Folker Meyer

Summary

Affiliation: Argonne National Laboratory
Country: USA

Publications

  1. pmc The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
    Daniel McDonald
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    Gigascience 1:7. 2012
  2. pmc Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
    William L Trimble
    Computation Institute, University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 13:183. 2012
  3. pmc Functional predictions from inference and observation in sequence-based inflammatory bowel disease research
    Folker Meyer
    Institute for Genomics and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
    Genome Biol 13:169. 2012
  4. pmc BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)
    Steffen Lemke
    University of Chicago, Dept, of Organismal Biology and Anatomy, CLSC 921B, 920 E, 58th Street, Chicago, IL 60637, USA
    BMC Genomics 12:278. 2011
  5. pmc Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
    Suparna Mitra
    Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 12:S21. 2011
  6. pmc FIGfams: yet another set of protein families
    Folker Meyer
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA
    Nucleic Acids Res 37:6643-54. 2009
  7. pmc A RESTful API for accessing microbial community data for MG-RAST
    Andreas Wilke
    Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America Computation Institute, University of Chicago, Chicago, Illinois, United States of America
    PLoS Comput Biol 11:e1004008. 2015
  8. pmc A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE
    Kevin P Keegan
    Argonne National Laboratory, Argonne, Illinois, United States of America
    PLoS Comput Biol 8:e1002541. 2012
  9. doi request reprint The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome
    Kim M Handley
    Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, IL, 60439, USA
    Environ Microbiol 16:3443-62. 2014
  10. doi request reprint A metagenomics portal for a democratized sequencing world
    Andreas Wilke
    Argonne National Laboratory, Lemont, Illinois, USA University of Chicago, Chicago, Illinois, USA
    Methods Enzymol 531:487-523. 2013

Collaborators

Detail Information

Publications17

  1. pmc The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
    Daniel McDonald
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    Gigascience 1:7. 2012
    ....
  2. pmc Short-read reading-frame predictors are not created equal: sequence error causes loss of signal
    William L Trimble
    Computation Institute, University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 13:183. 2012
    ....
  3. pmc Functional predictions from inference and observation in sequence-based inflammatory bowel disease research
    Folker Meyer
    Institute for Genomics and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
    Genome Biol 13:169. 2012
    ..Meta-omics approaches such as metagenomics, metatranscriptomics and metaproteogenomics have the potential to improve our understanding of how the human microbiome affects digestive health and disease...
  4. pmc BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)
    Steffen Lemke
    University of Chicago, Dept, of Organismal Biology and Anatomy, CLSC 921B, 920 E, 58th Street, Chicago, IL 60637, USA
    BMC Genomics 12:278. 2011
    ..These findings raise the question of whether the complement of BMP signaling components changed with the origin of the amnioserosa...
  5. pmc Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
    Suparna Mitra
    Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 12:S21. 2011
    ..The program has subsequently been extended to support comparative analyses of multiple datasets...
  6. pmc FIGfams: yet another set of protein families
    Folker Meyer
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA
    Nucleic Acids Res 37:6643-54. 2009
    ..FIGfams are freely available under an open source license. These can be downloaded at ftp://ftp.theseed.org/FIGfams/. The web site for FIGfams is http://www.theseed.org/wiki/FIGfams/..
  7. pmc A RESTful API for accessing microbial community data for MG-RAST
    Andreas Wilke
    Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America Computation Institute, University of Chicago, Chicago, Illinois, United States of America
    PLoS Comput Biol 11:e1004008. 2015
    ..We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service. ..
  8. pmc A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE
    Kevin P Keegan
    Argonne National Laboratory, Argonne, Illinois, United States of America
    PLoS Comput Biol 8:e1002541. 2012
    ....
  9. doi request reprint The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome
    Kim M Handley
    Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, IL, 60439, USA
    Environ Microbiol 16:3443-62. 2014
    ..Results expand upon recent findings highlighting the potential importance of sulfur and hydrogen metabolism in the terrestrial subsurface...
  10. doi request reprint A metagenomics portal for a democratized sequencing world
    Andreas Wilke
    Argonne National Laboratory, Lemont, Illinois, USA University of Chicago, Chicago, Illinois, USA
    Methods Enzymol 531:487-523. 2013
    ..As a result of the plummeting cost of sequencing and the readily available analytical power of MG-RAST, over 78,000 metagenomic datasets have been analyzed, with over 12,000 of them publicly available in MG-RAST. ..
  11. pmc Draft genome sequence of Agrobacterium albertimagni strain AOL15
    William L Trimble
    Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, USA
    J Bacteriol 194:6986-7. 2012
    ..1 Mb in 55 contigs with 61.2% GC content and includes a 21-gene arsenic gene island. This is the first available genome for this species and the second Agrobacterium arsenic gene island...
  12. pmc Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset
    Peter E Larsen
    Argonne National Laboratory, 9700, S, Cass Ave, Argonne, Illinois, USA
    Microb Inform Exp 1:4. 2011
    ..abstract:..
  13. doi request reprint From genomics to metagenomics
    Narayan Desai
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
    Curr Opin Biotechnol 23:72-6. 2012
    ..Data sharing and interoperability between tools are critical, since computation for metagenomic datasets is very high...
  14. ncbi request reprint Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes
    Elizabeth M Glass
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
    CSH Protoc 2010:pdb.prot5368. 2010
    ..A submitted metagenome is visible only to the user, unless the user makes it public or shares with other registered users. Public metagenomes are available to all...
  15. pmc Draft genome sequence of Achromobacter piechaudii strain HLE
    William L Trimble
    Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, USA
    J Bacteriol 194:6355. 2012
    ..This draft genome of 6.89 Mb is the second available genome for this species in the opportunistic pathogen Alcaligenaceae family...
  16. pmc The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
    Andreas Wilke
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
    BMC Bioinformatics 13:141. 2012
    ..Sequence similarity search results encoded in an open, exchangeable format have the potential to limit the needs for computational reanalysis of these data sets. A prerequisite for sharing of similarity results is a common reference...
  17. doi request reprint Connecting genotype to phenotype in the era of high-throughput sequencing
    Christopher S Henry
    Argonne National Laboratory, Argonne, IL 60439, USA
    Biochim Biophys Acta 1810:967-77. 2011
    ....