Containing pandemics through targeted testing of households.

Background: While invasive social distancing measures have proven efficient to control the spread of pandemics failing wide-scale deployment of vaccines, they carry vast societal costs. The development of a diagnostic methodology for identifying COVID-19 infection through simple testing was a reality only a few weeks after the novel virus was officially announced. Thus, we were interested in exploring the ability of regular testing of non-symptomatic people to reduce cases and thereby offer a non-pharmaceutical tool for controlling the spread of a pandemic.

ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models.

Motivation: The number and complexity of genome-scale metabolic models is steadily increasing, empowered by automated model-generation algorithms. The quality control of the models, however, has always remained a significant challenge, the most fundamental being reactions incapable of carrying flux. Numerous automated gap-filling algorithms try to address this problem, but can rarely resolve all of a model's inconsistencies.

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions.

Background: Genome-scale metabolic network reconstructions are low level chemical representations of biological organisms. These models allow the system-level investigation of metabolic phenotypes using a variety of computational approaches. The link between a metabolic network model and an organisms' higher-level behaviour is usually found using a constraint-based analysis approach, such as FBA (Flux Balance Analysis).

Hypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability.

Background: Genetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs. In the realm of synthetic biology, it is of great interest to engineer genetic circuits that can change their mode of operation from monostable to bistable, or even to multistable, based on the experimental fine-tuning of readily accessible parameters. In order to successfully design robust, bistable synthetic circuits to be used as biomolecular probes, or understand modes of operation of such naturally occurring circuits, we must identify parameters that are key in determining their characteristics.

Nanopore analysis of amyloid fibrils formed by lysozyme aggregation.

The measurement of single particle size distributions of amyloid fibrils is crucial for determining mechanisms of growth and toxicity. Nanopore sensing is an attractive solution for this problem since it gives information on aggregates' shapes with relatively high throughput for a single particle technology. In this paper we study the translocation of lysozyme fibrils through quartz glass nanopores.