Senior Scientist, Phenotypic Screening

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.

We are seeking a Senior Scientist to help build the high-content imaging and phenotypic screening arm of our drug discovery pipeline. This role will help to translate insights from disease biology into biologically relevant assays, and executing drug discovery screens.

Assay Development

• Design and develop image-based phenotypic assays in 96- and 384-well format, including cell painting, high-content readouts of subcellular protein localization, translocation assays, and multiparametric morphological profiling.
• Translate disease biology into screenable phenotypes by defining disease vs. healthy cell signatures, select robust primary readouts, and design appropriate counter-screens.
• Establish and validate assay performance metrics (Z′-factor, %CV, signal-to-background, edge effects) and drive miniaturization from bench-scale to plate-based formats compatible with high-throughput screening.
• Build and optimize image analysis pipelines using IN Carta, CellProfiler, Columbus, or equivalent platforms, including segmentation (watershed and propagation), feature extraction, co-localization metrics (Pearson's, Manders'), puncta detection, and downstream phenotypic classification, with deep-learning approaches where appropriate.
• Optimize multi-channel staining panels through antibody validation and titration, two-step surface vs. permeabilized protocols, substrate (ECM) effects on phenotype, and selection of imaging modality.

• Lead the execution of primary and secondary phenotypic screens from pilot, validation, and full-scale campaigns to ensure data quality and reproducibility.
• Manage day-to-day operation of the high-content imaging platform including scheduling, QC, instrument operation and performance of experimental work.
• Generate, curate, and analyze large image datasets to produce clear reports and recommendations for project teams and program reviews.
• Partner with the laboratory automation team to integrate assays into automated workflows.
• Establish rigorous documentation standards (SOPs, electronic lab notebook entries and QC records) to ensure assays are transferable and communicated across the team and to future hires.

• Collaborate closely with disease modeling, automation, and computational biology functions to align upstream biology with downstream data analysis.
• Contribute to internal scientific reviews, present results clearly in cross-functional meetings, and help shape the long-term direction of the screening platform.
• Partner with program leadership to translate screening results into actionable next steps for therapeutic programs.

• Mentor and train Senior Research Associates and Research Associates on imaging assays and image analysis workflows.
• Help define the screening team's longer-term operating model and shape what the platform looks like as the Institute moves into full-scale campaigns.
• Build a culture of scientific excellence, reproducibility, and operational urgency within the screening function.

Required

• PhD in Cell Biology, Molecular Biology, Biochemistry, Bioengineering, or a closely related discipline.
• At least 3-5 years of post-PhD experience in industry drug discovery, with demonstrated experience taking cell-based or imaging assays from development through to a screening campaign.
• Hands-on expertise with high-content imaging platforms (e.g., ImageXpress, Opera Phenix, CellInsight, or equivalent).
• Working proficiency with image analysis software (IN Carta, CellProfiler, Columbus, Harmony, or comparable), including building custom analysis pipelines.
• Strong cell culture fundamentals: maintaining mammalian cell lines and primary cells under aseptic conditions (iPSC culture a plus).
• Excellent scientific communication skills, with the ability to present data, write clear technical documentation, and mentor team members.

This position is based in the San Francisco Bay Area, with the primary work location in Redwood City, CA.

This is a hands-on senior scientist role for someone who combines expertise in high-content imaging and phenotypic assay development with operational discipline in screen execution. The Senior Scientist will collaborate closely with cross-functional scientific and project management teams to translate disease biology into screenable assays and to deliver high-quality data.