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You searched for +publisher:"Université du Luxembourg" +contributor:("Schneider, Reinhard [president of the jury]"). Showing records 1 – 3 of 3 total matches.

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Université du Luxembourg

1. Nielsen, Sune Steinbjorn. Diversity Preserving Genetic Algorithms - Application to the Inverted Folding Problem and Analogous Formulated Benchmarks.

Degree: 2016, Université du Luxembourg

Protein structure prediction is an essential step in understanding the molecular mechanisms of living cells with widespread applications in biotechnology and health. Among the open problems in the field, the Inverse Folding Problem (IFP) that consists in finding sequences that fold into a defined structure is, in itself, an important research problem at the heart of most rational protein design approaches. In brief, solutions to the IFP are protein sequences that will fold into a given protein structure, contrary to conventional structure prediction where the solution consists of the structure into which a given sequence folds. This inverse approach is viewed as a simplification due to the fact that the near infinite number of structure conformations of a protein can be disregarded, and only sequence to structure compatibility needs to be determined. Additional emphasis has been put on the generation of many sequences dissimilar from the known reference sequence instead of finding only one solution. To solve the IFP computationally, a novel formulation of the problem was proposed in which possible problem solutions are evaluated in terms of their predicted secondary structure match. In addition, two specialised Genetic Algorithms (GAs) were developed specifically for solving the IFP problem and compared with existing algorithms in terms of performance. Experimental results outlined the superior performance of the developed algorithms, both in terms of model score and diversity of the generated sets of problem solutions, i.e. new protein sequences. A number of landscape analysis experiments were conducted on the IFP model, enabling the development of an original benchmark suite of analogous problems. These benchmarks were shown to share many characteristics with their IFP model counterparts, but are executable in a fraction of the time. To validate the IFP model and the algorithm output, a subset of the generated solutions were selected for further inspection through full tertiary structure prediction and comparison to the original protein structure. Congruence was then assessed by super-positioning and secondary structure annotation statistics. The results demonstrated that an optimisation process relying on a fast secondary structure approximation, such as the IFP model, permits to obtain meaningful sequences. Advisors/Committee Members: AFR [sponsor], Bouvry, Pascal [superviser], Schneider, Reinhard [president of the jury], Talbi, El-Ghazali [member of the jury], Danoy, Grégoire [member of the jury], Jurkowski, Wiktor [member of the jury], University of Luxembourg: High Performance Computing - ULHPC [research center].

Subjects/Keywords: Genetic Algorithms; Inverted Folding Problem; Diversity Preservation; Engineering, computing & technology :: Computer science [C05]; Ingénierie, informatique & technologie :: Sciences informatiques [C05]

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Nielsen, S. S. (2016). Diversity Preserving Genetic Algorithms - Application to the Inverted Folding Problem and Analogous Formulated Benchmarks. (Doctoral Dissertation). Université du Luxembourg. Retrieved from http://orbilu.uni.lu/handle/10993/28226

Chicago Manual of Style (16th Edition):

Nielsen, Sune Steinbjorn. “Diversity Preserving Genetic Algorithms - Application to the Inverted Folding Problem and Analogous Formulated Benchmarks.” 2016. Doctoral Dissertation, Université du Luxembourg. Accessed October 18, 2019. http://orbilu.uni.lu/handle/10993/28226.

MLA Handbook (7th Edition):

Nielsen, Sune Steinbjorn. “Diversity Preserving Genetic Algorithms - Application to the Inverted Folding Problem and Analogous Formulated Benchmarks.” 2016. Web. 18 Oct 2019.

Vancouver:

Nielsen SS. Diversity Preserving Genetic Algorithms - Application to the Inverted Folding Problem and Analogous Formulated Benchmarks. [Internet] [Doctoral dissertation]. Université du Luxembourg; 2016. [cited 2019 Oct 18]. Available from: http://orbilu.uni.lu/handle/10993/28226.

Council of Science Editors:

Nielsen SS. Diversity Preserving Genetic Algorithms - Application to the Inverted Folding Problem and Analogous Formulated Benchmarks. [Doctoral Dissertation]. Université du Luxembourg; 2016. Available from: http://orbilu.uni.lu/handle/10993/28226

2. Narayanasamy, Shaman. Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community.

Degree: 2017, Université du Luxembourg

Microbial communities are ubiquitous and dynamic systems that inhabit a multitude of environments. They underpin natural as well as biotechnological processes, and are also implicated in human health. The elucidation and understanding of these structurally and functionally complex microbial systems using a broad spectrum of toolkits ranging from in situ sampling, high-throughput data generation ("omics"), bioinformatic analyses, computational modelling and laboratory experiments is the aim of the emerging discipline of Eco-Systems Biology. Integrated workflows which allow the systematic investigation of microbial consortia are being developed. However, in silico methods for analysing multi-omic data sets are so far typically lab-specific, applied ad hoc, limited in terms of their reproducibility by different research groups and suboptimal in the amount of data actually being exploited. To address these limitations, the present work initially focused on the development of the Integrated Meta-omic Pipeline (IMP), a large-scale reference-independent bioinformatic analyses pipeline for the integrated analysis of coupled metagenomic and metatranscriptomic data. IMP is an elaborate pipeline that incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning as well as genomic signature-based visualizations. The IMP-based data integration strategy greatly enhances overall data usage, output volume and quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python while relying on Docker for reproducibility. The IMP pipeline was then applied to a longitudinal multi-omic dataset derived from a model microbial community from an activated sludge biological wastewater treatment plant with the explicit aim of following bacteria-phage interaction dynamics using information from the CRISPR-Cas system. This work provides a multi-omic perspective of community-level CRISPR dynamics, namely changes in CRISPR repeat and spacer complements over time, demonstrating that these are heterogeneous, dynamic and transcribed genomic regions. Population-level analysis of two lipid accumulating bacterial species associated with 158 putative bacteriophage sequences enabled the observation of phage-host population dynamics. Several putatively identified bacteriophages were found to occur at much higher abundances compared to other phages and these specific peaks usually do not overlap with other putative phages. In addition, there were several RNA-based CRISPR targets that were found to occur in high abundances. In summary, the present work describes the development of a new bioinformatic pipeline for the analysis of coupled metagenomic and metatranscriptomic datasets derived from microbial communities and its application to a study focused on the dynamics of bacteria-virus interactions. Finally, this work demonstrates the power of integrated multi-omic investigation of microbial consortia towards the… Advisors/Committee Members: Fonds National de la Recherche - FnR [sponsor], Wilmes, Paul [superviser], Schneider, Reinhard [president of the jury], Goncalves, Jorge [secretary], Williams, Rohan [member of the jury], Anders, Andersson [member of the jury], Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center].

Subjects/Keywords: Multi-omics data integration; Metagenomics; Metatranscriptomics; Microbial ecology; Microbiome; Reproducibility; Reproducibility; Bacteriophages; Dynamics; Life sciences :: Biotechnology [F06]; Sciences du vivant :: Biotechnologie [F06]; Life sciences :: Environmental sciences & ecology [F08]; Sciences du vivant :: Sciences de l'environnement & écologie [F08]; Life sciences :: Microbiology [F11]; Sciences du vivant :: Microbiologie [F11]; Life sciences :: Multidisciplinary, general & others [F99]; Sciences du vivant :: Multidisciplinaire, généralités & autres [F99]; Engineering, computing & technology :: Multidisciplinary, general & others [C99]; Ingénierie, informatique & technologie :: Multidisciplinaire, généralités & autres [C99]; Human health sciences :: Multidisciplinary, general & others [D99]; Sciences de la santé humaine :: Multidisciplinaire, généralités & autres [D99]

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Narayanasamy, S. (2017). Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community. (Doctoral Dissertation). Université du Luxembourg. Retrieved from http://orbilu.uni.lu/handle/10993/29800

Chicago Manual of Style (16th Edition):

Narayanasamy, Shaman. “Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community.” 2017. Doctoral Dissertation, Université du Luxembourg. Accessed October 18, 2019. http://orbilu.uni.lu/handle/10993/29800.

MLA Handbook (7th Edition):

Narayanasamy, Shaman. “Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community.” 2017. Web. 18 Oct 2019.

Vancouver:

Narayanasamy S. Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community. [Internet] [Doctoral dissertation]. Université du Luxembourg; 2017. [cited 2019 Oct 18]. Available from: http://orbilu.uni.lu/handle/10993/29800.

Council of Science Editors:

Narayanasamy S. Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community. [Doctoral Dissertation]. Université du Luxembourg; 2017. Available from: http://orbilu.uni.lu/handle/10993/29800


Université du Luxembourg

3. Killcoyne, Sarah. Insilico genomes for high-throughput sequencing cancer-specific analysis.

Degree: 2015, Université du Luxembourg

As a genomic disease cancer is unique in that the entire genome can be highly unstable, with new mutations accumulating at a rapid rate and massive alterations to the chromosomal structure. Structural aberrations can be highly significant to a patient’s disease, resulting in aberrant proteins that can drive a cancer to progress faster or metastasize. Such aberrations may also have more subtle effects, enabling the cellular population to more rapidly develop drug resistance or simply generate highly diverse populations within a tumor making targeted therapies less effective. In fact it is these diverse or heterogeneous cellular populations, with highly mutated and frequently structurally aberrant genomes, that make understanding the extent of a tumor genome’s variation so challenging. Large scale sequencing efforts through the Cancer Genome Atlas and the International Cancer Genome Consortium have sequenced thousands of cancer genomes, and while small-scale variants have enabled researchers to begin to trace the evolutionary history and diversity of tumor genomes, large-scale structural variations have continued to be difficult to identify.Current methods and technologies for short-read sequencing generally rely on fitting genomes to a single reference assembly that is assumed to be representative of all individuals. Tumor genomes, which consist of heterogeneous cellular populations with unique aberrations can vary significantly from a ‘normal’ genome. This means that such single references are poor representations of a cancerous cell population, and so methods that rely less directly on the reference offer better opportunities to investigate these aberrations. In this project, a new method for large-scale structural variant identification, called MultiSieve, is proposed. This method uses prior knowledge to generate and test multiple references for each patient genome. Validation using simulated data establishes the utility of the method, and a comparison with commonly used methods demonstrates that MultiSieve is capable of finding variations often missed by traditional methods and that there are likely to be more structural variants in patients than have been identified previously. Advisors/Committee Members: Fonds National de la Recherche - FnR [sponsor], del Sol Mesa, Antonio [superviser], Schneider, Reinhard [president of the jury], Balling, Rudi [member of the jury], Galas, David [member of the jury], Andrade, Miguel [member of the jury], Luxembourg Centre for Systems Biomedicine (LCSB): Computational Biology (Del Sol Group) [research center], University of Luxembourg: High Performance Computing - ULHPC [research center].

Subjects/Keywords: Cancer genomics; structural variation; Life sciences :: Genetics & genetic processes [F10]; Sciences du vivant :: Génétique & processus génétiques [F10]

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Killcoyne, S. (2015). Insilico genomes for high-throughput sequencing cancer-specific analysis. (Doctoral Dissertation). Université du Luxembourg. Retrieved from http://orbilu.uni.lu/handle/10993/22512

Chicago Manual of Style (16th Edition):

Killcoyne, Sarah. “Insilico genomes for high-throughput sequencing cancer-specific analysis.” 2015. Doctoral Dissertation, Université du Luxembourg. Accessed October 18, 2019. http://orbilu.uni.lu/handle/10993/22512.

MLA Handbook (7th Edition):

Killcoyne, Sarah. “Insilico genomes for high-throughput sequencing cancer-specific analysis.” 2015. Web. 18 Oct 2019.

Vancouver:

Killcoyne S. Insilico genomes for high-throughput sequencing cancer-specific analysis. [Internet] [Doctoral dissertation]. Université du Luxembourg; 2015. [cited 2019 Oct 18]. Available from: http://orbilu.uni.lu/handle/10993/22512.

Council of Science Editors:

Killcoyne S. Insilico genomes for high-throughput sequencing cancer-specific analysis. [Doctoral Dissertation]. Université du Luxembourg; 2015. Available from: http://orbilu.uni.lu/handle/10993/22512

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