Todd Z DeSantis

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Simrank: Rapid and sensitive general-purpose k-mer search tool
    Todd Z DeSantis
    Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, USA
    BMC Ecol 11:11. 2011
  2. ncbi request reprint High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment
    Todd Z DeSantis
    Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Microb Ecol 53:371-83. 2007
  3. pmc PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip
    Kristen M DeAngelis
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Appl Environ Microbiol 77:6313-22. 2011
  4. doi request reprint Deep-sea oil plume enriches indigenous oil-degrading bacteria
    Terry C Hazen
    MS 70A 3317, One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 330:204-8. 2010
  5. doi request reprint Selective progressive response of soil microbial community to wild oat roots
    Kristen M DeAngelis
    Ecology Department, Lawrence Berkeley National Lab, Berkeley, CA, USA
    ISME J 3:168-78. 2009
  6. doi request reprint High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment
    Kim M Handley
    Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
    FEMS Microbiol Ecol 81:188-204. 2012
  7. pmc Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators
    Cindy H Wu
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 5:e11285. 2010
  8. doi request reprint Environmental genomics reveals a single-species ecosystem deep within Earth
    Dylan Chivian
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 322:275-8. 2008
  9. pmc Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
    Kimberlee A West
    Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720 1170, USA
    Appl Environ Microbiol 74:3533-40. 2008
  10. pmc Urban aerosols harbor diverse and dynamic bacterial populations
    Eoin L Brodie
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:299-304. 2007

Detail Information

Publications13

  1. pmc Simrank: Rapid and sensitive general-purpose k-mer search tool
    Todd Z DeSantis
    Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, USA
    BMC Ecol 11:11. 2011
    ..However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available...
  2. ncbi request reprint High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment
    Todd Z DeSantis
    Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Microb Ecol 53:371-83. 2007
    ..Furthermore, the microarray allowed samples to be rapidly evaluated with replication, a significant advantage in studies of microbial ecology...
  3. pmc PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip
    Kristen M DeAngelis
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Appl Environ Microbiol 77:6313-22. 2011
    ....
  4. doi request reprint Deep-sea oil plume enriches indigenous oil-degrading bacteria
    Terry C Hazen
    MS 70A 3317, One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 330:204-8. 2010
    ..Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown...
  5. doi request reprint Selective progressive response of soil microbial community to wild oat roots
    Kristen M DeAngelis
    Ecology Department, Lawrence Berkeley National Lab, Berkeley, CA, USA
    ISME J 3:168-78. 2009
    ..This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones...
  6. doi request reprint High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment
    Kim M Handley
    Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
    FEMS Microbiol Ecol 81:188-204. 2012
    ..Data implies complex membership among highly stimulated taxa and, by inference, biogeochemical responses to acetate, a nonfermentable substrate...
  7. pmc Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators
    Cindy H Wu
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 5:e11285. 2010
    ..A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring...
  8. doi request reprint Environmental genomics reveals a single-species ecosystem deep within Earth
    Dylan Chivian
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 322:275-8. 2008
    ....
  9. pmc Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
    Kimberlee A West
    Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720 1170, USA
    Appl Environ Microbiol 74:3533-40. 2008
    ....
  10. pmc Urban aerosols harbor diverse and dynamic bacterial populations
    Eoin L Brodie
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:299-304. 2007
    ..Finally, using multivariate regression techniques, we demonstrate that temporal and meteorological influences can be stronger factors than location in shaping the biological composition of the air we breathe...
  11. pmc Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation
    Eoin L Brodie
    Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:6288-98. 2006
    ..High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner...
  12. pmc Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
    Daniel Dalevi
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    BMC Bioinformatics 8:402. 2007
    ..Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies...
  13. ncbi request reprint Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray
    Todd Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    FEMS Microbiol Lett 245:271-8. 2005
    ..Notably, gentle extractions produced peak intensities for Mycoplasmatales and Burkholderiales, whereas a vigorous disruption produced peak intensities for Vibrionales, Clostridiales, and Bacillales...