Robert Schmieder

Summary

Affiliation: San Diego State University
Country: USA

Publications

  1. pmc PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity
    Bhakti Dwivedi
    College of Marine Science, University of South Florida, St, Petersburg, FL 33701, USA
    BMC Bioinformatics 13:37. 2012
  2. pmc Identification and removal of ribosomal RNA sequences from metatranscriptomes
    Robert Schmieder
    Department of Computer Science, San Diego State University, San Diego, CA 92182, USA
    Bioinformatics 28:433-5. 2012
  3. pmc Quality control and preprocessing of metagenomic datasets
    Robert Schmieder
    Department of Computer Science, Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
    Bioinformatics 27:863-4. 2011
  4. pmc Fast identification and removal of sequence contamination from genomic and metagenomic datasets
    Robert Schmieder
    Department of Computer Science, San Diego State University, San Diego, California, United States of America
    PLoS ONE 6:e17288. 2011
  5. pmc TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
    Robert Schmieder
    Department of Computer Science, San Diego State University, CA, USA
    BMC Bioinformatics 11:341. 2010
  6. pmc Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, California, USA
    J Clin Microbiol 52:425-37. 2014
  7. doi request reprint Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, California, USA
    J Clin Microbiol 52:425-37. 2014
  8. pmc Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, CA, 92182, USA Electronic address
    J Cyst Fibros 12:154-64. 2013
  9. pmc Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation
    Katrine L Whiteson
    Department of Biology, San Diego State University, San Diego, CA, USA
    ISME J 8:1247-58. 2014
  10. pmc Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, California, USA
    PLoS ONE 8:e64285. 2013

Collaborators

  • Yan Wei Lim
  • Heather Maughan
  • Dana Willner
  • David L Kirchman
  • Folker Meyer
  • Elizabeth A Dinsdale
  • John D McPherson
  • Katrine L Whiteson
  • Juris A Grasis
  • Bhakti Dwivedi
  • Matthew Haynes
  • Forest Rohwer
  • Robert A Edwards
  • Florent E Angly
  • Robert Quinn
  • Sebastian Fraune
  • Sören Franzenburg
  • Philip Rosenstiel
  • Tim Lachnit
  • Friederike Anton-Erxleben
  • Santiago Insua
  • Robert Kimble
  • Mark Little
  • Douglas Conrad
  • Gloriamay Machado
  • Simone Meinardi
  • Forest L Rohwer
  • Thomas C G Bosch
  • Donald R Blake
  • Mya Breitbart
  • Dawn B Goldsmith
  • Egbert Mundt
  • Rick Stevens
  • Baoli Zhu
  • Beltran Rodriguez-Mueller
  • Christelle Desnues
  • Rebecca Vega-Thurber
  • Katie Barott
  • Robert K Naviaux
  • Matthew R Henn
  • R Michael Miller
  • Yongfei Hu
  • Dionysios A Antonopoulos
  • Alejandra Prieto-Davo
  • Tracey McDole
  • Lixin Zhang
  • Matthew T Cottrell
  • Linda Wegley
  • Mike Furlan

Detail Information

Publications13

  1. pmc PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity
    Bhakti Dwivedi
    College of Marine Science, University of South Florida, St, Petersburg, FL 33701, USA
    BMC Bioinformatics 13:37. 2012
    ....
  2. pmc Identification and removal of ribosomal RNA sequences from metatranscriptomes
    Robert Schmieder
    Department of Computer Science, San Diego State University, San Diego, CA 92182, USA
    Bioinformatics 28:433-5. 2012
    ..riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications...
  3. pmc Quality control and preprocessing of metagenomic datasets
    Robert Schmieder
    Department of Computer Science, Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
    Bioinformatics 27:863-4. 2011
    ..Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis...
  4. pmc Fast identification and removal of sequence contamination from genomic and metagenomic datasets
    Robert Schmieder
    Department of Computer Science, San Diego State University, San Diego, California, United States of America
    PLoS ONE 6:e17288. 2011
    ..DeconSeq is available at http://deconseq.sourceforge.net/...
  5. pmc TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
    Robert Schmieder
    Department of Computer Science, San Diego State University, CA, USA
    BMC Bioinformatics 11:341. 2010
    ..Because of the potential for downstream inaccuracies introduced by unwanted sequence contaminations, it is important to use reliable tools for pre-processing sequence data...
  6. pmc Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, California, USA
    J Clin Microbiol 52:425-37. 2014
    ..Thus, this pilot study provides an example of how metagenomic data might be used with clinical assessments for the development of treatments tailored to individual patients. ..
  7. doi request reprint Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, California, USA
    J Clin Microbiol 52:425-37. 2014
    ..Thus, this pilot study provides an example of how metagenomic data might be used with clinical assessments for the development of treatments tailored to individual patients. ..
  8. pmc Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, CA, 92182, USA Electronic address
    J Cyst Fibros 12:154-64. 2013
    ..This study describes metagenomic and metatranscriptomic methods that address these issues...
  9. pmc Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation
    Katrine L Whiteson
    Department of Biology, San Diego State University, San Diego, CA, USA
    ISME J 8:1247-58. 2014
    ..We hypothesize that this may also increase phenazine production by P. aeruginosa, increasing reactive oxygen species and providing additional electron acceptors to CF microbes. ..
  10. pmc Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data
    Yan Wei Lim
    Department of Biology, San Diego State University, San Diego, California, USA
    PLoS ONE 8:e64285. 2013
    ..The results also highlight the remarkable evolutionary and ecological similarities of many CF pathogens; further examination of these similarities has the potential to guide patient care and treatment...
  11. pmc Species-specific viromes in the ancestral holobiont Hydra
    Juris A Grasis
    Department of Biology, San Diego State University, San Diego, California, United States of America Zoological Institute, Christian Albrechts University Kiel, Kiel, Germany
    PLoS ONE 9:e109952. 2014
    ....
  12. pmc Spatial distribution of microbial communities in the cystic fibrosis lung
    Dana Willner
    Department of Biology, San Diego State University, San Diego, CA, USA
    ISME J 6:471-4. 2012
    ....
  13. pmc The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes
    Florent E Angly
    Biology Department, San Diego State University, San Diego, California, United States of America
    PLoS Comput Biol 5:e1000593. 2009
    ....