Publications

gbtools: interactive visualization of metagenome bins in r.	improvements in dna sequencing technology have increased the amount and quality of sequences that can be obtained from metagenomic samples, making it practical to extract individual microbial genomes from metagenomic assemblies ("binning"). however, while many tools and methods exist for unsupervised binning with various statistical algorithms, there are few options for visualizing the results, even though visualization is vital to exploratory data analysis. we have developed gbtools, a software ...	2015	26732662
metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use.	low nutrient and energy availability has led to the evolution of numerous strategies for overcoming these limitations, of which symbiotic associations represent a key mechanism. particularly striking are the associations between chemosynthetic bacteria and marine animals that thrive in nutrient-poor environments such as the deep sea because the symbionts allow their hosts to grow on inorganic energy and carbon sources such as sulfide and co(2). remarkably little is known about the physiological ...	2012	22517752
high content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm olavius algarvensis.	selenocysteine (sec) and pyrrolysine (pyl) are rare amino acids that are cotranslationally inserted into proteins and known as the 21st and 22nd amino acids in the genetic code. sec and pyl are encoded by uga and uag codons, respectively, which normally serve as stop signals. herein, we report on unusually large selenoproteomes and pyrroproteomes in a symbiont metagenomic dataset of a marine gutless worm, olavius algarvensis. we identified 99 selenoprotein genes that clustered into 30 families, ...	2007	17626042
coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (oligochaeta) from the peru margin.	olavius crassitunicatus is a small symbiont-bearing worm that occurs at high abundance in oxygen-deficient sediments in the east pacific ocean. using comparative 16s rrna sequence analysis and fluorescence in situ hybridization, we examined the diversity and phylogeny of bacterial symbionts in two geographically distant o. crassitunicatus populations (separated by 385 km) on the peru margin (water depth, approximately 300 m). five distinct bacterial phylotypes co-occurred in all specimens from b ...	2005	15746360