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Item type:Publication, Access status: with files , Design and implementation of molecular circuits for mitigating genetic diseasesRNA-based tools (e.g. synthetic small RNAs, sRNAs) are designed and developed for engineering novel molecular circuits and theranostic approaches of genetic nonsense mutation- associated diseases, particularly cystic fibrosis (CF). Cellular computation combined with de novo approaches to gene regulation were explored for the diagnosis and mitigation of CF. Diagnostic rules based on Boolean expressions using miRNA profiles were proposed.Publicationtype: Doctoral Thesis312 2374 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Detection of pathogenic infections in neurological disorders through recycling of gene expression dataPublicationtype: Doctoral Thesis97 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , LWE-based encryption schemes and their applications in privacy-friendly data aggregationWe construct new Learning With Errors-based encryption schemes in order to solve two problems: privacy-preserving data aggregation and privacy-friendly social media marketing.The former allows for the aggregation of privacy-sensitive data from multiple users without trusting the aggregator. Our schemes improve over the state-of-the-art both in terms of runtime and bandwidth e ciency. In particular, our decryption routine is about 150 times faster compared to previous results. Secondly, we propose the first known solution for privacy-friendly social media marketing. Our construction maintains strong security and privacy guarantees and provides cryptographic proofs of correctness.Publicationtype: Doctoral Thesis664 3499 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Mapping dynamic programming algorithms on graphics processing unitsAlignment is the fundamental operation used to compare biological sequences. It also serves to identify regions of similarity that are eventually consequences of structural, functional, or evolutionary relationships. Today, the processing of sequences from large DNA or protein databases is a big challenge. Graphics Processing Units (GPUs) are based on a highly parallel, many-core streaming architecture and can be used to tackle the processing of large biological data. In the thesis, progressive alignment methods and their parallel implemenation by modern GPUs are studied. It turns out that wavefront and matrix-matrix product techniques can cope best with the data dependencies and so are highly appropriate for the implementation on a GPU. The performance of these methods is analyzed and the method with the highest speed-up is used to realize the alignment stage in the well-known software package ClustalW. Similar studies are made for the hidden Markov model. General principles and guidelines for GPU programming of matrix-based algorithms are discussed.Publicationtype: Doctoral Thesis914 1234 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Topics in abstract order geometryAn interval space is a set with a ternary relation satisfying some axioms that support the interpretation of the ternary relation as location of a point between two points. Some new concepts, including those of a topological, a quadrimodular and a quadrimedian interval space and a geodesic quadrimedian closure are developed. A sufficient criterion for embeddability of an interval space into a median metric space is proved. For two central structure theorems of analysis and algebra it is proved that analogues are valid for quadrimedian spaces, but do not hold in general for median spaces.Publicationtype: Doctoral Thesis424 1061 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Graph-based Methods for the Design of DNA ComputationsThe reliability of results in DNA based computations strongly depends on the DNA sequences representing the units of information. The task of finding appropriate sequences is currently handled by means of conventional computing. The most accurate criterium for this purpose is the free energy of hybridization complexes built by two DNA single strands. This thesis addresses two issues in this area. First, finding of a secondary structure of DNA/DNA complexes having minimal free energy. For this, a novel graph-based representation of DNA/DNA complexes is introduced and two advanced methods calculating the free energy based on dynamic programming are proposed. Second, the validation of a given set of DNA words to encode a particular assignment of a mathematical problem. For this, a method is developed based on free energy assessment. It is suitable for DNA computing models that are based on an interdependent encoding of DNA words, which represent two different types of entities in the mathematical problem. Another accomplishment of the thesis is an optimization of the Floyd-Warshall algorithm for finding shortest paths in a weighted graph. A memory reduction method for the particular case of bipartite graphs is established.Publicationtype: Doctoral Thesis475 1792 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Coding theory via Groebner basesCoding theory plays an important role in efficient transmission of data over noisy channels.In this thesis efficient encoding procedure for linear codes is developed using an algebraic approach. Description of linear codes as ideals in a residue class ring are given in terms of Groebner basis. While investigating primitive Reed Muller codes, a special family of linear codes with designed Hamming distance is obtained. A result proves their superiority over existing primitive Reed Muller codes. Furthermore, codes associated to a particular binomial ideal, defined as a sum of toric ideal and a prime ideal, are explored through minimal generators and Groebner basis. For these non-toric binomial ideals universal Groebner bases, Graver bases and circuits are also found. It is shown that each such binomial ideal has a natural reduced Groebner basis which provides a very compact encoding procedure. Finally, the binomial ideal of a linear code is presented in terms of its syzygy modules and the corresponding finite free resolution is also given.Publicationtype: Doctoral Thesis561 1117