Scientific Lead, Molecular Characterization

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. At Lilly, we unite caring with discovery to help make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana.

Our employees around the world work to discover and bring life‑changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world.

The Scientific Lead position would be the principal architect for spatial biology within the Molecular Characterization team in Discovery Technologies, responsible for developing, optimizing, and scaling these platforms in support of Oncology drug discovery  Molecular Characterization team sits at the intersection of genomics, proteomics, and emerging molecular technologies, providing cutting‑edge platform capabilities across Lilly's discovery portfolio. The central mandate is invention: defining what next‑generation spatial can do, and building the infrastructure to realize their full potential within the group.

The successful candidate will possess deep, applied expertise in spatial transcriptomics (e.g., Visium HD, Cos Mx, Xenium). Of equal importance is an entrepreneurial scientific mindset, a genuine drive to evaluate and deploy emerging tools that have not yet been established as standard practice within the field. This is a hands‑on role where direct experimentation and platform development are central to scientific impact, with growing opportunities to shape scientific direction and mentor junior team members as the platforms mature.

This position requires close collaboration with Oncology project teams, automation specialists, histology, and discovery informatics to translate novel molecular insights into actionable biology.

• Design and lead the development of spatial transcriptomics and multi‑modal spatial workflows, encompassing tissue optimization, library construction, and end‑to‑end data generation using platforms such as Visium HD, Cos Mx, and Xenium.
• Drive the integration of spatial transcriptomics with complementary modalities, including spatial proteomics (e.g., Cos Mx protein panels, CODEX/Pheno Cycler) and single‑cell data, to generate comprehensive tissue‑level molecular maps.
• Establish and continuously improve tissue processing standards for diverse sample types relevant to Oncology (FFPE, fresh‑frozen, bone marrow, cryosections), with a focus on maximizing data quality from challenging or low‑input specimens.
• Develop image analysis pipelines in collaboration with discovery informatics, including tissue segmentation, cell type deconvolution, and morphological co‑registration using tools such as QuPath, HALO, or equivalent platforms.
• Evaluate emerging spatial technologies on an ongoing basis and translate promising platforms into internal capabilities through systematic feasibility assessment and implementation planning.
• Contribute to automation of NGS…