Principal / Sr. Principal Scientist - Molecular Biology & Protein Expression (PM schedule)

Eli Lilly and Company; San Diego (CA); On-site; USD 72,000 - 189,000; Full time

Benefits offered by this job

401(k)

Health benefits

Paid time off

Flexible benefits

Life insurance

Job summary

Eli Lilly and Company in San Diego seeks a Principal Scientist in Molecular Biology & Protein Expression to join a centralized platform. You will own complex expression challenges, mentor staff, and drive platform automation and high-throughput workflows across multiple host systems.

The role emphasizes design of constructs, multi-host expression, and collaboration with purification and structural biology teams to deliver material for projects.

Qualifications

• B.S./M.S. in Biological Sciences or related field with 5+ years of hands‑on cloning and protein expression experience.
• Authorized to work in the United States on a full‑time basis. No visa sponsorship provided.

Responsibilities

• Design and execute molecular cloning strategies and construct design.
• Perform small‑scale expression in multiple host systems to screen constructs and conditions.
• Scale up expression in E. coli and insect cells to provide material for purification and projects.
• Assess expression using SDS‑PAGE, Western blot, SEC, and UV spectroscopy.
• Develop and improve platform workflows to increase throughput and reproducibility.
• Collaborate with purification, structural biology, and project teams to align strategies.
• Maintain accurate records in LIMS and electronic notebooks with rigor.
• Communicate progress, results, and risks clearly to stakeholders.

Skills

Molecular cloning

Protein expression

Gibson assembly

Golden Gate

In-Fusion

Site-directed mutagenesis

E. coli expression

Baculovirus/insect cells

Mammalian expression cells

Transient transfection

Baculovirus infection

Bioreactor development

High-throughput workflows

Laboratory automation

LIMS / electronic notebooks

Data integrity

Education

Bachelor's or Master's in Biological Sciences

Tools

AKTA FPLC

Benchling

LIMS

Job description

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.

Molecular Biology & Protein Expression – Principal Scientist / Senior Principal Scientist 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.

Assignment Details

Employment type: Fixed Duration Employee (FDE) Assignment length: 12 months Schedule: eight‑hour shift beginning at 2:00PM local time; including some weekends Location: San Diego,CA

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.
• Qualified applicants must be authorized to work in the United States on a full‑time basis. Vaccine Company will not provide support for or sponsor work authorization or visas for this role, including but not limited to F‑1CPT, F‑1OPT, F‑1STEMOPT, J‑1, H‑1B, TN, O‑1, E‑3, H‑1B1, or L‑1.

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, 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 (≥10L) 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 25lbs., 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.

#WeAreLilly At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe! #WeAreLilly