AI-Enabled Spatial Neuropathology & Multi-Omics

Sanofi•Cambridge, MA

4d•$75,000 - $108,333•Hybrid

About The Position

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. Join the engine of Sanofi’s mission — where deep immunoscience meets bold, AI-powered research. In R&D, you’ll drive breakthroughs that could turn the impossible into possible for millions.

Requirements

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, GeoMx, CODEX/PhenoCycler, 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 StarDist/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.

Nice To Haves

Working knowledge of R or Python or AI tools (Cursor, Claude) sufficient to perform QC, generate exploratory plots, and interface with computational collaborators.
Direct experience with postmortem human CNS tissue and familiarity with brain bank operations and consent/IRB frameworks.
Experience with in vivo rodent procedures including blood micro-sampling, terminal collections, brain dissection and microdissection, CSF collection, and analyzing tissue samples from in vivo studies using molecular assays including NULISA, MSD, ELISA, and Western Blot.
Background in neurodegenerative disease research (ALS, FTD, Alzheimer's disease, Parkinson's disease, or multiple sclerosis).
Familiarity with iPSC-derived neuronal or glial models.
Prior pharmaceutical or biotechnology industry experience and exposure to GLP/GxP-adjacent documentation practices.
Co-authorship on peer-reviewed publications.

Responsibilities

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 NanoString GeoMx DSP) and spatial proteomics workflows (CODEX/PhenoCycler, GeoMx 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.