Affiliation: University of Maryland
- MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasetsBo Liu
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
BMC Proc 5:S9. 2011..Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic datasets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge...
- Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequencesBo Liu
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA
BMC Genomics 12:S4. 2011..One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels...
- DNACLUST: accurate and efficient clustering of phylogenetic marker genesMohammadreza Ghodsi
Department of Computer Science, University of Maryland, College Park, MD 20742, USA
BMC Bioinformatics 12:271. 2011..g., only one sequence per cluster needs to be provided to downstream analyses)...
- Gene prediction with Glimmer for metagenomic sequences augmented by classification and clusteringDavid R Kelley
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, 3115 Biomolecular Sciences Building 296, University of Maryland, College Park, MD 20742, USA
Nucleic Acids Res 40:e9. 2012..In a comparison among multiple gene finding methods, Glimmer-MG makes the most sensitive and precise predictions on simulated and real metagenomes for all read lengths and error rates tested...
- Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detectionBrianna Lindsay
University of Maryland, School of Medicine, Baltimore, Maryland, USA
J Clin Microbiol 51:3263-9. 2013..The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens. ..
- Deep sequencing of the oral microbiome reveals signatures of periodontal diseaseBo Liu
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
PLoS ONE 7:e37919. 2012....