New DNA sequencing technologies can sequence up to one billion bases in a single day at
low cost, putting large-scale sequencing within the reach of many scientists. Many …

… & Pop, M. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read …
& Pop, M. Parametric complexity of sequence assembly: theory and applications to next …

Advances in sequencing technologies have led to the increased use of high throughput
sequencing in characterizing the microbial communities associated with our bodies and our …

The human intestinal microbiota is composed of 10 13 to 10 14 microorganisms whose collective
genome (“microbiome”) contains at least 100 times as many genes as our own genome…

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been
certified as a biosafety host for the cloning of foreign genes. The bacterium also has …

… to align three sets of 2 M untrimmed reads, a 36-bp set, a 50-bp set and a 76-bp set, to the
human genome on the server platform. Each set of 2 M is randomly sampled from a larger set (…

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the
diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 …

… We assume raw data are given as count matrix M(m, n), where m and n are the number of
features and samples, respectively. The raw data in this matrix are represented by counts c i,j , …

Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax 1 .
Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded …

Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which
is a significant source of morbidity and mortality in developing countries 1 . Here we present …