Great efforts have been devoted to decipher the sequence composition of the genomes and transcriptomes of diverse organisms. Continuing advances in high-throughput sequencing technologies have led to a decline in associated costs, facilitating a rapid increase in the amount of available genetic data. In particular genome studies have undergone a fundamental paradigm shift where genome projects are no longer limited by sequencing costs, but rather by computational problems associated with assembly. There is an urgent demand for more efficient and more accurate methods. Most recently, “hybrid” methods that integrate short- and long-read data have been devised to address this need. LazyB is a new, low-cost hybrid genome assembler. It starts from a bipartite overlap graph between long reads and restrictively filtered short-read unitigs. This graph is translated into a long-read overlap graph. By design, unitigs are both unique and almost free of assembly errors. As a consequence, only few spurious overlaps are introduced into the graph. Instead of the more conventional approach of removing tips, bubbles, and other local features, LazyB extracts subgraphs whose global properties approach a disjoint union of paths in multiple steps, utilizing properties of proper interval graphs. A prototype implementation of LazyB, entirely written in Python, not only yields significantly more accurate assemblies of the yeast, fruit fly, and human genomes compared to state-of-the-art pipelines, but also requires much less computational effort. An optimized C++ implementation dubbed MuCHSALSA further significantly reduces resource demands. Advances in RNA-seq have facilitated tremendous insights into the role of both coding and non-coding transcripts. Yet, the complete and accurate annotation of the transciptomes of even model organisms has remained elusive. RNA-seq produces reads significantly shorter than the average distance between related splice events and presents high noise levels and other biases The computational reconstruction remains a critical bottleneck. Ryūtō implements an extension of common splice graphs facilitating the integration of reads spanning multiple splice sites and paired-end reads bridging distant transcript parts. The decomposition of read coverage patterns is modeled as a minimum-cost flow problem. Using phasing information from multi-splice and paired-end reads, nodes with uncertain connections are decomposed step-wise via Linear Programming. Ryūtōs performance compares favorably with state-of-the-art methods on both simulated and real-life datasets. Despite ongoing research and our own contributions, progress on traditional single sample assembly has brought no major breakthrough. Multi-sample RNA-Seq experiments provide more information which, however, is challenging to utilize due to the large amount of accumulating errors. An extension to Ryūtō enables the reconstruction of consensus transcriptomes from multiple RNA-seq data sets, incorporating consensus calling at low level features. Benchmarks show stable improvements already at 3 replicates. Ryūtō outperforms competing approaches, providing a better and user-adjustable sensitivity-precision trade-off. Ryūtō consistently improves assembly on replicates, demonstrable also when mixing conditions or time series and for differential expression analysis. Ryūtōs approach towards guided assembly is equally unique. It allows users to adjust results based on the quality of the guide, even for multi-sample assembly.:1 Preface 1.1 Assembly: A vast and fast evolving field 1.2 Structure of this Work 1.3 Available 2 Introduction 2.1 Mathematical Background 2.2 High-Throughput Sequencing 2.3 Assembly 2.4 Transcriptome Expression 3 From LazyB to MuCHSALSA - Fast and Cheap Genome Assembly 3.1 Background 3.2 Strategy 3.3 Data preprocessing 3.4 Processing of the overlap graph 3.5 Post Processing of the Path Decomposition 3.6 Benchmarking 3.7 MuCHSALSA – Moving towards the future 4 Ryūtō - Versatile, Fast, and Effective Transcript Assembly 4.1 Background 4.2 Strategy 4.3 The Ryūtō core algorithm 4.4 Improved Multi-sample transcript assembly with Ryūtō 5 Conclusion & Future Work 5.1 Discussion and Outlook 5.2 Summary and Conclusion

La choroïde ou uvée, située entre la rétine et la sclérotique, est une membrane vasculaire qui tapisse la paroi de l’œil, son rôle est d’assurer l’apport en nutriment de la rétine et de l’iris. Ce tissu peut être le siège de nombreuses tumeurs, bénignes ou malignes. Le mélanome de la choroïde est la tumeur intra-oculaire la plus fréquente de l’adulte mais les facteurs de risque sont mal connus: l’exposition aux ultraviolets n’est pas clairement établi dans la genèse de la tumeur, de même que l’âge ou le sexe.L’énucléation a longtemps été considérée comme la seule option thérapeutique, mais depuis de nombreuses années, des techniques dites conservatrices de l’œil se sont développées. Des études ont montré qu’il n’y a pas de différence significative de survie entre les patients ayant subis une énucléation et les patients traités avec des méthodes conservatrices. De plus, à ce jour, aucune thérapie adjuvante n’a montré son efficacité après le traitement du mélanome oculaire primaire. En effet, malgré un traitement initial bien adapté, la moitié des patients va récidiver sur le mode métastatique. Environ 30\% des patients récidivent dans les 5 ans, ce chiffre augmente jusqu’à 50\% à 15 ans.L’œil étant dépourvu de structures lymphatiques, la diffusion métastatique du melanome uvéal se fait par voie hématogène. Le foie est le site privilégié de développement de métastases, faisant toute la gravité du pronostic. La médiane de survie après apparition de métastases est de 2 à 6 mois en l’absence de traitement. Il peut exister de façon plus anecdotique des métastases pulmonaires, ganglionnaires, osseuses ou cutanées.Sur un plan génétique, les critères les plus fréquemment détectés pour le mélanome uvéal sont la perte du chromosome 3 et le gain du 8q. Plusieurs études montrent dans beaucoup de cas des aberrations chromosomiques non aléatoires sur les chromosomes 1, 3, 6 et 8 et que la perte du chromosome 3 et le gain du 8q sont associés significativement à une survie réduite et au développement de métastase. Plusieurs rapports suggèrent deux entités distinctes de mélanome uvéal (avec et sans monosomie du chromosome 3) qui ne peuvent pas être différenciées du fait de leur aspect clinico-pathologique similaire.Afin d’améliorer le diagnostic et le traitement du mélanome de la choroïde, nous proposons d’effectuer des analyses d’expression et du nombre de copie d’ADN de ce mélanome particulier, avec pour objectifs : l’identification des gènes liés à l’apparition de métastase pour classer les patients à haut risque afin qu’ils puissent bénéficier d’une immunothérapie adjuvante spécifique, la caractérisation de ces gènes au niveau moléculaire, et l’étude du potentiel de ces gènes en tant que cibles thérapeutiques.Dans ce manuscrit je décrirai en détail le lignage mélanocytaire afin de comprendre les particularités du mélanome de la choroïde par rapport au mélanome cutané, puis j'aborderai l'importance des approches haut débit dans l'étude des cancers et les techniques d'analyse bioinformatiques utilisées. Je présenterai ensuite les différents résultats obtenus comme la mise en évidence d'une phosphatase, PTP4A3, qui semble avoir de l'importance dans le développement métastatique du mélanome de la choroïde. / The choroid is a layer of highly vascularised tissue surrounding the eye. Choroidal blood nourishes the retinal pigment epithelium and the photoreceptors on the outer layer of the retina. Uveal melanoma occurs to the detriment of uveal melanocytes (located in the iris, ciliary body and choroid) and is the most common intraocular malignancy in adults. The etiological factors involved in the process of malignant transformation are poorly understood. There is a doubtful role of environmental factors such exposure to sunlight, age or sexe in the emergence of uveal melanoma.The management of uveal melanomas has greatly evolved, moving towards more focused and conservative treatments (such as observation, photocoagulation, thermotherapy, radiotherapy). According to literature, there is no significant difference in survival between patients treated with enucleation and those treated with conservative methods. To date, no adjuvant therapy has proven effective following the initial treatment of ocular melanoma. The metastatic pattern for uveal melanoma differs from that of skin melanoma and is usually located in the liver. About 50\% of patients will develop metastases after a median time of three years, and will ultimately die of their disease. Once the disease becomes metastatic, median survival ranges from two to six months, and only 15\% of the patients survive more than one year. Surgical resection of metastases is feasible only if occurring in limited areas. Genetic differences may be the origin of the various types of melanoma and their different features. Multivariate analyses of genomic imbalances, showed that cutaneous and uveal melanomas presnted different copy number changes. The most frequently detected imbalances in uveal melanoma is the loss of chromosome 3 and gain of 8q. Further studies revealed that most cases show non-random chromosomal aberrations of chromosomes 1, 3, 6 and 8 and that the loss of chromosome 3 and gain of 8q were significantly associated with overall survival and the development of metastases. Some reports suggested two distinct entities of uveal melanoma (with or without chromosome 3 monosomy) previously unrecognized because of their similar clinicopathological features. In order to improve diagnosis and treatment of uveal melanoma, we propose to perform transcriptome and DNA copy number analysis with following objectives : identify genes linked to metastasis behaviour to identify high risk patients who could take advantage of specific adjuvant therapy ; characterize these genes at molecular level ; study if these genes could be powerful therapeutic target.In this thesis, I will describe the melanocyte lineage in order to understand differences observed between cutaneous and uveal melanoma, then I will discuss the importance of high-throughput approaches in the study of cancer and bioinformatics analysis techniques used. I will finally present the different results as the significance of a phosphatase, PTP4A3, which seems to be relevant in metastatic behaviour in uveal melanoma.

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