Zymergen, Inc

About Zymergen

Founded in 2013, Zymergen marries the latest innovations in data science, automation, and molecular biology to both discover and engineer new molecular products and to improve existing ones. Zymergen uses hypothesis testing based on our deep and broad knowledge, coupled with an atheoretic and automated approach in order to navigate the genomic search space for our customers. This methodology is designed to make discoveries beyond the bounds of human intuition by collecting and analyzing promising data we otherwise might never encounter.

To do this innovative and interdisciplinary research, Zymergen works equally as a software company and a biology company. On the software front, our proprietary infrastructure helps us simultaneously design thousands of “test everything” experiments targeting both on- and off-pathway genes, while allowing us to include other experiments based on rational hypotheses. Our software and IT infrastructure are layered on top of our innovative factory, an automated, modular, full-production facility. This factory is designed so scientists can safely and accurately conduct experiments using automated equipment and workflows. We also combine our platform and data infrastructure with a “host agnostic” approach: Zymergen has proven capabilities to work with the full range of microbes currently used for industrial production, as well as unconventional microbial species. Alongside canonical hosts such as S. cerevisiae and E. coli, we work with a range of other yeasts and other Gram-negative bacteria, as well as filamentous fungi and Gram-positive bacteria.

Our company ultimately sits at the intersection of molecular biology, industrial chemistry, machine learning, data science, and automation systems design. This enables Zymergen to deliver material diversity and performance capabilities not previously possible, with applications across industries — from electronics to agriculture, to pharmaceuticals and more.

Internship Project Description

–This description represents a potential internship project and is subject to change.–

(Updated 10/30/2020)

Zymergen’s intern projects may include work on novel industrial organisms (e.g. but not limited to: filamentous fungi, novel yeasts, Corynebacterium strains), pathway engineering, metagenomic library generation, bioinformatics using large datasets, library creation for enzyme engineering, and high throughput/automated methods. In case of a remote internship (which will likely be the case for our 2021 interns), projects will focus especially on bioinformatics, data science, and some aspects of technology development for example in context of large metagenomic data sets.

Additionally, our Advanced Technology Program may have an opportunity for an intern (remote, if needed) to help research and develop Deep Learning models for the prediction of molecular structures produced by biosynthetic gene clusters found in our metagenomics library. Another potential project may include RNAseq Optimization and Machine Learning, an effort focused on driving down the costs of RNAseq by an order of magnitude, while increasing reliability and repeatability. Depending on the skills of the intern, this project may focus on improving data handling pipelines and automated QC steps, advanced data analysis to enable efficient use of smaller samples, creation of software tools for use in the RNAseq process, or the creation of machine learning tools to use the resulting RNAseq datasets to predict the efficient optimization of the desired phenotype. This project can be done entirely remotely and may work in collaboration with on-site staff capable of running lab experiments.

Lastly, within our Computational Product Discovery Program, we may have an opportunity for a biochemistry/bioinformatics/systems biology intern to help with research and development of technologies for the prediction of biosynthetic pathways and the construction of biological reaction rules from large empirical datasets of enzymatic reactions.

In addition to providing a useful scientific experience for our interns, Zymergen also strives to help them learn about all aspects of our company and working in an industry setting. This includes special workshops and talks for interns about company departments and goals; ability to attend group, department, and company-wide meetings and educational presentations; and assistance to connect and network with other employees and groups of personal interest.