Scientist II – Spatial Biology, Epigenomics & Tumor Microenvironment

The Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda (MD); On-site; USD 93,100 - 120,000; Full time

Job summary

The Henry M. Jackson Foundation for the Advancement of Military Medicine seeks a Scientist II to lead breast cancer research using integrated single-cell and spatial multi-omic approaches at the Walter Reed National Military Medical Center in Bethesda, MD.

You will develop spatial genomics workflows, supervise technicians, and contribute to grant reporting and manuscript preparation. You will work with PhenoCycler platforms, spatial ATAC-seq and scRNA-seq, and collaborate with pathologists and

Qualifications

• Doctoral degree required with strong record in single-cell genomics or spatial biology.
• 5-8 years of relevant experience in breast cancer research or related fields.
• Experience with high-plex imaging platforms and spatial biology workflows.
• Strong communication and ability to supervise and train staff.

Responsibilities

• Plan, execute, and oversee lab research using ultra-high-plex spatial biology and single-cell multi-omic technologies.
• Operate and maintain Akoya PhenoCycler and optimize staining and imaging workflows.
• Develop spatial epigenomic and single-cell protocols (spatial ATAC-seq, scRNA-seq).
• Integrate imaging with genomics data to interpret tumor microenvironment architecture.
• Prepare reports, manuscripts, and grant applications; assist in QA/QC processes.
• Mentor staff and supervise technicians; manage space, equipment, and supplies.

Skills

Breast cancer research

Single-cell biology

NGS technologies

Quantitative image analysis

Computational multi-omics

Communication skills

Independence & supervision

Troubleshooting imaging procedures

Animal cancer research experience

Education

Doctoral Degree

PhD in Molecular Biology/Oncology/Immunology/Bioinformatics/Genetics/Genomics/Biological Sciences

Tools

Akoya PhenoCycler

HALO

QuPath

Seurat/Signac/Scanpy

Job description

Job Description

Join the HJF Team! 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). Investigates the feasibility of applying a wide variety of scientific principles and concepts to potential inventions, products, and problems. Develops new technologies, high-plex panel designs, spatial multi-omic workflows, and advanced single-cell protocols. This position entails various aspects of laboratory management. The incumbent is to be responsible for the day-to-day operations of the laboratory. Teaches the most advanced laboratory procedures, including ultra-high-plex multiplexing, single-cell multi-omics, and computational spatial analysis, and supervises the work of laboratory technicians. Provides administrative oversight to space management, personnel management, and laboratory supply management and equipment upkeep. Keeps up to date with laboratory goals of grant submissions and progress reports. This position will be in support of the John P. Murtha Cancer Center located at the Walter Reed National Military Medical Center, in Bethesda, Maryland. This position will support Dr. Geeta Upadhyay, Scientific Director of the Clinical Breast Care Project (CBCP) at the CBCP labs at USUHS campus 4301 Jones Bridge Road, Bethesda, MD. 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. The Murtha Cancer Center is a modern, patient-centric, tri-service military healthcare facility. Its comprehensive core of military and civilian oncologists and other cancer-trained clinicians and researchers provide multidisciplinary cancer-care delivery and patient-family support services. Our Cancer Center, the only DoW Cancer Center of Excellence within the Military Health System, offers its patients access to cutting-edge cancer diagnostic and treatment technologies. The Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) is a nonprofit organization dedicated to advancing military medicine. We serve military, medical, academic and government clients by administering, managing and supporting preeminent scientific programs that benefit members of the armed forces and civilians alike. Since its founding in 1983, HJF has served as a vital link between the military medical community and its federal and private partners. HJF's support and administrative capabilities allow military medical researchers and clinicians to maintain their scientific focus and accomplish their research goals.

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.
• Monitors scientific literature regarding spatial transcriptomics/epigenomics, single-cell biology, and digital pathology. Prepares written reports and manuscripts for submission to scientific journals and prepares patent applications.
• Coordinates and prepares new grant and funding applications focused on spatial oncology and translational multi-omics.
• Processes, normalizes, and interprets high-dimensional spatial and sequencing datasets.
• Makes scientific observations, maintains detailed workbooks/documentation, and ensures 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. Assists in the development of the quality assurance and quality control (QA/QC) plans and procedures for digital imaging, tissue arrays, and genomic sequencing data.
• Participates in identifying disease situations and designs proper laboratory support for such projects.
• May include budgetary responsibility to include plan/forecast, prepare, and approve.
• Maintains laboratory information systems and spatial/genomic data storage infrastructures for two laboratory sections. 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.
• May perform other duties and responsibilities as assigned or directed by the supervisor. This may include attendance of and participation in required training for role.

Qualifications

Education and Experience

• 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.

Required Knowledge, Skills And Abilities

• Experience in breast cancer research.
• 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.

Work Environment

• This position will take place primarily in a laboratory setting.

Compensation

• The annual salary range for this position is $93,100 - $120,000. Actual salary will be determined based on experience, education, etc.

Benefits

• HJF offers a comprehensive suite of benefits focused on your health and well‑being, from medical, dental, and vision coverage to health savings and retirement plans, and more.

Employment with HJF is contingent upon successful completion of a background check, which may include, but is not limited to, contacting your professional references, verification of previous employment, education and credentials, a criminal background check, and a department of motor vehicle (DMV) check if applicable. Any qualifications to be considered as equivalents, in lieu of stated minimums, require the prior approval of the Chief Human Resources Officer.

Equal Opportunity Employer/Protected Veterans/Individuals With Disabilities