Yan Wei Lim

Summary

Affiliation: San Diego State University
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. doi request reprint A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation
    Robert A Quinn
    Department of Biology, San Diego State University, San Diego, CA, USA
    ISME J 9:1024-38. 2015
  9. 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
  10. pmc Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors
    Linda W Kelly
    Department of Biology, San Diego State University, San Diego, CA 92182
    Proc Natl Acad Sci U S A 111:10227-32. 2014

Collaborators

  • Robert Schmieder
  • Heather Maughan
  • Dana Willner
  • Enric Sala
  • Peter Salamon
  • Craig E Nelson
  • Elizabeth A Dinsdale
  • David Metzgar
  • John L Mokili
  • Forest Rohwer
  • Robert A Quinn
  • Linda W Kelly
  • Matthew Haynes
  • Juris A Grasis
  • Katrine L Whiteson
  • Don Blake
  • Simone Mienardi
  • Doug Conrad
  • Savannah E Sanchez
  • Barbara Bailey
  • Katrine Whiteson
  • Andreas F Haas
  • Robert A Edwards
  • Merry Youle
  • Stuart A Sandin
  • Mark J A Vermeij
  • Simone Meinardi
  • Mark Little
  • Tim Lachnit
  • Donald R Blake
  • Gloriamay Machado
  • Robert Quinn
  • Robert Kimble
  • Gareth J Williams
  • Craig A Carlson
  • Douglas Conrad
  • Philip Rosenstiel
  • Tracey McDole
  • Sören Franzenburg
  • Jennifer E Smith
  • Sebastian Fraune
  • Katie L Barott
  • Thomas C G Bosch
  • Santiago Insua
  • Forest L Rohwer
  • Friederike Anton-Erxleben

Detail Information

Publications12

  1. 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...
  2. 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...
  3. 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. ..
  4. 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
    ....
  5. 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. ..
  6. 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. ..
  7. 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...
  8. doi request reprint A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation
    Robert A Quinn
    Department of Biology, San Diego State University, San Diego, CA, USA
    ISME J 9:1024-38. 2015
    ..Treatment targeting the Attack Community may better resolve exacerbations and resulting lung damage. ..
  9. 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
    ....
  10. pmc Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors
    Linda W Kelly
    Department of Biology, San Diego State University, San Diego, CA 92182
    Proc Natl Acad Sci U S A 111:10227-32. 2014
    ..These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes. ..
  11. 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...
  12. pmc Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness
    John L Mokili
    Department of Biology, San Diego State University, San Diego, California, USA
    PLoS ONE 8:e58404. 2013
    ..The metagenomic procedures, coupled with the bioinformatic methods described herein are well suited to detect small circular genomes such as those of human papillomaviruses...