Principal Scientist, Cell Modeling

Job Description

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.

Responsibilities

Scientific Leadership and Strategy

• 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.

Program Execution at the Bench

• 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.

Characterization and Quality Standards

• 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.

Cross-Functional Collaboration

• 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.
• Work with the phenotypic screening and assay development functions to ensure cell models are compatible with high-throughput and high-content workflows.
• Communicate results clearly to program leads, contribute to scientific discussions shaping next experiments, and present at internal scientific reviews.

Team and External Engagement

• Mentor and, where applicable, develop and train a team of scientists supporting the cell modeling function.
• Support knowledge transfer of methods and models between the Redwood City and Cambridge sites, even though the role itself is Redwood City-based.
• Manage external collaborations and vendor relationships relevant to cell modeling, including academic partners and contract providers for specialized lines or services.
• Represent the Institute's cell modeling work in select external scientific settings as appropriate.

Qualifications

Required

• PhD in cell biology, stem cell biology, molecular biology, or a closely related discipline.
• Minimum of ten years of post-PhD experience in industry or a translational research setting, with substantial time spent on iPSC-based disease modeling and engineered cell line generation.
• Deep hands-on expertise in iPSC or other stem cell culture, including antibiotic-free maintenance and extended differentiation protocols into multiple lineages.
• Demonstrated experience building three-dimensional and organoid models, particularly of lung or related epithelial tissues.
• End-to-end experience generating CRISPR-edited cell lines, including design, delivery across multiple methods, clonal isolation, and validation.
• Experience leading CRISPR screening campaigns, including arrayed or pooled formats and the functional genomics readouts that follow.
• Strong scientific communication skills and the judgment to set technical standards that others can follow.

Preferred

• Direct experience with lung-lineage differentiation, including airway and alveolar epithelial protocols.
• Familiarity with RNA-seq and single-cell approaches, including sample preparation and interpretation of results.
• Experience with liquid handling platforms and laboratory automation in a cell biology context.
• Prior work in fibrosis, pulmonary biology, or transplant-focused disease modeling R&D setting.
• Experience contributing to IND-enabling or regulatory-facing studies, even indirectly through model provision.

Location and Work Environment

This position is based in the San Francisco Bay Area, with primary work location in the Redwood City laboratory. The role is fully on-site, with daily presence required to support cell culture, engineering workflows, and team supervision. Occasional travel to the Cambridge site and to academic collaborators is expected.

About the Role

This role is intended for someone who has a strong background in the development of high-fidelity cell-based models that capture the complex context of epithelial biology. The right person possesses broad-based technical knowledge across stem cell biology, organoid culture, and genome engineering and is motivated by the prospect of seeing models they develop be brought to bear on decisions in therapies for patients with lung disease and beyond.