Aria S. Hahn

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UNLABELLED Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present(More)
A fundamental step in the analysis of environmental sequence information is the prediction of potential genes or open reading frames (ORFs) encoding the metabolic potential of individual cells and entire microbial communities. FragGeneScan, a software designed to predict intact and incomplete ORFs on short sequencing reads combines codon usage bias,(More)
Ecosystem recovery following disturbance requires the reestablishment of key soil biogeochemical processes. This long-term 7 year study describes effects of organic material, moisture, and vegetation on soil microbial community development in the Athabasca Oil Sands Region of Western Canada. Phospholipid fatty acid analysis was used to characterize and(More)
Accurate description of the microbial communities driving matter and energy transformations in complex ecosystems such as soils cannot yet be effectively accomplished using assembly-based approaches despite the rise of next generation sequencing technologies. Here we present SOFA, an open source pipeline enabling comparative functional annotation of(More)
Enhanced biological phosphorus removal (EBPR) relies on diverse but specialized microbial communities to mediate the cycling and ultimate removal of phosphorus from municipal wastewaters. However, little is known about microbial activity and dynamics in relation to process fluctuations in EBPR ecosystems. Here, we monitored temporal changes in microbial(More)
Processes governing the fixation, partitioning, and mineralization of carbon in soils are under increasing scrutiny as we develop a more comprehensive understanding of global carbon cycling. Here we examined fixation by Douglas-fir seedlings and transfer to associated ectomycorrhizal fungi, soil microbes, and full-sibling or nonsibling neighbouring(More)
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between(More)
A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this(More)
FAST is a multi-threaded, I/O optimized Seed-and-Extend alignment program. FAST is extensible to nucleotide sequences making it comparable to both BLASTn and BLASTp, and also features several new usage flags reporting only HSPs meeting user defined e-value cut-offs. FASTs threaded database construction allows fast, low memory database construction e.g.,(More)
Anoxygenic photosynthesis evolved prior to oxygenic photosynthesis and harnessed energy from sunlight to support biomass production on the early Earth. Models that consider the availability of electron donors predict that anoxygenic photosynthesis using Fe(II), known as photoferrotrophy, would have supported most global primary production before the(More)