Scientist II – Spatial Biology, Epigenomics & Tumor Microenvironment

Scientist II – Spatial Multi‑Omic Biology

HJF is seeking a Scientist II to develop and supervise research projects focused on multi‑omic mapping of the spatial biology and epigenetic landscape of the breast cancer tumor microenvironment (TME). The role involves laboratory management, technology development, and grant preparation at the John P. Murtha Cancer Center in Bethesda, Maryland.

• Plan, execute, and oversee laboratory research utilizing ultra‑high‑plex spatial biology and single‑cell multi‑omic technologies, formulating experimental hypotheses and designing complex multiplex antibody validation and spatial sequencing workflows.
• Operate and maintain advanced multiplex imaging platforms, specifically the Akoya Pheno Cycler, optimizing automated cyclic fluidics, tissue staining, and image acquisition workflows.
• Establish and execute spatial epigenomic and single‑cell biology protocols, including tissue preparation and library construction for spatial ATAC‑seq, single‑cell RNA‑seq, and/or single‑cell ATAC‑seq.
• Execute complex spatial and multi‑omic analysis pipelines to integrate high‑plex proteomic imaging with spatial chromatin accessibility data, interpreting cellular states, tissue segmentation, and morphological features of the breast cancer microenvironment.
• Monitor scientific literature regarding spatial transcriptomics/epigenomics, single‑cell biology, and digital pathology; prepare written reports and manuscripts for submission to scientific journals and for patent applications.
• Coordinate and prepare new grant and funding applications focused on spatial oncology and translational multi‑omics.
• Process, normalize, and interpret high‑dimensional spatial and sequencing datasets.
• Make scientific observations, maintain detailed workbooks/documentation, and ensure documentation fulfills generally accepted professional/industry standards.
• Collaborate with other technical and professional staff, including pathologists and bioinformaticians; train and supervise technical staff in tissue processing, multiplex IF, NGS library preparation, and software tools.
• Manage, lead, and mentor staff; ensure productivity is monitored, identify peak and slack periods, and make operational or staffing adjustments as necessary.
• Work with section supervisors and the laboratory director on complex problems; identify, evaluate, and present solutions.
• Ensure standardization, enforce good clinical practices for CAP accreditation, and assist in developing QA/QC plans for digital imaging, tissue arrays, and genomic sequencing data.
• Participate in identifying disease situations and design proper laboratory support for such projects.
• May include budgetary responsibility for planning/forecasting, preparing, and approving budgets.
• Maintain laboratory information systems and spatial/genomic data storage infrastructures for two laboratory sections; identify information needs and recommend improvements.
• Ensure appropriate training for employees, write user manuals, establish priorities, and maintain security and confidentiality of clinical/patient information.
• Perform other duties and responsibilities assigned or directed by the supervisor, including attendance at required training.

• Doctoral Degree required; preference for a degree in Molecular Biology, Oncology, Immunology, Bioinformatics, Genetics/Genomics, or Biological Sciences.
• Minimum of 5–8 years of experience with a documented track record in single‑cell genomics, spatial biology, or multiplex tissue profiling.

• Deep technical knowledge of multiplex immunofluorescence (mIF) assay development and hands‑on experience operating the Akoya Biosciences Pheno Cycler (formerly CODEX) or comparable high‑plex imaging platforms.
• Hands‑on expertise in single‑cell biology workflows and next‑generation sequencing (NGS) technologies, with specific experience in spatial ATAC‑seq or single‑cell ATAC/RNA library preparation.
• Proficiency in quantitative image analysis and computational multi‑omics; experience using spatial biology software such as HALO, QuPath, and bioinformatics toolkits for single‑cell/spatial data…