Research Topics
| Mihai PopSummaryAffiliation: University of Maryland Country: USA Publications
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Detail Information
Publications
We are what we eat: how the diet of infants affects their gut microbiomeMihai Pop
Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
Genome Biol 13:152. 2012..Simultaneous analysis of the gut microbiome and host gene expression in infants reveals the impact of diet (breastfeeding versus formula) on host-microbiome interactions...- Genome assembly reborn: recent computational challengesMihai Pop
Department of Computer Science and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park, MD 20742, USA
Brief Bioinform 10:354-66. 2009..In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain... - 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)... - Alignment and clustering of phylogenetic markers--implications for microbial diversity studiesJames R White
Department of Computer Science, University of Maryland College Park, College Park, MD 20742, USA
BMC Bioinformatics 11:152. 2010..To date, however, there exists significant variability in analysis methods employed in these studies... - 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... - Scaffolding and validation of bacterial genome assemblies using optical restriction mapsNiranjan Nagarajan
University of Maryland, College Park, MD 20742, USA
Bioinformatics 24:1229-35. 2008..In this article we propose methods to overcome such limitations by incorporating information from optical restriction maps... 
Sequencing and genome assembly using next-generation technologiesNiranjan Nagarajan
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies and Department of Computer Science, University of Maryland, College Park, MD, USA
Methods Mol Biol 673:1-17. 2010..This paper surveys the recent software packages aimed specifically at analyzing new generation sequencing data...- Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of informationSaket Navlakha
Department of Computer Science, University of Maryland, College Park, Maryland 20742, USA
J Comput Biol 17:503-16. 2010..For these two applications, we test the quality of our clusters by using them to predict complex and species membership, respectively. We find that our approach generally outperforms the commonly used heuristic methods... - Assembly complexity of prokaryotic genomes using short readsCarl Kingsford
Department of Computer Science, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
BMC Bioinformatics 11:21. 2010..We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes... - Genome assembly forensics: finding the elusive mis-assemblyAdam M Phillippy
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
Genome Biol 9:R55. 2008..The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net... - 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.... - Bambus 2: scaffolding metagenomesSergey Koren
Department of Computer Science, University of Maryland, College Park, MD 20742, USA
Bioinformatics 27:2964-71. 2011..The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources... - Bioinformatics challenges of new sequencing technologyMihai Pop
Center for Bioinformatics and Computational Biology, University of Maryland, MD 20742, USA
Trends Genet 24:142-9. 2008.... - Minimus: a fast, lightweight genome assemblerDaniel D Sommer
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
BMC Bioinformatics 8:64. 2007..Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run... - ARDB--Antibiotic Resistance Genes DatabaseBo Liu
Center for Bioinformatics and Computational Biology and Department of Computer Science, University of Maryland, College Park, MD 20742, USA
Nucleic Acids Res 37:D443-7. 2009..Currently, ARDB contains resistance information for 13,293 genes, 377 types, 257 antibiotics, 632 genomes, 933 species and 124 genera. ARDB is available at http://ardb.cbcb.umd.edu/... - Figaro: a novel statistical method for vector sequence removalJames Robert White
Center for Bioinformatics and Computational Biology, University of Maryland College Park, MD 20742, USA
Bioinformatics 24:462-7. 2008..Correct clipping information is essential to scientists attempting to validate, improve and even finish the increasingly large number of genomes released at a 'draft' quality level... - Parametric complexity of sequence assembly: theory and applications to next generation sequencingNiranjan Nagarajan
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland 20742, USA
J Comput Biol 16:897-908. 2009..Our work suggests at least two ways in which existing assemblers can be extended in a rigorous fashion, in addition to delineating directions for future theoretical investigations... - Statistical methods for detecting differentially abundant features in clinical metagenomic samplesJames Robert White
Applied Mathematics and Scientific Computation Program, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
PLoS Comput Biol 5:e1000352. 2009..g. SAGE). A web server implementation of our methods and freely available source code can be found at http://metastats.cbcb.umd.edu/... - Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeBen Langmead
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
Genome Biol 10:R25. 2009..Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu)... - Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assembliesJoshua Wetzel
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
BMC Bioinformatics 12:95. 2011.... - Next generation sequence assembly with AMOSTodd J Treangen
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
Curr Protoc Bioinformatics . 2011..Additionally, we provide three tutorial examples that include bacterial, viral, and metagenomic datasets with specific tips for improving assembly quality... 
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracisTimothy D Read
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
Science 296:2028-33. 2002..These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks...- AGORA: Assembly Guided by Optical Restriction AlignmentHenry C Lin
Center for Bioinformatics and Computational Biology, University of Maryland College Park, College Park, MD, USA
BMC Bioinformatics 13:189. 2012.... - 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...