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David M. Schruth


Database/Web Developer
Research Consultant



Education

   Univeristy of Washington, Seattle

  • Bachelors in Biochemistry (w/ College Honors)
  • Minors in Chemistry

Software

  • metapathmapR -  an R package for mapping expression data onto metabolic pathways
  • manta -  an R package for comparative (meta) transcriptomic normalization and analysis of microbial assemblages
  • flowPhyto -  a continuous flow cytometry Bioconductor R package  (with Francois Ribalet)

    • Other Open Source Contributions

    Armbrust Lab Web Interfaces

    • DiatomDB - back end database and user interfaces to the lab's diatom specific data repo
    • ArmBlast - The Armbrust Lab Blast interface (along with Chris Berthaiume)
    • SeaFlow - The web interface to the flowPhyto R package (with major contributions from Chris Fox)
    • Anno-J - Lab Anno-J Genome Web Browser Instance (with contributions from Vaughn Iverson)

    Professional Development

    • Annual Bioconductor Conference 2010 & 2011
    • Life Technologies: "Sequencing at the Tipping Point" Meeting 2010
    • Advanced R Programming for Bioinformatics, Bioconductor Course, June 2010
    • PostGreSQL West Conference 2009
    • SOLiD Users Group Meeting 2008 & 2009

    Publications

    • Marchetti*, A., Schruth*, D., Durkin, C., Parker, M.S., Kodner, R.,Berthiaume, C., Morales, R., Allen, A., and Armbrust, E.V. Comparative Metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. PNAS Feb 7 2012
    • Ribalet*, F., Schruth*, D., and Armbrust, E.V. flowPhyto: enabling automated analysis of continuous flow cytometric data from SeaFlow repository. Bioinformatics Jan 2011

    Posters

    • Parker, M.S., Schruth, D., Berthiaume, C., Morales,R.,Rocap, G.,Jenkins, B.,Bates, S.S., Marchetti, A. & Armbrust, E. V., Transcriptome Analysis of the Toxin Producing Diatom Pseudo-Nitschia Multiseries,  HAB 2011
    • Marchetti, A., Schruth, D., Durkin, C., Morales, R., Berthiaume, C., Parker, M. and Armbrust, E.V.Taxonomic and metabolic shifts in an iron-stimulated eukaryotic marine plankton community from the NE Pacific revealed through comparative metatranscriptomics.   ASLO 2010
    • Ribalet, F. ., Morales, R. ., Swalwell, J. ., Marchetti, A. ., Durkin, C. A., Schruth, D. ., van den Engh, G. & Armbrust, E. V., , Patchiness and Diel Variability Of Phytoplankton Communities in the NE Subartic Pacific Ocean Revealed by Continuous-Monitoring Flow Cytometry,  ASLO 2009
    • Ribalet, F., Swalwell, J., Schruth, D., Fox, C. & Armbrust, E.V. SeaFlow Software: Novel underway flow-cytometer for continuous observation of phytoplankton distributions in the ocean. ASLO 2010
    • Parker, M.S., Jenkins B., Lin, E.O., Schruth, D., Berthiaume, C., Kudela, R., Iverson, V.S., Rocap, G., Rodrigues, H. & Armbrust, E.V.  Comparative Genomics of Pseudo-nitzschia ESTs from multiple species. Oceans and Human Health [OHH] Gordon Research Conference 2010
    • Parker, M.S., Schruth, D., Berthiaume, Iverson, V.S., Rocap, G., Jenkins, Samantha, M., Bates, S.S. & Armbrust, E.V. Genome Sequencing of the toxin-producing diatom Pseudo-nitzschia multiseries. Harmful Algal Bloom [HAB] Conference 2009

    Presentations

    • Bender, S.J., Durkin, C.A., Schruth, D.M., Morales, R.L. and Armbrust, E.V. Identifying shared responses to nitrate starvation among three diatoms using whole-cell transcriptomics. Ocean Sciences Meeting 2012
    • Marchetti, A., Moreno, C., Oleinikov, I., Durkin, C., Schruth, D., Hubbard, K. & Armbrust, E.V., Development of Molecular Indicators for the Iron Nutritional Status of Diatoms.   PSA 2011
    • Schruth, D.  Visual Comparative Transcriptomics using MANTA / RA.  PSA Genomics Workshop 2011

    Aknowledgements

    • Vaughn Iverson, Robert M. Morris, Christian D. Frazar, Chris T. Berthiaume, Rhonda L. Morales, and E. Virginia Armbrust, Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota, Science, Vol. 335 no. 6068 pp. 587-590, February 3rd, 2012
    • Sara J. Bender, Micaela S. Parker, E. Virginia Armbrust, Coupled Effects of Light and Nitrogen Source on the Urea Cycle and Nitrogen Metabolism over a Diel Cycle in the Marine Diatom Thalassiosira pseudonana. 2011 Protist Online
    • Swalwell, J.E., Ribalet, F., and Armbrust, E.V. SeaFlow: A novel underway flow-cytometer for continuous observations of phytoplankton in the ocean. In prep for Limnology & Oceanography: Methods.
    • Matsen, F.A., Kodner, R. B., and Armbrust, E. V., pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of metagenomic sequences on a reference tree. 2010. BMC Bioinformatics


    * Authors contributed equally to the work