Principal / Sr. Principal Scientist - Molecular Biology & Protein Expression

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us. 

Position Summary

The Principal Scientist / Senior Principal Scientist in Molecular Biology & Protein Expression will join a centralized molecular biology and protein expression platform team within Lilly Small Molecule Discovery (LSMD). This role focuses on molecular biology and recombinant expression of diverse protein targets, including challenging targets such as membrane proteins, across multiple host systems. The scientist will serve as a key member of the technical team, owning complex expression challenges, mentoring less experienced colleagues, and driving platform development, including automation and higher-throughput workflows.  

Key Responsibilities

• Independently design and execute molecular cloning strategies, including Gibson assembly, Golden Gate, In-Fusion, restriction/ligation cloning, SLIC, and site-directed mutagenesis, and design constructs (tags, truncations, fusion partners, codon optimization) tailored to each target.
• Perform small-scale expression of recombinant proteins across multiple host systems, including E. coli, baculovirus/insect cells, and mammalian cells, using transient transfection, baculovirus infection, and adherent/suspension cell culture workflows to screen constructs, hosts, and expression conditions.
• Execute large-scale expression of recombinant proteins in E. coli and insect cells, using shake flasks, Wave/rocker bag systems, and stirred-tank bioreactors to deliver material for purification and project needs.
• Assess expression and small-scale material using SDS-PAGE, Western blot, capillary electrophoresis, analytical SEC, and UV spectroscopy in support of construct triage and expression optimization.
• Develop and improve platform workflows, including parallelization, standardization, and automation of cloning and expression screening, to increase throughput and reproducibility.
• Collaborate with purification, structural biology, and project teams to align construct design and expression strategies with downstream needs.
• Maintain accurate and timely records of all experimental data in a Laboratory Information Management System (LIMS) and electronic laboratory notebooks, upholding high standards of scientific rigor and data integrity.
• Communicate experimental progress, key results, and risks clearly, verbally and in writing, to project stakeholders and team leadership, ensuring consistent visibility into program status and proposed next steps.

Basic Qualifications

• B.S. or M.S. in Biological Sciences, Biochemistry, Molecular Biology, Chemistry, Biophysics, or a related discipline, with typically 5 or more years of relevant hands-on molecular cloning and recombinant protein expression experience, or equivalent demonstrated impact.

Preferred Qualifications

• Proficiency with molecular cloning techniques (Gibson, Golden Gate, In-Fusion, site-directed mutagenesis) and proven ability to design constructs for structurally and biochemically diverse targets.
• Hands-on proficiency across all three host systems (E. coli and baculovirus/insect), with experience selecting the appropriate host for a given target.
• Strong organizational skills and attention to detail.
• Effective written and verbal communication skills.
• Proficient with standard laboratory and office software.
• Experience with yeast expression and large-scale mammalian expression (e.g., CHO, HEK293).
• Experience with membrane protein expression (e.g., GPCRs, transporters, ion channels); this is required at the Senior Principal Scientist level.
• Experience with bioreactor process development (DO, pH, feeding strategy) and Wave/rocker bag scale-up workflows.
• Experience with large-scale (≥10 L) purification workflows, including AKTA FPLC.
• Experience with laboratory automation and high-throughput cloning/expression workflows (e.g., liquid handling, colony picking).
• Familiarity with cell-free protein synthesis systems and/or other specialized expression strategies.
• Demonstrated experience mentoring and providing technical guidance to junior scientists is highly valued and may indicate suitability for the more senior level.
• Experience with electronic laboratory notebooks (e.g., Benchling), LIMS, or protein sample tracking databases.

Work Environment & Physical Demands

• This role is based on-site in laboratory/bench setting.
• Must be able to meet the physical requirements of the position, including lifting up to 25 lbs., with or without reasonable accommodation.

 

Additional Information:

• The appointed candidate will work on site, full-time, in San Diego, California. 

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.  The anticipated wage for this position is

$72,000 - $189,200

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

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