The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical para...

A method is developed to automatically generate an assembling procedure for an assembly. In this work, an assembly is described by its components and their relationship in an assembly, especially the mating conditions. From the mating conditions of the components, an assembling procedure is generated in two steps. First, a hierarchical structure of the assembly is generated. Second, an assembly...

Self-assembling peptide nanofiber scaffolds are an excellent material for applications such as tissue repair, tissue regeneration, instant stopping of bleeding, and slow drug release. We report a new self-assembling peptide D-EAK16 consisting purely of D-amino acids. D-EAK16 and L-EAK16 display mirror-image CD spectra at 20 degrees C. Like L-EAK16, D-EAK16 self-assembles into nanofibers, thus d...

We present a tile system for assembling a counter of width K and height N = 2 on top of a seed-row in optimum time Θ(N). Our counter works at temperature 2. Earlier known constructions either took sub-optimal time or required temperature 3. Using existing techniques, our system for assembling a counter from a seed row can be extended into a system for assembling an N × N square in optimum time ...

Four representative species from three genera of gram-negative bacteria that secrete exopolysaccharides acquired resistance to the antibiotic bacitracin by stopping synthesis of the exopolysaccharide. Xanthomonas campestris, Sphingomonas strains S-88 and NW11, and Escherichia coli K-12 secrete xanthan gum, sphingans S-88 and NW11, and colanic acid, respectively. The gumD gene in X. campestris i...

Gene structure prediction is one of the most important problems in computational molecular biology. It involves two steps: the first is finding the evidence (e.g., predicting splice sites) and the second is interpreting the evidence, that is, trying to determine the whole gene structure by assembling its pieces. In this paper, we suggest a combinatorial solution to the second step, which is als...