Principal Scientist, Cell Modeling

Job Description

The Allman Institute is a translational research organization applying personalized medicine to treat severe and historically difficult-to-treat diseases, beginning with pulmonary fibrosis and chronic lung transplant dysfunction. The Institute combines deep molecular profiling, longitudinal clinical data, and a pragmatic mix of mechanism‑guided and large‑scale empirical approaches to accelerate therapeutic discovery and translation.

We pursue an ambitious and pragmatic, modality‑agnostic therapeutic strategy spanning genetic medicines, molecular and pharmacologic therapies, cell and immune‑based interventions, and engineered biological systems, in close collaboration with leading academic and biotech partners across the U.S. and abroad. The Institute is established as a nonprofit, backed by substantial long‑term capital committed directly to the mission. Where strategically valuable, we may pursue mission‑aligned for‑profit ventures, spin‑outs, and partnerships to accelerate therapeutic development and patient impact.

We are a small but rapidly growing team of approximately 20, scaling to 40–50 over the next year across labs and offices in Redwood City, CA and Cambridge, MA, driven by scientific rigor, translational urgency, and a patient‑anchored mandate.

The Institute is seeking a Principal Scientist, Cell Modeling to lead the design, generation, and characterization of the human cell systems that underpin its therapeutic programs across gene therapy, drug repurposing, transplant, and lung regeneration. This is a hands‑on role with technical ownership of the iPSC, organoid, and engineered cell line platforms that inform downstream programs. The Principal Scientist will set the scientific direction for cell modeling at the Institute, work at the bench on the most difficult model‑building challenges, and may manage a team as the function scales.

• Define the cell modeling strategy across active programs, including which iPSC lines, differentiation protocols, and engineered systems are required to support gene therapy, fibrosis, transplant, and regeneration work.
• Anticipate downstream needs by working closely with program leads to align model selection with the specific therapeutic questions each program must answer.
• Evaluate emerging technologies in stem cell biology, organoid culture, and genome engineering, and decide which to bring in‑house versus access through collaboration.
• Establish technical standards for iPSC handling, differentiation, and engineered line validation that hold across the cell modeling function as it grows.

• Establish and implement protocols to generate and maintain iPSC cultures under antibiotic‑free conditions, including the long differentiation timelines required for mature lung epithelial phenotypes.
• Develop and execute directed differentiation protocols into lung lineages and other cell types relevant to active programs, including transcription factor‑based and small molecule‑driven approaches.
• Generate three‑dimensional and organoid systems, particularly of lung and related epithelial tissues, to capture biological context that 2D cultures cannot provide.
• Design and execute CRISPR‑based editing strategies to produce isogenic, disease‑relevant, and reporter cell lines, including end‑to‑end ownership from design through clonal isolation and validation.
• Lead CRISPR screening efforts where program requirements call for functional genomics readouts, including arrayed and pooled formats.

• Implement industry best practices to characterize differentiated cells and engineered lines using qPCR, immunofluorescence, RNA‑seq, and other molecular and cellular assays appropriate to the model.
• Maintain rigorous quality control across iPSC culture, including karyotype, identity, and pluripotency monitoring, and define what fit‑for‑purpose validation means for each model class.
• Document protocols, results, and deviations in a manner that supports reproducibility, cross‑program transfer, and audit‑ready records.
• Collaborate with team members and external collaborators to troubleshoot differentiation methods when results fall outside expected ranges.

• Partner with scientists across gene therapy, drug repurposing, transplant, and regenerative medicine programs to deliver fit‑for‑purpose cell models on program‑relevant timelines.
• Coordinate with computational and AI colleagues to align experimental design with downstream analytical needs, including sample structure for sequencing‑based readouts.