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Ben Heavner

Research Scientist

Institute for Systems Biology
401 Terry Ave North
Seattle, WA 98109-5234

  • Summary
  • Technical Skills
  • Background
  • Publications
  • Summary

    I'm a research scientist affiliated with the Nathan Price Group at the Institute for Systems Biology in Seattle, Washington, USA.

    My work focuses on integrating multi-omic data sets to enable biological discovery (e.g. doi:10.1093/jamia/ocv077). I build cloud-based computational infrastructure and work with bioinformatic and statistical inference approaches to analyze things like short-read sequence data ("data science").

    Lately, I've really been enjoying working to become a better software developer and to adapt an action-biased culture of software engineering (e.g. my work with the Minimal Identifier Pilot Project).

    Previously, my doctoral research focused on the computational reconstruction of the metabolic network of the yeast Saccharomyces cerevisiae (e.g. doi:10.1089/ind.2012.0002, doi:10.1186/1752-0509-6-55, doi:10.1093/database/bat059).

    As a postdoc in the Price lab, I continued to work on metabolic network reconstruction research, (e.g. doi:10.1016/j.copbio.2014.12.010, doi:10.1371/journal.pcbi.1004530), and expanded my research focus as I began learning more about probabalistic modeling, such as those used for reconstructing gene regulatory networks or evaluating short-read sequence data.

    Technical Skills

    I am a tech generalist, and have had professional exposure to things like Amazon Web Services (S3, EC2, IAM management) for cluster computing using Sun Grid Engine controlled by StarCluster, basic developer tools like version control (github), shell scripting, full stack web development tools like HTML5, Bootstrap, jQuery, Javascript, Angular JS, and node.js (hi Free Code Camp!). I've used Matlab for metabolic network reconstruction, R for differential expression analysis (bioconductor), and have exposure to Python, and Perl. I've completed coursework in Statistical Learning. I've seen python, but not written much code there.

    Academic and Professional Background

    Ph.D. Cornell University 2012
    Biological and Environmental Engineering
    M.S. University of Colorado at Boulder 2004
    Civil and Environmental Engineering
    B.S. University of Puget Sound 1999
    Majors: Mathematics, Natural Sciences with an emphasis in Physics

    Peer Reviewed Publications

    • Heavner BD, Price ND. 2015. "Comparative Analysis of Yeast Metabolic Network Models Reveals Progress, Opportunities for Metabolic Reconstruction." PLOS Computational Biology. doi:10.1371/journal.pcbi.1004530

    • Toga AW, Foster I, Kesselman C, Madduri R, Chard K, Deutsch EW, Price ND, Glusman G, Heavner BD, Dinov ID, Ames J, Van Horn J, Kramer R, Hood L. 2015. "Big Biomedical data as the key resource for discovery science." Journal of the American Medical Informatics Association. Ocv077. doi:10.1093/jamia/ocv077

    • Heavner BD, Price ND. 2015. "Transparency in metabolic network reconstruction enables scalable biological discovery." Current opinion in biotechnology. 34:105-109. doi:10.1016/j.copbio.2014.12.010

    • Richards MA, Cassen V, Heavner BD, Ajami NE, Hermann A, Simeonidis E, Price ND. 2014. "MediaDB: A Database of Microbial Growth Conditions in Defined Media." PLOS one 2014, no. 9 e103548. doi:10.1371/journal.pone.0103548

    • Heavner BD, Smallbone K, Price ND, Walker LP. 2013. "Version 6 of the Consensus Yeast Metabolic Network Refines Biochemical Coverage and Improves Model Performance." Database 2013, no. 0 (August 9, 2013): bat059–bat059. doi:10.1093/database/bat059.i

    • Heavner B.D., Smallbone K., Barker B., Mendes P., Walker L.P. 2012. "Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network." BMC Systems Biology, 6:55. [doi:10.1186/1752-0509-6-55]

    • Heavner B.D., Henry S.A., and Walker L.P. 2012. "Evaluating Sphingolipid Biochemistry in the Consensus Reconstruction of Yeast Metabolism." Industrial Biotechnology, 8(2):72-78. [doi:10.1089/ind.2012.0002]

    Last updated: November 18, 2015