Assessment of Predictive Genomic Biomarkers for Response to Cisplatin-based Neoadjuvant Chemotherapy in Bladder Cancer

Cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy is recommended for patients with muscle-invasive bladder cancer (MIBC). It has been shown that somatic deleterious mutations in ERCC2, gain-of-function mutations in ERBB2, and alterations in ATM, RB1, and FANCC are correlated with pathological response to NAC in...

Comparing Current Noise in Biological and Solid-State Nanopores

Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of...

Genetic factors associated with a poor outcome in head and neck cancer patients receiving definitive chemoradiotherapy

About half of advanced stage head and neck squamous cell carcinoma (HNSCC) patients can be cured by chemoradiotherapy. Patient outcome may be partially determined by the genetic alterations in HNSCC, rendering these alterations promising candidate prognostic factors and/or therapeutic targets. However, their relevance in patient outcome...

DNA sensing with nanopores in graphene nanoribbons

The information that can be extracted from DNA base sequences, is important for our understanding of biology, for insights in disease, and the way we practice medicine. The technology that one uses to determine DNA-base sequences is called ‘DNA sequencing’. A portable device that enables fast and accurate sequencing, can potentially greatly...

Probing DNA Translocations with Inplane Current Signals in a Graphene Nanoribbon with a Nanopore

Many theoretical studies predict that DNA sequencing should be feasible by monitoring the transverse current through a graphene nanoribbon while a DNA molecule translocates through a nanopore in that ribbon. Such a readout would benefit from the special transport properties of graphene, provide ultimate spatial resolution because of the single...

Algorithms for sequence-based reverse metabolic engineering

Microorganisms are employed on a large scale in a variety of industrial production processes, such as production of food and ingredients, beverages, pharmaceutical compo- nents and fine- and bulk chemicals. Improving the behaviour of these microorganisms is of crucial importance in the design of efficient production processes. In this thesis we...