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 …

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence
reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie …

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…

Advances in sequencing technologies and increased access to sequencing services have
led to renewed interest in sequence and genome assembly. Concurrently, new applications …

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 …

We introduce a methodology to assess differential abundance in sparse high-throughput
microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq …

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 …

Numerous studies are currently underway to characterize the microbial communities inhabiting
our world. These studies aim to dramatically expand our understanding of the microbial …

The treatment of infections is increasingly compromised by the ability of bacteria to develop
resistance to antibiotics through mutations or through the acquisition of resistance genes. …

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