AI-Enabled Spatial Neuropathology & Multi-Omics

Job title : AI-Enabled Spatial Neuropathology & Multi-Omics Location : Cambridge, MA About the Job 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. Main 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. About You Education 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. Experience & Technical Skills 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. Soft Skills 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. Preferred Qualifications 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. Why Choose Us Bring the miracles of science to life alongside a supportive, future‑focused team. Discover endless opportunities to grow your talent and drive your career, whether it’s through a promotion or lateral move, at home or internationally. Enjoy a thoughtful, well‑crafted rewards package that recognizes your contribution and amplifies your impact. Take good care of yourself and your family, with a wide range of health and wellbeing benefits including high‑quality healthcare, prevention and wellness programs and at least 14 weeks’ gender‑neutral parental leave. Be part of a pioneering biopharma company that engages patients early in drug development and uses their insights to design studies that reflect real‑world needs. Help improve the lives of millions of people globally by making drug development quicker and more effective. Work at the forefront of drug discovery, harnessing cutting‑edge AI, data, and digital platforms to push the boundaries of science. Sanofi Inc. and its U.S. affiliates are Equal Opportunity and affirmative Action employers committed to a culturally diverse workforce. All qualified applicants will receive consideration for employment without regard to race; color; creed; religion; national origin; age; ancestry; nationality; marital, domestic partnership or civil union status; sex, gender, gender identity or expression; affectional or sexual orientation; disability; veteran or military status or liability for military status; domestic violence victim status; atypical cellular or blood trait; genetic information (including the refusal to submit to genetic testing) or any other characteristic protected by law. All compensation will be determined commensurate with demonstrated experience. Employees may be eligible to participate in Company employee benefit programs, and additional benefits information can be found here. #J-18808-Ljbffr Sanofi