Scientist - Assay Development (TE3)

Ginkgo is a high-growth, well-capitalized public biotech company in Boston that is redesigning the living world to solve some of the globe's growing challenges in health, energy, food, materials, and more. Ginkgo is constructing, editing, and redesigning the living world in order to answer the globe's growing challenges in health, energy, food, materials, and more. Our mission to "make biology easier to engineer" is poised to disrupt multiple industries by leveraging our innovative data, automation, and scale in biological engineering.

In order to support Ginkgo's mission of making biology easier to engineer, the Enzymology, Biochemistry and Biocatalysis (EBB) team is seeking a motivated biochemist with experience in applied enzymology, using enzymes to produce novel small molecules, proteins and oligonucleotides for applications across a broad range of chemical and pharmaceutical industries. The successful candidate will become an integral part of Ginkgo's programs, supporting the use of enzymes in applications ranging from bioremediation to pathway engineering to chemical synthesis and everything in between.

Responsibilities

• Science (Assay Development)
  • Provide expert guidance leveraging a deep understanding of chemical principles in designing metagenomic sourcing and protein engineering projects to discover novel biotransformations of small molecules, proteins, and oligonucleotides.
  • Collaborate with analytical chemistry colleagues to deploy molecular detection strategies for new-to-science chemical transformations, including enantioselective small molecule transformations, peptide or protein post-translational decoration, and oligonucleotide biosynthesis
  • Apply knowledge of chemical, biochemical, biophysical, and enzymological principles to design assays that can be executed in high throughput to measure enzyme activity, small molecule concentration, protein abundance, and protein function.
  • Understand the impact of microbial growth and fermentation on assays of interest and design small-scale fermentation conditions that will be predictive of assay results at larger scales
  • Design, execute, and analyze assay development experiments to demonstrate proof of principle of new assays, de-risk sources of assay interference or bias, optimize and validate the assays in high-throughput workcells
• Science (Screen Execution)
  • Execute screens in high-throughput using a suite of automated instruments and integrated workcells, including liquid handlers, microplate readers, mass spectrometers, HPLCs, high to mid-dimensional screens, and others, working in high-density microplate formats (384- and 1536-well plates)
  • Coordinate with Core and Operations teams to support their work in Screen Execution
• Software
  • Use a variety of software packages and write scripts for programming liquid handlers (in-house and third-party tools), designing and viewing DNA sequences, processing data, and performing statistical analysis (Spotfire, Python, JMP) laboratory information management system (LIMS), database management (in-house and third-party tools), and third-party lab instrumentation and automation software
• Data science, data management, and statistical analysis
  • Use Spotfire to analyze and apply advanced statistical techniques to assay development experiments and executed high-throughput screens, and upload these results in a structured, standardized format into company databases
  • Build robust applications capable of managing complex, large volumes of data resulting in new biological insights.
  • Apply statistical Design of Experiment principles to design assay optimization experiments and analyze the results to identify optimal conditions for future experiments and screens
• Automation
  • Establish an understanding of automated liquid handlers to be able to create and execute new liquid handling procedures on complex liquids (high viscosity and volatility) at small volumes (ranging from nanoliters to microliters) and independently troubleshoot errors that arise during the execution
  • Understand and incorporate the constraints of automated liquid handlers into experiment and procedure design, and understand how different instruments may introduce bias into experimental data
• Project scoping/planning/sales
  • Work with Commercial teams in planning and scoping new projects, meet with potential and current customers to understand their needs, and propose both standardized and bespoke solutions to their problems, review proposals, and plan project timelines in alignment with customer requirements and milestone deadlines
• Project leadership
  • Within a project, lead a group of several scientists in assay development and screen execution, including planning and designing experiments, delegating tasks, and being accountable for on-time delivery of results
  • Work collaboratively with the project leader to coordinate the inputs and outputs of high throughput screening work on the project, including technical strategy, timeline, and presentation of results internally and externally
• Project management
  • Within a project, work with the project leader to coordinate on strategic elements of the project that may impact, but are not necessarily within the scope of work of, HTS. This can include strategic components of genetic design, protein engineering, cell transformation, analytical chemistry teams, and fermentation
  • In some cases, may serve as project lead for internal development projects or projects that heavily lean on HTS capabilities
• Communication
  • Communicate to a broad range of stakeholders, including providing detailed technical communications to scientific stakeholders and high-level, abstracted, accessible communications to leadership, executive, and external audiences, including customers

Minimum Requirements

• PhD in biochemistry, bioengineering, chemistry, chemical engineering or equivalent; OR BS or MS with 4+ years of prior experience in an industry laboratory setting working as part of a multi-disciplinary team
• Demonstrated experience in protein engineering, biocatalysis or protein biochemistry
• Demonstrated ability to deliver results while working independently as a laboratory scientist

Preferred Capabilities and Experience

• Established capability to design, conduct, optimize, and execute novel analytical assay development efforts in the lab supporting HTS and project deliverables.
• Experience developing biochemical assays (e.g., assessing enzymatic activity & kinetics, molecular interactions, protein modifications) and/or biophysical techniques & approaches (e.g., SPR, ITC, TSA, etc.)
• Experience with modern analytical chemistry techniques and platforms (HPLC, LC-MS, GC-MS, etc)
• Understanding of microbial metabolism and physiology
• Experience using laboratory automation equipment
• Experience in computational analysis of biological data and large data sets using general-purpose programming languages (such as Python, R, or Matlab)
• Familiarity with software and statistical platforms for documenting (ELN) and analyzing large data sets (e.g., JMP, Spotfire, or MODDE pro/DoE)