Bio


Amy earned a PhD in Molecular Biophysics and Biochemistry from Yale University, where she studied cell cycle regulation in the yeast Saccharomyces cerevisiae. Prior to joining Stanford Libraries in 2012, Amy worked on scientific databases in the biotech and biofuels industries, developing methods for collecting and synthesizing sophisticated information into easy-to-understand formats.

Current Role at Stanford


Amy assists members of the Stanford community with the sharing and preservation of research data and other research products in the Stanford Digital Repository (SDR). She serves as the Product Owner for the Libraries' self-deposit application for the SDR and as the Product Owner for the upcoming Data Catalog project. Amy assists researchers with large data deposits for the SDR and serves on several groups that work to better enable access to research data at Stanford. Amy also co-manages Stanford Libraries' campus DOI service. Visit the Data Management Services web site to find out more.

Education & Certifications


  • PhD, Yale University, Molecular Biophysics and Biochemistry
  • MPhil, Yale University, Molecular Biophysics and Biochemistry
  • BS, Centre College of Kentucky, Biochemistry and Molecular Biology
  • Agile Scrum Product Owner, Scrum Alliance/Agile Learning Labs (2017)
  • Agile ScrumMaster, Scrum Alliance/Agile Learning Labs (2017)
  • Certified Instructor Trainer, Software/Data Carpentry (2017)
  • Certified Instructor, Software/Data Carpentry (2015)

Service, Volunteer and Community Work


  • Vice President and Board Member, Friends of the Paul Sawyier Public Library (2005 - 2006)

    Location

    Frankfort, KY

Work Experience


  • Director of Curation Research, Garbrook Knowledge Resources (September 2007 - December 2008)

    Crafted standards and protocols for gathering and assimilating market intelligence on the green technology industry from scientific, industry, and other sources into topical online reports. Upgraded and expanded ABR content by researching and assimilating findings on government and institution policies related to green technology. Instituted quality control routines and exhaustively tested and documented proprietary Java-based database management software.

    Location

    Beverly, MA

  • Database Editor, Garbrook Knowledge Resources (February 2007 - August 2007)

    Crafted standards and protocols for gathering and assimilating market intelligence on the green technology industry from scientific, industry, and other sources into topical online reports. Upgraded and expanded ABR content by researching and assimilating findings on government and institution policies related to green technology. Instituted quality control routines and exhaustively tested and documented proprietary Java-based database management software.

    Location

    Beverly, MA

  • Scientific Curator, Pharmacogenomics Knowledgebase (PharmGKB), Stanford University (April 2006 - January 2007)

    Curation and analysis of pharmacogenomics research data and creation of enhanced knowledge annotation process.

    Location

    Stanford, CA

  • Editor, Proteome Databases, Biobase Corporation (February 2005 - March 2006)

    Managed US- and India-based teams of curators and editors collecting scientific data from the published literature for seven different major databases and projects. In-house and distance curator training; development of methodologies, manuals, and training materials; assisted with design of user interfaces for internal and external applications; creation and implementation of QA/QC procedures.

    Location

    Beverly, MA

  • Editor, Proteome Databases, Incyte Corporation (January 2001 - February 2005)

    Managed US--based teams of curators and editors collecting scientific data from the published literature. Distance curator training; development of methodologies and manuals; assisted with design of user interfaces for internal and external applications; creation and implementation of QA/QC procedures.

    Location

    Beverly, MA

  • Scientific Curator, Proteome, Inc. (February 2000 - January 2001)

    Compiled and submitted data from the scientific literature to the company's proprietary databases.

    Location

    Beverly, MA

  • Instructor of Microbiology, Midway College (July 2000 - December 2000)

    Prepared and delivered twice-weekly lectures. Set up and supervised student laboratory experiments.

    Location

    Midway, KY

Skills and Expertise


    Information Technology
      Data Management
      Project Management
      Research Data
      Service Management

Professional Affiliations and Activities


  • Member, Stanford CORES Executive Committee (2020 - Present)
  • Member, DataCite Community Engagement Steering Group (2018 - Present)
  • Member, PLOS Data Guidelines Board (2015 - Present)
  • Chair of Executive Council, The Carpentries (2019 - 2019)
  • Elected Member of Executive Council, The Carpentries (2018 - 2020)
  • Invited Member, DataONE Community Engagement & Outreach Working Group (2014 - 2016)
  • Mentor, Association for Women in Science (2014 - 2015)
  • Invited Participant, NSF-sponsored iNeuro workshop (2014 - 2014)

All Publications


  • Using Peer Review to Support Development of Community Resources for Research Data Management Journal of eScience Librarianship Soyka, H. E., Budden, A., Hutchinson, V., Bloom, D., Duckles, J., Hodge, A., Mayernik, M., Poisot, T., Rauch, S., Steinhart, G., Wasser, L., Whitmire, A. L., Wright, S. 2017

    View details for DOI 10.7191/jeslib.2017.1114

  • Making the Case for Institutional Data Repositories Curating research data, Practical strategies for your digital repository Vitale, C. R., Carlson, J., Hodge, A. E., Hswe, P., Johns, E., Johnston, L. R., Kozlowski, W., Nurnberger, A., Petters, J., Rolando, E., Shorish, Y., Schneider, J., Zilinski, L. edited by Johnston, L. R. Chicago Association of College and Research Libraries. 2017
  • The PharmGKB: integration, aggregation, and annotation of pharmacogenomic data and knowledge CLINICAL PHARMACOLOGY & THERAPEUTICS Hodge, A. E., Altman, R. B., Klein, T. E. 2007; 81 (1): 21-24

    Abstract

    The Pharmacogenetics and Pharmacogenomics Knowledge Base, PharmGKB (http://www.pharmgkb.org), curates pharmacogenetic and pharmacogenomic information to generate knowledge concerning the relationships among genes, drugs, and diseases, and the effects of gene variation on these relationships. PharmGKB curators collect information on genotype-phenotype relationships both from the literature and from the deposition of primary research data into our database. Their goal is to catalyze pharmacogenetic and pharmacogenomic research.

    View details for DOI 10.1038/sj.clpt.6100048

    View details for Web of Science ID 000242874200010

    View details for PubMedID 17185992

  • The cyclin-dependent kinase inhibitory domain of the yeast Sic1 protein is contained within the C-terminal 70 amino acids MOLECULAR AND GENERAL GENETICS Hodge, A., Mendenhall, M. 1999; 262 (1): 55-64

    Abstract

    By inhibiting the activity of Cdc28/Clb cyclin-dependent protein kinase (CDK) complexes, Sic1 prevents the premature initiation of S phase in the yeast Saccharomyces cerevisiae. By testing a series of Sic1 truncation mutants, we have mapped the minimal domain necessary for Cdc28/Clb inhibition in vivo to the C-terminal 70 amino acids of Sic1. Site-directed mutagenesis was used to show that a sequence that matches the zRxL motif found in mammalian CDK inhibitors is essential for Sicl function. This motif is not found in the Schizosaccharomyces CDK inhibitor p25rum1, which appears to be a structural and functional homolog of Sicl. Based on the mutational data and sequence comparisons, we argue that Sic1 and p25rum1 are structurally distinct from the known mammalian CDK inhibitors, but may bind CDK complexes in a manner more closely resembling CDK substrates like the retinoblastoma and E2F proteins.

    View details for Web of Science ID 000082577300007

    View details for PubMedID 10503536

  • Analysis of the Saccharomyces cerevisiae cyclin-dependent kinase inhibitor Sic1 [Dissertation] Hodge, A. E. Yale University. New Haven, CT. 1999
  • Regulation of cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS Mendenhall, M. D., Hodge, A. E. 1998; 62 (4): 1191-?

    Abstract

    The cyclin-dependent protein kinase (CDK) encoded by CDC28 is the master regulator of cell division in the budding yeast Saccharomyces cerevisiae. By mechanisms that, for the most part, remain to be delineated, Cdc28 activity controls the timing of mitotic commitment, bud initiation, DNA replication, spindle formation, and chromosome separation. Environmental stimuli and progress through the cell cycle are monitored through checkpoint mechanisms that influence Cdc28 activity at key cell cycle stages. A vast body of information concerning how Cdc28 activity is timed and coordinated with various mitotic events has accrued. This article reviews that literature. Following an introduction to the properties of CDKs common to many eukaryotic species, the key influences on Cdc28 activity-cyclin-CKI binding and phosphorylation-dephosphorylation events-are examined. The processes controlling the abundance and activity of key Cdc28 regulators, especially transcriptional and proteolytic mechanisms, are then discussed in detail. Finally, the mechanisms by which environmental stimuli influence Cdc28 activity are summarized.

    View details for Web of Science ID 000077376400007

    View details for PubMedID 9841670