Mash extends the MinHash dimensionality-reduction technique to include a pairwise
mutation distance and P value significance test, enabling the efficient clustering and search of …

Background A critical output of metagenomic studies is the estimation of abundances of
taxonomical or functional groups. The inherent uncertainty in assignments to these groups …

Whole-genome sequences are now available for many microbial species and clades,
however existing whole-genome alignment methods are limited in their ability to perform …

Although gene expression has been studied in bacteria for decades, many aspects of the
bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and …

The MinHash algorithm has proven effective for rapidly estimating the resemblance of two
genomes or metagenomes. However, this method cannot reliably estimate the containment of …

Here, we report the development of SOCS (short oligonucleotide color space), a program
designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a …

… The bar charts in the present work and that of Ondov et al. [20] were horizontally extended,
an increasingly common design [8]. Other variants even of bar charts might reveal the use of …

Data visualizations convert numbers into visual marks so that our visual system can extract
data from an image instead of raw numbers. Clearly, the visual system does not compute …

… (BD) Expression coverage plots illustrating 3 categories of sense plus AS transcription for
6 genomic regions. Genome Coordinates from B. anthracis Ames Ancestor genome: (B) left = …

When performing bioforensic casework, it is important to be able to reliably detect the presence
of a particular organism in a metagenomic sample, even if the organism is only present …