Research Specialist, Senior

Job Title

The Spraggins group develops integrated molecular imaging technologies to elucidate the molecular basis of health and disease. Modern instrumentation and computing capabilities have enabled researchers to move beyond reductionist biology and, instead, probe how the components of biological entities (e.g., molecules, cells, and tissues) interact globally to reveal the underlying biology of disease. This systems biology approach has been accelerated by advancements in high-throughput 'omics' technologies, however, genetic and molecular information are only part of the story.

The challenge lies in understanding how these parts interact and how perturbations to the system relate to disease. To address this challenge, we are advancing instrumental capabilities and developing the computational tools necessary to integrate and mine multimodal data sets that bring together imaging mass spectrometry, highly multiplexed immunofluorescence microscopy, and spatial transcriptomics.

The Spraggins laboratory is part of the Mass Spectrometry Research Center (MSRC) and Department of Cell & Developmental Biology at Vanderbilt University. The MSRC consists of two research groups, including the Spraggins and Schey groups, and three cores that offer analytical services in proteomics, small molecules, and tissue imaging using mass spectrometry. The MSRC conducts collaborative research programs with investigators in nearly every Center and department in the Medical Center and Vanderbilt University as well as many trans-institutional initiatives.

Team members have access to state-of-the-art instrumentation including 6 imaging mass spectrometers, a CODEX highly multiplexed immunofluorescence platform, 2 fluorescence slide scanners, a laser capture microdissection system, a Xenium in situ platform, and a Geo Mx spatial transcriptomics instrument, as well as a collection of commercial and custom software for the analysis of imaging, multi-omics, and microscopy data. The group's research is embedded in large national consortia, including the Human Bio Molecular Atlas Program (HuBMAP), the Kidney Precision Medicine Project (KPMP), and the Human Tumor Atlas Network (HTAN).

Data Analysis and Method Development

• Develop, validate, document, and maintain computational pipelines for multimodal biomedical imaging data, including preprocessing, quality control, normalization, image registration, cell segmentation, and feature extraction.
• Analyze single-cell and spatial transcriptomics data, including clustering, marker-based cell type annotation, neighborhood enrichment, and cell–cell interaction analysis.
• Integrate imaging mass spectrometry, multiplexed immunofluorescence microscopy, and spatial transcriptomics data acquired from the same or serial tissue sections into common coordinate frameworks.
• Apply statistical and machine learning approaches to identify molecular and spatial features associated with disease state, progression, or treatment response.
• Design and execute analyses independently, selecting appropriate methods and evaluating model performance and robustness to confounding variables.
• Work closely with team members to interpret data generated by imaging and 'omics assays and to inform experimental design.
• Produce data visualizations and publication-quality figures for presentations, manuscripts, and grant applications.

Data and Software Management

• Management of large imaging and multi-omics datasets, including organization, storage, backup, and metadata capture.
• Execution of analysis workflows in high-performance and cloud computing environments.
• Use of version control and reproducible research practices for all analysis code.
• Preparation and submission of data and derived products to consortium data portals and public repositories in accordance with FAIR data standards.
• Record-keeping and documentation of analytical protocols.

Collaborations and Education

• Assist team members with implementing biocomputational, single-cell, and spatial transcriptomics workflows.
• Train students, postdoctoral fellows, and staff on biocomputational tools and analysis methods.
• Effective delivery of…