AI-Enabled Spatial Neuropathology & Multi-Omics

Job title
: AI-Enabled Spatial Neuropathology & Multi-Omics

Location
:
Cambridge, MA

Sanofi is building a next-generation neuroscience research engine focused on defining the molecular mechanisms of neurodegenerative disease — Alzheimer's disease, ALS, frontotemporal dementia, Parkinson's disease, and multiple sclerosis — through high-resolution interrogation of human brain and spinal cord tissues. We are seeking a Senior Associate Scientist II to join a newly established research group that integrates single-cell genomics, spatial transcriptomics and proteomics, and human neuropathology to identify and credential novel therapeutic targets.

This role sits at the experimental core of the group. The successful candidate will execute end-to-end multi-omics workflows on postmortem human CNS tissue and patient-derived models, partnering closely with computational biologists, neuropathologists, and program teams to translate human tissue insights into drug discovery programs.

• Generate high-quality single-cell and single-nucleus RNA-seq libraries (10x Genomics Chromium, multiome ATAC + GEX) from human postmortem brain and spinal cord, iPSC-derived neural cultures, and rodent CNS tissues.
• Execute spatial transcriptomics workflows (10x Atera, Xenium, or Nano String Geo Mx DSP) and spatial proteomics workflows (CODEX/Pheno Cycler, Geo Mx protein, imaging mass cytometry) on FFPE and fresh-frozen CNS sections.
• Perform precision dissection, cryosectioning, and FFPE sectioning of human postmortem CNS tissue under appropriate biosafety conditions; manage tissue biobank inventory, sample QC, and chain-of-custody documentation.
• Conduct multiplex immunohistochemistry and immunofluorescence to characterize disease-relevant pathology (e.g., TDP-43 proteinopathy, tau, α-synuclein, demyelination markers) and to validate findings from single-cell and spatial datasets.
• Operate and maintain confocal, widefield, and slide-scanning microscopy platforms; capture and curate imaging data to support quantitative neuropathology.
• Execute first-pass QC and exploratory analysis of single-cell and spatial datasets using standard pipelines (Cell Ranger, Space Ranger, Seurat, Scanpy, Squidpy); partner with computational team members for downstream analysis.
• Develop, optimize, and document standard operating procedures; train junior team members on established assays.
• Maintain rigorous electronic lab notebook records, contribute to internal data reviews, present results at group and cross-functional meetings, and contribute to publications, posters, and patent filings.
• Coordinate with external academic collaborators, brain banks, and CRO partners on tissue acquisition, IRB documentation, and assay execution.

• BS with 4+ years OR MS with 2+ years, of relevant laboratory experience in neuroscience, molecular biology, cell biology, biomedical engineering, or a related discipline.

• Demonstrated hands‑on proficiency with single-cell or single-nucleus RNA‑seq library preparation (10x Genomics Chromium platform required).
• Direct hands‑on experience with at least one spatial transcriptomics or spatial proteomics platform (Visium, Xenium, MERFISH, Geo Mx, CODEX/Pheno Cycler, or equivalent).
• Demonstrated experience handling and processing primary tissue, including cryosectioning and/or FFPE sectioning, with a track record of producing publication‑quality histology.
• Hands‑on competence in immunohistochemistry, immunofluorescence, and fluorescence microscopy.
• Hands‑on experience applying AI/machine learning approaches to digital neuropathology, including the use of deep learning‑based tools (e.g., QuPath with Star Dist/Cellpose, HALO AI, Aiforia, or custom Python/PyTorch pipelines) for automated cell segmentation, tissue classification, and quantitative pathology readouts on whole‑slide images.

• Strong organizational skills, meticulous record‑keeping, and the ability to manage multiple parallel workflows in a deadline‑driven environment.
• Excellent written and verbal communication; comfort presenting data to scientific audiences.

• Working knowledge…