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 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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

Collaborators

  • Heather Maughan
  • Dana Willner
  • David L Kirchman
  • Folker Meyer
  • Elizabeth A Dinsdale
  • John D McPherson
  • Yan Wei Lim
  • Bhakti Dwivedi
  • Mike Furlan
  • Matthew Haynes
  • Forest Rohwer
  • Robert A Edwards
  • Florent E Angly
  • Christopher S Hayes
  • David A Low
  • Katrine Whiteson
  • T David Matthews
  • Stephen J Poole
  • Robert Edwards
  • Douglas Conrad
  • Mya Breitbart
  • Dawn B Goldsmith
  • R Michael Miller
  • Beltran Rodriguez-Mueller
  • Katie Barott
  • Matthew R Henn
  • Rebecca Vega-Thurber
  • Lixin Zhang
  • Egbert Mundt
  • Robert K Naviaux
  • Rick Stevens
  • Baoli Zhu
  • Yongfei Hu
  • Dionysios A Antonopoulos
  • Alejandra Prieto-Davo
  • Matthew T Cottrell
  • Tracey McDole
  • Christelle Desnues
  • Linda Wegley

Detail Information

Publications8

  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 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...
  4. 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
    ..The source code, user help and additional information are available at http://prinseq.sourceforge.net/...
  5. 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/...
  6. 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...
  7. 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
    ....
  8. 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
    ....