Cory Strope

Experience

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  University of Nebraska-Lincoln

  Aug 2005 - Jan 2010

  Maintain and expand sequence simulation software developed during dissertation work, indel-Seq-Gen. Collaborate with Ph.D. student developing a GUI interface for software. Produce a large-scale nucleotide benchmark dataset. Developed biological sequence evolution simulator, indel-Seq-Gen (version 1.0 and 2.0). Authored publications detailing each method. Supervised undergraduate student in converting indel-Seq-Gen from a PERL wrapper to a C program to C++. Full responsibility instructor for 3-hour undergraduate non-major computer science courses. Developed and presented lecture materials. Drafted homework assignments, quizzes, and exams to evaluate student performance. Supervised grader. Collaborated with lab instructor to coordinate activities for the lab and course.

  • Postdoctoral Researcher

    Dec 2009 - Jan 2010

  • Research Assistant

    Jun 2007 - Nov 2009

  • Teaching Assistant

    Aug 2005 - May 2007
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  North Carolina State University

  Jan 2011 - Oct 2012

  Postdoctoral Researcher

  Developed a computationally feasible statistical method for modeling biological sequence evolution under a dependent-sites model, where mutations at a site depend on the states of the flanking sites, for both forward simulation and inference of phylogenetically related endpoint sequence evolutionary history inference. Inference mechanism uses Markov-chain Monte Carlo inference method to generate a distribution of high-likelihood molecular evolutionary paths along a phylogenetic tree relating fixed endpoint leaf sequences. Show less

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  At U.S. Environmental Protection Agency

  Oct 2012 - Sept 2014

  ORISE Postdoctoral Fellowship

  - Implement a R package for the Exposure Forecasting (ExpoCast) project that performs the Bayesian Markov chain Monte Carlo inferences of parent chemical exposure given NHANES urine metabolites. - Develop and implement a pharmacokinetic method to infer exposures based on serum exposure information, and merge this serum exposure data into the Bayesian model.- Grow and maintain a metabolism mapping, i.e., parent-to-product chemical metabolism pathways. - Create a javascript application to visualize the relationships between parent and product chemicals in the metabolism mapping.- Work in a team to plan, implement and release a web-based interface for exploring and prioritizing chemicals and releasing chemical endpoints from high-throughput ToxCast assay. Show less

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  The Hamner Institutes for Health Sciences

  Sept 2014 - Dec 2015

  Research Scientist

  - Developed classification scheme to categorize chemicals into chemical classes (Pharmaceutical, near- and far-field environmental) based on Use categories in ACToR. Developed method to infer chemical ionizable sites and the pK a using chemical substructures. Assessed the uncertainty of downstream predictions elicited by inference scheme.- Collected and collated physicochemical properties, molecular descriptors, chemical structures, and ACToR Use categories for EPA data set of 32583 chemicals comprising the “exposure universe.” Computationally curated data set to remove duplicates and resolve conflicting CAS registration numbers, reducing data set to 32413 chemicals.- Collected and unified data sets for measuring PAH concentrations from the Deepwater Horizon oil spill in the Gulf of Mexico from the National Oceanic and Atmospheric Agency and British Petroleum. Predicted fish internal PAH concentrations using PBPK model.- Set up and administered Linux web server for the implementation of organization-wide workflow management software (http://icss.thehamner.org). Show less

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  Aperiomics

  Feb 2016 - Jan 2017

  Bioinformatics Scientist

  - Formulated a blueprint for Monte Carlo metagenomic sample benchmark data set construction varying genomic content, genomic and sample read abundance, sequencing error profiles, and host genome content. Developed pipeline for generating data sets using Python and Luigi- Generated Python scripts to assess four leading metagenomic software methods, testing prediction accuracy, ROC analyses, and abundance prediction.

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  US Environmental Protection Agency (EPA)

  Jan 2017 - now

  Biologist