Jack A Gilbert

Summary

Publications

  1. ncbi request reprint Microbial metagenomics: beyond the genome
    Jack A Gilbert
    Plymouth Marine Laboratory, Plymouth PL1 3DH, United Kingdom
    Ann Rev Mar Sci 3:347-71. 2011
  2. pmc Metagenomics - a guide from sampling to data analysis
    Torsten Thomas
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, The University of New South Wales, Sydney, NSW 2052, Australia
    Microb Inform Exp 2:3. 2012
  3. pmc The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist
    Jack A Gilbert
    Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
    Microb Inform Exp 1:5. 2011
  4. 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
  5. pmc The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation
    Jack A Gilbert
    Plymouth Marine Laboratory, Plymouth, United Kingdom
    PLoS ONE 5:e15545. 2010
  6. doi request reprint The seasonal structure of microbial communities in the Western English Channel
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK
    Environ Microbiol 11:3132-9. 2009
  7. doi request reprint Metagenomics
    Jack A Gilbert
    Plymouth Marine Laboratory, The Hoe, Plymouth, UK
    Methods Mol Biol 733:173-83. 2011
  8. doi request reprint Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK
    Environ Microbiol 11:111-25. 2009
  9. ncbi request reprint Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing
    Ben Temperton
    Plymouth Marine Laboratory, Plymouth, UK
    ISME J 3:792-6. 2009
  10. pmc Defining seasonal marine microbial community dynamics
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, Plymouth, UK
    ISME J 6:298-308. 2012

Detail Information

Publications23

  1. ncbi request reprint Microbial metagenomics: beyond the genome
    Jack A Gilbert
    Plymouth Marine Laboratory, Plymouth PL1 3DH, United Kingdom
    Ann Rev Mar Sci 3:347-71. 2011
    ....
  2. pmc Metagenomics - a guide from sampling to data analysis
    Torsten Thomas
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio Innovation, The University of New South Wales, Sydney, NSW 2052, Australia
    Microb Inform Exp 2:3. 2012
    ..As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared...
  3. pmc The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist
    Jack A Gilbert
    Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
    Microb Inform Exp 1:5. 2011
    ..The fact that evolution remains a 'theory', at least to the general public, suggests that surveys for new data need to be taken to a new level...
  4. 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...
  5. pmc The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation
    Jack A Gilbert
    Plymouth Marine Laboratory, Plymouth, United Kingdom
    PLoS ONE 5:e15545. 2010
    ..Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function...
  6. doi request reprint The seasonal structure of microbial communities in the Western English Channel
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK
    Environ Microbiol 11:3132-9. 2009
    ..There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations...
  7. doi request reprint Metagenomics
    Jack A Gilbert
    Plymouth Marine Laboratory, The Hoe, Plymouth, UK
    Methods Mol Biol 733:173-83. 2011
    ..We hope that the information provided here will be useful to establish the techniques in most reasonably equipped molecular biology laboratories...
  8. doi request reprint Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK
    Environ Microbiol 11:111-25. 2009
    ..The fact that the capacity to utilize phosphonoacetate was evident in each of the three coastal environments suggests the potential for widespread utilization of this bioavailable P source...
  9. ncbi request reprint Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing
    Ben Temperton
    Plymouth Marine Laboratory, Plymouth, UK
    ISME J 3:792-6. 2009
    ..This study suggests that, although fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic fosmid libraries...
  10. pmc Defining seasonal marine microbial community dynamics
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, Plymouth, UK
    ISME J 6:298-308. 2012
    ..Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables...
  11. pmc Isolation and initial characterization of a novel type of Baeyer-Villiger monooxygenase activity from a marine microorganism
    Andrew Willetts
    Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, UK
    Microb Biotechnol 5:549-59. 2012
    ..Although low, abundance was detected in samples from many marine provinces, confirming the potential for biodiscovery in marine microorganisms...
  12. doi request reprint Bioturbation: impact on the marine nitrogen cycle
    Bonnie Laverock
    Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
    Biochem Soc Trans 39:315-20. 2011
    ..In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study...
  13. pmc Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, Plymouth, United Kingdom
    PLoS ONE 3:e3042. 2008
    ..The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities...
  14. 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...
  15. doi request reprint Gene expression profiling: metatranscriptomics
    Jack A Gilbert
    Plymouth Marine Laboratory, The Hoe, Plymouth, UK
    Methods Mol Biol 733:195-205. 2011
    ..Also, a section is dedicated for outlining a bioinformatic procedure for the analysis of metatranscriptomic datasets...
  16. pmc Novel analysis of oceanic surface water metagenomes suggests importance of polyphosphate metabolism in oligotrophic environments
    Ben Temperton
    School of Biological Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 6:e16499. 2011
    ....
  17. doi request reprint Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments
    Bonnie Laverock
    Plymouth Marine Laboratory, Plymouth, UK
    ISME J 4:1531-44. 2010
    ..In an area of high macrofaunal abundance, this could lead to alterations in the microbial transformations of important nutrients at the sediment-water interface...
  18. pmc Modeling microbial community structure and functional diversity across time and space
    Peter E Larsen
    Argonne National Laboratory, Lemont, IL, USA
    FEMS Microbiol Lett 332:91-8. 2012
    ..We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways...
  19. doi request reprint Predicting bacterial community assemblages using an artificial neural network approach
    Peter E Larsen
    Argonne National Laboratory Biosciences Division, Illinois, USA
    Nat Methods 9:621-5. 2012
    ....
  20. doi request reprint Toward effective probiotics for autism and other neurodevelopmental disorders
    Jack A Gilbert
    Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
    Cell 155:1446-8. 2013
    ..Thus probiotics may provide therapeutic strategies for neurodevelopmental disorders. ..
  21. 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...
  22. 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:..
  23. doi request reprint A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome
    Jack A Gilbert
    Plymouth Marine Laboratory, Prospect Place, Plymouth, UK
    ISME J 2:790-3. 2008
    ..Variation in SAR11 genomes from different locations might explain why SAR11 is abundant in so many diverse marine provinces...