• Publications
  • Influence
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, whenExpand
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JIGSAW: integration of multiple sources of evidence for gene prediction
TLDR
JIGSAW is a new gene finding system designed to automate the process of predicting gene structure from multiple sources of evidence, with results that often match the performance of human curators. Expand
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Scalable metagenomic taxonomy classification using a reference genome database
TLDR
A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Expand
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JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
BackgroundPredicting complete protein-coding genes in human DNA remains a significant challenge. Though a number of promising approaches have been investigated, an ideal suite of tools has yet toExpand
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Computational gene prediction using multiple sources of evidence.
This article describes a computational method to construct gene models by using evidence generated from a diverse set of sources, including those typical of a genome annotation pipeline. The program,Expand
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Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces
Antimicrobial resistance (AMR) is a global health issue. In an effort to minimize this threat to astronauts, who may be immunocompromised and thus at a greater risk of infection from antimicrobialExpand
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Three-dimensional nanoscale composition mapping of semiconductor nanowires.
We demonstrate the three-dimensional composition mapping of a semiconductor nanowire with single-atom sensitivity and subnanometer spatial resolution using atom probe tomography. A new class of atomExpand
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Metagenomic Analysis of the Airborne Environment in Urban Spaces
The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examineExpand
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Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs
BackgoundHigh throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sampleExpand
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Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission
One of the hurdles to understanding the role of viral quasispecies in RNA virus cross-species transmission (CST) events is the need to analyze a densely sampled outbreak using deep sequencing inExpand
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