Steven J Hallam

Summary

Publications

  1. pmc Metabolic pathways for the whole community
    Niels W Hanson
    Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100 570 West 7th Avenue, Vancouver, British Columbia V5Z 4S6, Canada
    BMC Genomics 15:619. 2014
  2. pmc MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
    Kishori M Konwar
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada
    BMC Bioinformatics 14:202. 2013
  3. doi request reprint Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones
    David A Walsh
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Science 326:578-82. 2009
  4. pmc Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle
    Jody J Wright
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    ISME J 8:455-68. 2014
  5. doi request reprint Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters
    Alyse K Hawley
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
    Methods Enzymol 531:305-29. 2013
  6. pmc Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
    Martin Hartmann
    Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
    ISME J 6:2199-218. 2012
  7. doi request reprint Microbial ecology of expanding oxygen minimum zones
    Jody J Wright
    Department of Microbiology and Immunology, University of British Columbia, Life Sciences Institute, 2552 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
    Nat Rev Microbiol 10:381-94. 2012
  8. doi request reprint Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands
    Martin Hartmann
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    Environ Microbiol 11:3045-62. 2009
  9. pmc Expanding the boundaries of local similarity analysis
    W Evan Durno
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    BMC Genomics 14:S3. 2013
  10. pmc Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils
    David Vaninsberghe
    Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
    ISME J 9:2435-41. 2015

Collaborators

Detail Information

Publications24

  1. pmc Metabolic pathways for the whole community
    Niels W Hanson
    Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100 570 West 7th Avenue, Vancouver, British Columbia V5Z 4S6, Canada
    BMC Genomics 15:619. 2014
    ....
  2. pmc MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
    Kishori M Konwar
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T1Z3, Canada
    BMC Bioinformatics 14:202. 2013
    ..The dominant paradigm in metabolic reconstruction is to assign functional annotations using BLAST. Functional annotations are then projected onto symbolic representations of metabolism in the form of KEGG pathways or SEED subsystems...
  3. doi request reprint Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones
    David A Walsh
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Science 326:578-82. 2009
    ..Our analysis provides a genomic foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential sensitivity to environmental changes...
  4. pmc Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle
    Jody J Wright
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    ISME J 8:455-68. 2014
    ..These results posit a potential role for specific MGA subgroups in the marine sulfur cycle. ..
  5. doi request reprint Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters
    Alyse K Hawley
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
    Methods Enzymol 531:305-29. 2013
    ....
  6. pmc Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
    Martin Hartmann
    Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
    ISME J 6:2199-218. 2012
    ....
  7. doi request reprint Microbial ecology of expanding oxygen minimum zones
    Jody J Wright
    Department of Microbiology and Immunology, University of British Columbia, Life Sciences Institute, 2552 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
    Nat Rev Microbiol 10:381-94. 2012
    ....
  8. doi request reprint Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands
    Martin Hartmann
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    Environ Microbiol 11:3045-62. 2009
    ..These effects warrant more comprehensive investigation of the effects of harvesting on the structure of forest soil microbial communities and the functional consequences...
  9. pmc Expanding the boundaries of local similarity analysis
    W Evan Durno
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    BMC Genomics 14:S3. 2013
    ..Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets...
  10. pmc Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils
    David Vaninsberghe
    Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
    ISME J 9:2435-41. 2015
    ..In addition, this study demonstrates how focusing research on economically important microorganisms can bias our understanding of the natural world. ..
  11. doi request reprint V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets
    Martin Hartmann
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    FEMS Microbiol Lett 319:140-5. 2011
    ..Thus, v-revcomp is highly efficient in detecting and reorienting reverse complementary 16S sequences of almost any length and can be used to detect various sequence anomalies...
  12. doi request reprint Molecular tools for investigating ANME community structure and function
    Steven J Hallam
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
    Methods Enzymol 494:75-90. 2011
    ....
  13. doi request reprint Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems
    Christopher E Lawson
    Department of Civil Engineering, University of British Columbia, Vancouver, BC, Canada
    Environ Microbiol 17:4979-93. 2015
    ..Taken together, these results point towards complex interactions selected for within the EBPR ecosystem and highlight a previously unrecognized functional potential among low abundance microorganisms in engineered ecosystems. ..
  14. pmc Metagenomic scaffolds enable combinatorial lignin transformation
    Cameron R Strachan
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 MetaMixis, Inc, Vancouver, BC, Canada V6J 3R3
    Proc Natl Acad Sci U S A 111:10143-8. 2014
    ..These results illuminate cellular and community-wide networks acting on aromatic polymers and expand the toolkit for engineering recombinant lignin transformation based on ecological design principles. ..
  15. pmc A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities
    Kaston Leung
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
    Proc Natl Acad Sci U S A 109:7665-70. 2012
    ..The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members...
  16. doi request reprint Phylogenetic diversity of transition and anoxic zone bacterial communities within a near-shore anoxic basin: Nitinat Lake
    Jana Schmidtova
    Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC, Canada
    Environ Microbiol 11:3233-51. 2009
    ..Overall, sequence diversity between different vertical zones was high, although the spatial segregation of gamma-Proteobacteria, Chlorobi, and epsilon-Proteobacteria did not appear to vary significantly between seasons...
  17. pmc MetaPathways v2.5: quantitative functional, taxonomic and usability improvements
    Kishori M Konwar
    Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada
    Bioinformatics 31:3345-7. 2015
    ..Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database...
  18. pmc Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities
    Christopher E Lawson
    MetaMixis Biologics, Inc, Vancouver, British Columbia, Canada Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
    Appl Environ Microbiol 81:7924-37. 2015
    ..Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity. ..
  19. doi request reprint Biocatalysts for biomass deconstruction from environmental genomics
    Zachary Armstrong
    Genome Science and Technology Program, University of British Columbia, Vancouver, Canada
    Curr Opin Chem Biol 29:18-25. 2015
    ..Here we review recent progress in recovering such biological devices from environmental genomes and consider how this information can be used to build better biorefining ecosystems. ..
  20. doi request reprint Synthesis and evaluation of a series of 6-chloro-4-methylumbelliferyl glycosides as fluorogenic reagents for screening metagenomic libraries for glycosidase activity
    Hong Ming Chen
    Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
    Carbohydr Res 421:33-9. 2016
    ..Hits were then readily deconvoluted with the individual substrates in a single plate to identify specific activities within each clone. The use of such a collection of substrates greatly accelerates the screening process. ..
  21. doi request reprint Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia
    Elena Zaikova
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
    Environ Microbiol 12:172-91. 2010
    ....
  22. pmc Illuminating microbial dark matter in meromictic Sakinaw Lake
    Esther A Gies
    Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
    Appl Environ Microbiol 80:6807-18. 2014
    ..Taken together, these observations point to previously unrecognized syntrophic networks in meromictic lake ecosystems with the potential to inform design and operation of anaerobic methanogenic bioreactors. ..
  23. doi request reprint The art and design of functional metagenomic screens
    Marcus Taupp
    Department of Microbiology and Immunology, University of British Columbia, Canada
    Curr Opin Biotechnol 22:465-72. 2011
    ....
  24. pmc Genomic and transcriptomic studies of an RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)-degrading actinobacterium
    Hao Ping Chen
    Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
    Appl Environ Microbiol 78:7798-800. 2012
    ..Aspects of this mycolic acid-containing actinobacterium's catabolic potential were experimentally verified and compared with those of rhodococci and mycobacteria...