as the position of amino acids under positive selection. The divergent evolution of all these genes could be involved in speciation or at least in the reinforcement of species barriers.Finally, the PhyleasProg web server was designed during the thesis. This tool permits to scientists with no experience in phylogenetic analyses to acquire a large number of results quickly and easily on the evolutionary history of their genes of interest
Ambellouis, Sébastien. "Analyse du mouvement dans les séquences d'images par une méthode récursive de filtrage spatio-temporel sélectif". Lille 1, 2000. https://pepite-depot.univ-lille.fr/LIBRE/Th_Num/2000/50376-2000-77-78.pdf.
Pełny tekst źródłaLiu, Jingtian. "Shaping Strategies to Embrace Nonlinear Effects in Optical Fiber Communications". Electronic Thesis or Diss., Institut polytechnique de Paris, 2024. http://www.theses.fr/2024IPPAT007.
Pełny tekst źródłaThe main impediment in long-distance communications is nonlinear interference (NLI), stemming from nonlinear effects in optical fibers. While Digital signal processing algorithms offer partial mitigation, the inherent nonlinear nature of the fiber, coupled with predominant dispersion effects, continues to challenge the increase of transmission throughputs. Addressing nonlinearity at the information source through signal modulation technology is at the heart of our research. Traditional modulation schemes, as spectral efficiency climbs, such as QAM, become increasingly susceptible to NLI while their Mean Squared Euclidean Distance (MSED) diminishes. While multi-dimensional (MD) modulation yields improved linear and partial nonlinear gains, it has not yet demonstrated tangible benefits. On the other hand, the emergence of probabilistic constellation shaping (PCS), preferred for its enhanced linear gain and compatibility with conventional modulation hardware and software, introduces additional NLI. Consequently, the design of nonlinear-tolerant PCS is emerging as a pivotal research direction. Our thesis begins with a novel MD modulation for uniformly distributed signals. Then, we propose a novel approach combining MD with PCS to examine performance variations. Delving into PCS, we investigate the enumerative sphere shaping distribution matcher (DM), initially from an MD stance, and design a DM optimized for nonlinear tolerance over shorter distances. Subsequently, we introduce a new NLI measurement technique, accounting for dispersion effects. Integrating this with the sequence selection framework of PCS, we achieve successful long-distance transmission with notable nonlinear gains
Thivin, Solenne. "Détection automatique de cibles dans des fonds complexes. Pour des images ou séquences d'images". Thesis, Université Paris-Saclay (ComUE), 2015. http://www.theses.fr/2015SACLS235/document.
Pełny tekst źródłaDuring this PHD, we developped an detection algorithm. Our principal objective was to detect small targets in a complex background like clouds for example.For this, we used the spatial covariate structure of the real images.First, we developped a collection of models for this covariate structure. Then, we selected a special model in the previous collection. Once the model selected, we applied the likelihood ratio test to detect the potential targets.We finally studied the performances of our algorithm by testing it on simulated and real images
Hamrouni, Abdelbasset. "Identification des clones de lymphocytes T spécifiques de l'antigène liés au m^eme réarrangement VDJβ ancestral". Lyon, École normale supérieure (sciences), 2003. http://www.theses.fr/2003ENSL0259.
Pełny tekst źródłaLebarbier, Emilie. "Quelques approches pour la détection de ruptures à horizon fini". Paris 11, 2002. http://www.theses.fr/2002PA112141.
Pełny tekst źródłaThis thesis is devoted to the detection of multiple change-points. The first part considers the case of change-points in the mean for Gaussien signal. In Chapter 1, we adopt a bayesien approach: the posterior distribution of the change-points sequence is estimated by Monte Carlo by Markov chain methods. A stochastic version of the EM algorithm is used for estimating the hyper-parameters of the model. In Chapter 2, the change-points and the means are simultaneously estimated by recovering the underlying piecewice constant function denoted by s which is a penalized least-square estimator. We give the penalty form and a non-asymptotic risk bound for the corresponding penalized estimator. The penalty depends on two constants and the noise level which are unknown. In Chapter 3, given known variance we determine the optimal values for the two constants for any function s and size of sample by simulation study. In Chapter 4, rather than estimating the noise level, a heuristic method is used to estimate the penalty itself using the data. We calibrate it and test it on various simulated data sets. In Chapter 5, we propose an hybrid algorithm combining the CART algorithm and a partial exhaustive search for the application for large samples. The second part considers the case of change-points in the distribution of a sequence of independant random variables. In Chapter 6, we associate the distribution to a function s which we estimate by maximizing the penalized likelihood and we give a risk bound for the obtained estimator. In Chapter 7, we adapt the hybrid algorithm proposed in Chapter 5 to detect homogeneous regions in DNA sequences of two bacteria
Darrier, Benoît. "Cartographie fine de la recombinaison, analyse des séquences locales et étude du déséquilibre de liaison chez le blé tendre (Triticum aestivum)". Thesis, Clermont-Ferrand 2, 2016. http://www.theses.fr/2016CLF22764/document.
Pełny tekst źródłaBetter knowledge of the factors that drive recombination (crossovers; COs) in bread wheat (Triticum aestivum L.) is of main interest since this process is the main tool allowing breeders to admix the genetic diversity and to introgress regions of interest in agronomic varieties. We used cytogenetic techniques previously developed on barley to compare the establishment of synapsis during meiosis in deletion lines missing part or whole of the long arm of chromosome 3B of bread wheat and which were previously shown as having a reduced chiasmata number compared to euploid varieties. Cytogenetic analysis combined with bioinformatics studies showed that the synapsis occurs almost normally in mutants and that deletion of some genes known to impact meiosis behavior may explain the observed phenotype. In addition, development of genomic resources (SNPs, sequence) for wheat breeders allowed simultaneous elaboration of high density genetic maps for the 21 chromosomes anchored on genome sequence. All chromosomes present the same recombination pattern with an increase of recombination in the distal parts and reduction in centromeric/pericentromeric regions of the chromosomes. Analysis of more than 250 COs mapped in windows lower than 25kb located on chromosome 3B used as model to study the impact of sequence features on recombination showed that current and ancestral recombination patterns are conserved and that COs preferentially occur in the promoter part of gene expressed in meiosis suggesting that chromatin conformation impacts recombination. Finally, these data were the opportunity to detect recombination-associated motif which presents similarities with the motif targeted by the PRDM9 protein driving recombination in human. This suggests that the control of recombination mechanisms is conserved among eukaryotes
Jonquières, Anne. "Influence de la structure des matériaux et perméants sur les propriétés de sorption et de transfert dans des systèmes polymère / liquides organiques : application à la séparation par pervoration de mélanges alcool-éther à l'aide de polyuréthaneimides (PUI) et modélisation du transfert dans le cas d'un système ternaire". Vandoeuvre-les-Nancy, INPL, 1994. http://www.theses.fr/1994INPL095N.
Pełny tekst źródłaGreene, Malorie. "Étude des conséquences génomiques et fonctionnelles de l'instabilité des microsatellites dans le cancer colorectal". Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066592/document.
Pełny tekst źródłaSince the discovery of a link between mismatch repair (MMR) deficiency and cancer, microsatellite instability (MSI) is thought as a process underlying cell transformation and tumour progression and invasion. MSI tumours are a subset of frequent human neoplasms, both inherited and sporadic, associated with several primary locations (colon, stomach, endometrium…). In MMR-deficient cells, MSI generates hundreds of frameshift mutations in genes (MSI Target Genes, MSI-TGs) containing coding microsatellite sequences (e.g. -1/+1 bp, insertions/deletions, i.e. indels). Some of these mutations affect genes with a role in human carcinogenesis and are thus expected to promote the MSI-driven tumorigenic process. During my PhD, I aimed to decipher the role of MSI in colon tumorigenesis. I exploited exome-sequencing data available in my lab that were generated from the analysis of a series of 47 human MSI primary colorectal cancer (CRC). Through biostatistics analysis and mathematical models that we designed to interpret mutation rates in the context of the high background for instability characterizing MSI in CRC, we identified a few microsatellites containing genes coding mutations that were negatively selected in MSI colon tumours (N=13). Under the hypothesis that these events may have a negative impact in colon tumorigenesis, I demonstrated that the silencing of these MSI target genes (siRNA/shRNA) was deleterious for MSI cancer cells using in vitro and in vivo models (impairment of proliferation and/or migration and/or response to chemotherapy and/or tumour growth) (Jonchère*, Marisa*, Greene* et al., submitted)
Bensmina, Imene. "Étude du promoteur de ZNF74 et des séquences d'ADN reconnues par ce répresseur transcriptionnel". Thèse, 2006. http://hdl.handle.net/1866/15221.
Pełny tekst źródłaLaurin-Lemay, Simon. "Modélisation des biais mutationnels et rôle de la sélection sur l’usage des codons". Thesis, 2019. http://hdl.handle.net/1866/24481.
Pełny tekst źródłaThe acquisition of genomic data continues to grow, as does the appetite to interpret them. But determining the processes that shaped the evolution of coding sequences (and their relative importance) is a scientific challenge that requires the development of statistical models of evolution that increasingly take into account heterogeneities in mutation and selection processes. Identifying selection is a task that typically requires comparing two models: a null model that does not allow for an adaptive evolutionary regime and an alternative model that allows it. When a test between these two models rejects the null, we consider to have detected the presence of adaptive evolution. The task is all the more difficult as the signal is weak and confounded with various heterogeneities neglected by the models. The detection of selection on codon usage is controversial, particularly in Vertebrates. There are several reasons for this controversy: (1) there is a sociological bias in seeing selection as the main driver of evolution, to such an extent that heterogeneities relating to mutation processes are historically neglected; (2) according to the principles of population genetics, the small effective size of vertebrate populations limits the power of selection over synonymous mutations conferring a minimal advantage; (3) On the other hand, selection on the use of codons could be very localized along the coding sequences, at specific sites, subject to selective constraints related to DNA patterns used by the splicing machinery, for example. Phylogenetic mutation-selection models are the preferred tools to address these issues, as they explicitly model mutation processes and selective constraints. All the heterogeneities neglected by the mutation-selection models of Yang and Nielsen [2008] can generate false positives, ranging from 20% (site-specific amino acid preference) to 100% (hypermutability of transitions in CpG context)[Laurin-Lemay et al., 2018b]. In particular, the hypermutability of transitions in the CpG context alone can explain the selection on codon usage detected by Yang and Nielsen [2008]. However, modelling phenomena that take into account data interdependencies (e.g., hypermutability of the CpG context) greatly increases the complexity of the likelihood function. On the other hand, today’s sophisticated models require high-dimensional parameter vectors to model the heterogeneity of the processes studied, in our case selective constraints on the protein. Approximate Bayesian Computation (ABC) is used to bypass the calculation of the likelihood function. This approach differs from the Markov Chain Monte Carlo (MCMC) sampling commonly used to approximate the posterior distribution. We explored the idea of combining these approaches for a specific problem involving high-dimensional parameters and new parameters taking into account dependencies between sites. Under certain conditions, when the high dimensionality parameters are weakly correlated to the new parameters of interest, it is possible to infer the high dimensionality parameters with the MCMC method, and then the parameters of interest using the ABC. This new approach is called Conditional Approximate Bayesian Computation (CABC) [Laurin-Lemay et al., 2018a]. We were able to verify the effectiveness of the CABC method in a case study, namely the hypermutability of transitions in the CpG context within Eutheria [Laurin-Lemay et al.,2018a]. We find that 100% of the 137 genes tested have significant hypermutability of transitions. We have also shown that models incorporating hypermutability of transitions in CpG contexts predict a codon usage closer to that of the genes studied. This suggests that a significant part of codon usage can be explained by mutational processes alone. Finally, we explore several avenues of research emanating from our methodological developments: the application of hypermutability detection of transitions in CpG contexts to the Vertebrate scale; the expansion of the model to recognize contexts other than only CpG (e.g., hypermutability of transitions and transversions in CpG and TpA context); and methodological perspectives to improve the performance of the CABC approach.
Fittipaldi, Nahuel. "Identification and characterization of novel virulence factors from the swine pathogen and zoonotic agent streptococcus suis". Thèse, 2008. http://hdl.handle.net/1866/6393.
Pełny tekst źródłaRoure, Béatrice. "Amélioration de l'exactitude de l'inférence phylogénomique". Thèse, 2011. http://hdl.handle.net/1866/5949.
Pełny tekst źródłaThe explosion of sequence number allows for phylogenomics, the study of species relationships based on large multi-gene alignments, to flourish. Without any doubt, phylogenomics is essentially an efficient way to eliminate the problems of single gene phylogenies due to stochastic errors, but numerous problems remain despite obvious progress realized in modeling evolutionary process. In this PhD-thesis, we are trying to characterize some consequences of a poor model fit and to study their impact on the accuracy of the phylogenetic inference. In contrast to heterotachy, the variation in the amino acid substitution process over time did not attract so far a lot of attention. We demonstrate that this heterogeneity is frequently observed within animals, but also that its existence can interfere with the quality of phylogenomic inference. In absence of an adequate model, the elimination of heterogeneous columns, which are poorly handled by the model, can eliminate an artefactual reconstruction. In a phylogenomic framework, the sequencing strategies often result in a situation where some genes are absent for some species. The issue about the impact of the quantity of empty cells was recently relaunched, but the majority of studies on missing data is performed on small datasets of simulated sequences. Therefore, we were interested on measuring the impact in the case of a large alignment of real data. With a reasonable amount of missing data, it seems that the accuracy of the inference is influenced rather by the choice of the model than the incompleteness of the alignment. For example, the addition of an incomplete sequence that breaks a long branch can at least partially re-establish an artefactual phylogeny. Because, model violations are always representing the major limitation of the accuracy of the phylogenetic inference, the improvement of species and gene sampling remains a useful alternative in the absence of an adequate model. Therefore, we developed a sequence-selection software, which allows the reproducible construction of datasets, based on the quantity of data, their evolutionary speed and their compositional bias. During this study, we did realize that the human expertise still furnishes an indispensable knowledge. The various analyses performed in the course of this PhD thesis agree on the primordial importance of the model of sequence evolution.
Croisetière, Sébastien. "Étude du polymorphisme du gène majeur d’histocompatibilité de classe IIb (MHIIb) chez l’omble de fontaine (Salvelinus fontinalis)". Thèse, 2009. http://hdl.handle.net/1866/3592.
Pełny tekst źródłaClassical major histocompatibility complex class II (MHCII) molecules are cell-surface glycoproteins specialized in the presentation of peptides, mainly derived from extracellular pathogens, to the antigen receptors of CD4+ T cells in the adaptive immune system. They are encoded, with those of the MHC class I, by the most polymorphic genes known to date, with multiple loci and high allelic diversity at each one. Moreover, the polymorphism within MHCII genes is not restricted to coding sequences. It has also been observed in promoters where it was shown to affect the expression level of the genes. Variation in gene regulation is believed to be an important factor from which modification in morphology, physiology or behaviour can be observed in all organisms. Repeated DNA sequences with functional roles in this regulation have been identified within the non-coding parts of the genomes. On the other hand, pathogen-driven selection is also believed to be important in the evolution and maintenance of the polymorphism of the MHC genes in vertebrates. Studies have shown the implication of different MHC alleles in disease resistance or susceptibility. In this study, our aims were to characterize the polymorphism of the MHIIb gene in brook charr (Salvelinus fontinalis), to document its effects on the survival conferred by specific alleles and/or genotypes following an infection and on the variation of the expression level of the gene in different environmental conditions. In a first part, we identified a total of 6 MHIIb alleles, designated Safo-DAB*0101 to Safo-DAB*0601, showing a high similarity to coding sequences from teleost fish and human. Analysis of the b1 domain sequences indicates the effect of a positive selection pressure to select polymorphic mutations in that region of the molecule. Four of these alleles were tested in a challenge experiment against the pathogen Aeromonas salmonicida to evaluate their effect on fish survival. We found that one allele, DAB*0101, was significantly associated with resistance to furonculosis. In addition to homozygotes for this allele, its resistance effect was also detected in the heterozygote individuals of the DAB*0101/*0201 genotype. In contrast, other allelic combinations, namely heterozygous genotypes DAB*0201/*0301 and DAB*0301/*0401 were significantly associated with increased susceptibility. Given that its frequency was relatively low in the population, the negative frequency dependant selection hypothesis could explain the advantage associated with the allele DAB*0101 over the other alleles and highlight the importance of this mechanism to sustain variation at the MHC in brook charr. In a second part, we reported the identification of a polymorphic minisatellite formed of a 32 nucleotides motif in the second intron of MHIIb gene, and for which distinctive repeat numbers of the motif were associated to each alleles (69, 27, 20, 40, 19 and 25 repeats for the DAB*0101 to DAB*0601 alleles respectively). Relative expression levels of four alleles were determined in heterozygous fish at temperature of 18 ºC and 6 ºC. Results indicate that alleles carrying the longest minisatellite showed a 1.67 to 2.56-fold reduction in the transcript expression relatively to the shortest one. In contrast, no significant differences were seen in the expression levels between alleles with comparable minisatellite length at both temperatures. Furthermore, the repressive activity associated to the longest minisatellite was more effective at temperature of 18 ºC in fish from three different genotypes. We finally observed a significant 2.08-fold up-regulation of the total MHII transcript amount at 6 ºC. The results support the implication of repeated DNA sequences in the regulation of the gene transcriptional activity and suggest that a temperature-sensitive minisatellite could potentially be submitted to selective forces and therefore play an important role in gene expression and evolution in ectothermic organisms.