Erin Wilson

PhD student, Computer Science and Engineering

I’m a second year PhD student at the University of Washington where I work at the intersection of data science, synthetic biology, and sustainability!

See my Research

EDUCATION

2nd year PhD student, Computer Science & Engineering
      University of Washington, Seattle, WA

BA Computational Biology
      Carleton College, Northfield, MN
      June 2014  

RESEARCH & PROJECTS

I am interested in engineering microorganisms into tiny biological factories that can sustainably produce everyday molecules. To do this, we can edit microorganism genomes to convert renewable feedstocks (sugar) or waste streams (methane) into a desired target molecule such as medicine, biofuel, or theoretically any molecule found in nature. My current research focus is to use computational methods to better understand the "genetic grammar" underlying how these organisms control gene expression and use these insights to more efficiently engineer them for sustainable molecule production.

Current Projects


 Discovering sequence patterns in Methanotroph promoter regions

  Mary Lidstrom & Dave Beck     Jan 2019 - present
Analyzing genomic sequence and RNA-seq data in the methanotroph Methylomicrobium buryatense to model sequence patterns that contribute to promoter strength.

 Decoding yeast gene regulation from millions of random sequences

  Georg Seelig     Sept 2018 - present
Training deep and machine learning models on massively parallel reporter data from millions of randomized sequences to characterize gene regulation in yeast.



Past Projects


 Understanding gene expression patterns in developing heart tissue

  Georg Seelig     Sept 2017 - June 2018
Analyzed single-cell RNA-sequencing data to understand gene expression patterns in differentiating cardiomyocytes. (In collaboration with the Allen Institute for Cell Science)

INDUSTRY & WORK EXPERIENCE

I began my research career as a biologist and have since grown into a computer scientist with an interest in understanding biological data. I am excited about opportunities that allow me to span across fields and require computational skillsets to dig into outstanding challenges in biology.

Zymergen, Intern, Data Science

  Seattle, WA     June 2018 - August 2018
Used sci-kit learn and Keras/Tensorflow to build machine learning and convolutional neural network models for predicting DNA regulatory features in non-standard microbe genomes.

Amyris, Associate Scientist, Scientific Computing

  Emeryville, CA     July 2014 - July 2017
In the Scientific Computing group at Amyris, I applied my background in genetics and computer science to various computational projects in R&D. My role as a scientist ranged from the designated computational resource for a given project, to a member on a team of computational experts, and a communication bridge between software engineers and biologists. Several specific projects I worked on include:
  • characterizing the genomic impact of chemical mutagens
  • maintaining the company's whole genome sequencing pipeline
  • developing and training the Amyris community in Genotype Specification Language (a DNA design tool invented at Amyris)
  • building a Genotype Generator tool to translate high level designs for metabolic pathways into concrete build instructions for strains that can carry out pathway designs

Amyris, Intern, Scientific Computing

  Emeryville, CA     December 2013
Coded a data visualization tool to help strain engineers overlay experimental data onto yeast metabolic pathways.

 University of Minnesota, Research Assistant, Myers Lab (Computational Biology)

  Minneapolis, MN     June 2013 - August 2013
Used genetic interaction and chemical genetic interaction data to code a target prediction pipeline in Python. Developed a benchmark standard for accurately predicting gene targets for chemicals of interest.

 Carleton College, Research Assistant, Goings Lab (Evolutionary Computing)

  Northfield, MN     June 2012 - August 2012
Performed experiments on evolving populations of digital organisms to examine the effects of limited CPU resources on the populations’ ability to evolve complex Boolean logic functions.

 UCSF, Research Assistant, Ahituv Lab (Genetics)

  San Francisco, CA     June 2011 - August 2011
Perfomed chromatin immunoprecipitation sequencing experiments on mouse limb tissue to find enhancer candidates involved in limb patterning and development.

SCIENCE COMMUNICATION

PUBLICATIONS

  • E. H. Wilson, C. Macklin, and D. Platt. (2018) "Engineering genomes with Genotype Specification Language." In Methods in Molecular Biology, Synthetic Biology. J.C. Braman, ed. Springer Publishing Company, New York, NY. PubMed

  • E. H. Wilson, S. Sagawa, J. Weis, M. Shubert, M. Bissell, B. Hawthorne, C. Reeves, J. Dean, and D. Platt. (2016) "Genotype Specification Language." ACS Synthetic Biology. 5(6), pp 471-478. PubMed

  • S. W. Simpkins, J. Nelson, R. Deshpande, S.C. Li, J. S. Piotrowski, E. H. Wilson, A. A. Gebre, R. Okamoto, M. Yoshimura, M. Costanzo, Y. Yashiroda, Y. Ohya, H. Osada, M. Yoshida, C. Boone, C. L. Myers. (2018) “Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions.” PLoS Computational Biology. PubMed

POSTERS

  • E. H. Wilson, D. Platt. “Genotype Specification Language: Programming in DNA!” Poster presentation at Synthetic Biology, Engineering, Evolution & Design (SEED) conference in Chicago, July 2016.

BLOG POSTS

  • Conny Scheitz and Erin Wilson "Genetic Constructor and GSL - Best of Both Worlds." (2016) Autodesk Bionano Research Blog. Blog Post

AWARDS & HONORS

NSF Graduate Research Fellow
      University of Washington     2019
Marilyn Fries Fellow
      University of Washington     2017-2018
      First year funding from UW CSE
Graduation Honors
      Carleton College     2014
      Magna Cum Laude
      Received "Distinction" on Senior Thesis
Clare Boothe Luce Scholar
      Carleton College     Summer 2012
      Summer research funding for women in physics and computer science

Miscellaneous Science Nerdisms

Sometimes my brain makes jokes. Often they involve Disney/Science puns. Here are a few of them :)

Inspired by working at Amyris


Inspired by UW classes (ML, NLP, SynBio)


Contact Me

I'm always excited to learn more about how a computer/data scientist can help solve problems in biology and sustainability! Feel free to connect :)

Also, if you're considering exploring the intersection of Biology and Computer Science, I'd be happy to chat about my experience navigating undergrad, working in industry, and transitioning back to grad school.

You can reach me at ewilson6 cs.washington.edu.

I also have a LinkedIn.