Scientist II – Spatial Biology, Epigenomics & Tumor Microenvironment

About the role

The Scientist II will lead projects investigating breast cancer architecture using integrated single-cell and spatial technologies—specifically the Akoya Biosciences PhenoCycler platform for complex spatial phenotyping, alongside spatial ATAC-seq (Assay for Transposase-Accessible Chromatin) and single-cell sequencing modalities to map the chromatin accessibility and structural cellular neighborhoods of the TME.

Responsibilities

• Plans, executes, and oversees laboratory research utilizing ultra-high-plex spatial biology and single-cell multi-omic technologies.
• Formulates experimental hypotheses and designs complex multiplex antibody validation and spatial sequencing workflows.
• Operates and maintains advanced multiplex imaging platforms, specifically the Akoya PhenoCycler, optimizing automated cyclic fluidics, tissue staining, and image acquisition workflows.
• Establishes and executes 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.
• Executes 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.
• Maintains detailed workbooks/documentation, ensuring documentation fulfills generally accepted professional/industry standards.
• Collaborates with other technical and professional staff, including pathologists and bioinformaticians.
• Trains and supervises technical staff in tissue processing, multiplex IF, NGS library preparation, and software tools.
• Manages, leads, and mentors staff. Ensures productivity is monitored, identifying peak and slack periods, and makes operational or staffing adjustments as necessary in both sections.
• Works with both section supervisors and the laboratory director on complex problems. Identifies, evaluates, and presents solutions.
• Ensures standardization, without duplicity, within the sections and enforces good clinical practices for the College of American Pathologists (CAP) accreditation.
• Participates in identifying disease situations and designs proper laboratory support for such projects.
• May include budgetary responsibility to include plan/forecast, prepare, and approve.
• Identifies information needs and problems and recommends improvements.
• Oversees and ensures the appropriate training for employees.
• Writes user manuals, establishes priorities, and maintains security and confidentiality of clinical/patient information.

Qualifications

• 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 required, 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 direct hands-on experience operating the Akoya Biosciences PhenoCycler (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 utilizing spatial biology software (e.g., HALO, QuPath) alongside bioinformatics toolkits for single-cell/spatial data analysis (e.g., Seurat, Signac, Scanpy, Giotto, or custom R/Python scripts).
• Strong understanding of the tumor microenvironment architecture, cell-to-cell interaction modeling, gene regulatory networks, and epigenetic regulation in cancer.
• Excellent communication skills and ability to bridge the gap between wet-lab biology, spatial imaging, and computational genomics.
• Ability to troubleshoot technical imaging procedures, tissue artifacts, and library generation failures.
• Ability to work independently and supervise others, directing work assignments for laboratory technicians and junior scientists.
• Animal cancer research experience and a strong inclination to work with human archival patient sample material (FFPE and frozen tissues) to address precision medicine challenges.
• Ability to obtain and maintain a T1/Public Trust background check.