Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome
data, but a lack of consensus about benchmarking complicates performance assessment. …

Microbiomes are vast communities of microorganisms and viruses that populate all natural
ecosystems. Viruses have been considered to be the most variable component of …

One of the major goals in metagenomics is to identify the organisms present in a microbial
community from unannotated shotgun sequencing reads. Taxonomic profiling has valuable …

The approximately 10 11 viruses and microbial cells per gram of fecal matter (dry weight) in
the large intestine are important to human health. The responses of three common gut …

… example data from the Citrobacter model discussed previously (Cuevas et al., 2014). A second
… to ER, and by a STEM scholarship award funded by NSF grant DUE-1259951 to Cuevas. …

Temperate phage genomes are highly variable mosaic collections of genes that infect a
bacterial host, integrate into the host’s genome or replicate as low copy number plasmids, and …

… Daniel A Cuevas , Daniel A Cuevas … The growth level metric, recapitulated from the
previous version of PMAnalyzer, represents a single quantitative value of growth (Cuevas et al., …

From the perspective of social learning theory, factors such as experiences with childhood
abuse, witnessing sibling and parental violence, having a distant relationship with one’s father…

Genomics and metagenomics have revolutionized our understanding of marine microbial
ecology and the importance of microbes in global geochemical cycles. However, the process …

… information on the accuracy and validity of the MAPs and PMAnalyzer see Cuevas et al. …
As described in Cuevas et al. , the PMAnalyzer is a single bash program written as a wrapper …