PhageScanner: a reconfigurable machine learning framework for bacteriophage genomic and metagenomic feature annotation.

Bacteriophages are the most prolific organisms on Earth, yet many of their genomes and assemblies from metagenomic sources lack protein sequences with identified functions. While most bacteriophage proteins are structural proteins, categorized as Phage Virion Proteins (PVPs), a considerable number remain unclassified. Complicating matters further, traditional lab-based methods for PVP identification can be tedious.

PhageBox: An Open Source Digital Microfluidic Extension With Applications for Phage Discovery.

Objective: Recent advancements demonstrate the significant role of digital microfluidics in automating laboratory work with DNA and on-site viral testing. However, since commercially available instruments are limited to droplet manipulation, our work addresses the need for accelerated integration of other components, such as temperature control, that can expand the application domain.

Methods: We developed PhageBox-an accessible device that can be used as a biochip extension.

Method for rapid MRI needle tracking.

A new method for MRI needle tracking within a given two-dimensional (2D) image slice is presented. The method is based on k-space investigation of the difference image between the current dynamic frame and a reference frame. Using only a few central k-lines of the difference image and a nonlinear optimization procedure, one can resolve the parameters that define the 2D sinc function that best characterizes the needle in k-space.

Substrate-directed formation of small biocatalysts under prebiotic conditions.

One of the most debated issues concerning the origin of life, is how enzymes which are essential for existence of any living organism, evolved. It is clear that, regardless of the exact mechanism, the process should have been specific and reproducible, involving interactions between different molecules. We propose that substrate templating played a crucial role in maintaining reproducible and specific formation of prebiotic catalysts.

Trapping of gas mixtures by amorphous water ice.

Our studies on gas trapping in amorphous water ice at 24-100 K were extended, by using mixtures of CH4, CO, N2, and Ar, rather than single gases. In 1:1 gas:(water vapor) mixtures, the competition among these gases on the available sites in the ice showed that the trapping capacity for the various gases is determined not only by the structure and dynamics of the ice, but is also influenced by the gas itself. Whereas at 24-35 K all four gases are trapped in the ice indiscriminantly, at 50-75 K there is a clear enhancement, in the order of CH4 > CO > N2 > or approximately Ar.