Genomic Signatures in De Bruijn Chains

Genomic Signatures from DNA Word Graphs

Genomes have both deterministic and random aspects, with the underlying DNA sequences exhibiting features at numerous scales, from codons and cis-elements through genes and on to regions of conserved or divergent gene order. The DNAWords program aims to identify mathematical structures that characterize genomes at multiple scales. The focus of this work is the fine structure of genomic sequence...

A Large Set of Secure Signatures for DS-SS Long Range Radars in Autonomous Cars

The current trend in the use of ICT to boost the development of the automotive sector is mainly addressed towards so called autonomous vehicles, equipped with appropriate sensors, actuators and processors, that make them able to move safely, without the intervention of a human driver. Actually, since several years, ICT permitted a widespread implementation of systems to help the driver maintain...

Thesis Advisory Committee Start-Up Meeting: Using de Bruijn graphs to assemble and compare genomic sequences

Reducing Genome Assembly Complexity with Optical Maps

De Bruijn graphs provide a framework for genome assembly, where the correct reconstruction of the genome is given by one of the many Eulerian tours through the graph. The assembly problem is complicated by genomic repeats, which allow for many possible Eulerian tours, thereby increasing the de Bruijn graph complexity. Optical maps provide an ordered listing of restriction fragment sizes for a g...

On the recognition of de Bruijn graphs and their induced subgraphs

The directed de Bruijn graphs appear often as models in computer science, because of the useful properties these graphs have. Similarly, the induced subgraphs of these graphs have applications related to the sequencing of DNA chains. In this paper, we show that the directed de Bruijn graphs can be recognized in polynomial time. We also show that it is possible to recognize in polynomial time wh...