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Single Cell Spatial Transcriptomics Jobs in Needham, MA

AA2IT

Bioinformatics Scientist - II

Cambridge, MA · On-site

$75/hr

Proven work with RNA-Seq, single-cell RNA-Seq, genotype data, spatial transcriptomics, and proteomics (e.g., OLINK). * Technical Skills: Strong programming skills in R, Python, and Bash. * Experience ...

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How much do single cell spatial transcriptomics jobs pay per hour?

As of Jun 4, 2026, the average hourly pay for single cell spatial transcriptomics in Needham, MA is $23.58, according to ZipRecruiter salary data. Most workers in this role earn between $18.32 and $29.57 per hour, depending on experience, location, and employer.

What are the key skills and qualifications needed to thrive as a Single Cell Spatial Transcriptomics Scientist, and why are they important?

To thrive as a Single Cell Spatial Transcriptomics Scientist, you need a strong background in molecular biology, genomics, and bioinformatics, typically supported by an advanced degree (PhD or MSc) in a relevant field. Familiarity with high-throughput sequencing platforms, spatial transcriptomics technologies (like 10x Genomics Visium or NanoString GeoMx), and data analysis tools such as R or Python is essential. Critical thinking, problem-solving, and effective communication are crucial soft skills for interpreting complex data and collaborating in multidisciplinary teams. These skills and qualities are vital for generating reliable insights into cellular function and spatial organization, which drive innovative research and discovery.

What are some typical challenges faced by professionals working in Single Cell Spatial Transcriptomics, and how can they be addressed?

Professionals in Single Cell Spatial Transcriptomics often encounter challenges related to handling large, complex data sets and integrating spatial information with single-cell transcriptomic profiles. These tasks demand strong computational skills and close collaboration with bioinformaticians and other researchers. Effective communication within interdisciplinary teams is essential to ensure experimental design aligns with downstream analysis needs. Staying updated with rapidly evolving technologies and best practices also helps professionals overcome technical hurdles and produce reliable, high-impact results.

What is single cell spatial transcriptomics?

Single cell spatial transcriptomics is a cutting-edge technique that allows researchers to analyze gene expression in individual cells while preserving their spatial location within a tissue. This method combines the high-resolution insights of single-cell RNA sequencing with spatial information, enabling scientists to understand how cells interact and organize within their native environments. It is widely used in biomedical research to study tissue architecture, disease mechanisms, and cellular heterogeneity.
What job categories do people searching Single Cell Spatial Transcriptomics jobs in Needham, MA look for? The top searched job categories for Single Cell Spatial Transcriptomics jobs in Needham, MA are:
What cities near Needham, MA are hiring for Single Cell Spatial Transcriptomics jobs? Cities near Needham, MA with the most Single Cell Spatial Transcriptomics job openings:
Single Cell Spatial Transcriptomics jobs near you
Infographic showing various Single Cell Spatial Transcriptomics job openings in Needham, MA as of May 2026, with employment types broken down into 4% Locum Tenens, 95% Full Time, and 1% Part Time. Highlights an 93% Physical, 1% Hybrid, and 6% Remote job distribution, with an average salary of $49,045 per year, or $23.6 per hour.
AI-Enabled Spatial Neuropathology & Multi-Omics

AI-Enabled Spatial Neuropathology & Multi-Omics

Sanofi

Cambridge, MA • On-site

$100K - $136.60K/yr

Full-time

This job post has expired 1 day ago. Applications are no longer accepted.

Sanofi rating

8.2

Company rating: 8.2 out of 10

Based on 58 frontline employees who took The Breakroom Quiz

26th of 71 rated pharmaceutical

Job description

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.
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.
About Sanofi:
We're an R&D-driven, AI-powered biopharma company committed to improving people's lives and delivering compelling growth. Our deep understanding of the immune system - and innovative pipeline - enables us to invent medicines and vaccines that treat and protect millions of people around the world. Together, we chase the miracles of science to improve people's lives.
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.
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Pursue progress, discover extraordinary
Better is out there. Better medications, better outcomes, better science. But progress doesn't happen without people - people from different backgrounds, in different locations, doing different roles, all united by one thing: a desire to make miracles happen. So, let's be those people.
At Sanofi, we provide equal opportunities to all regardless of race, colour, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, ability or gender identity.
Watch our ALL IN video and check out our Diversity Equity and Inclusion actions at sanofi.com!
US and Puerto Rico Residents Only
Sanofi Inc. and its U.S. affiliates are Equal Opportunity and Affirmative Action employers committed to a culturally inclusive and diverse workforce. All qualified applicants will receive consideration for employment without regard to race; color; creed; religion; national origin; age; ancestry; nationality; natural or protective hairstyles; 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.
North America Applicants Only
The salary range for this position is:
$75.000,00 - $108.333,33
All compensation will be determined commensurate with demonstrated experience. Employees may be eligible to participate in Company employee benefit programs. Additional benefits information can be found through the LINK.

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About Sanofi

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At Sanofi R&D North America, we deliver meaningful solutions for patients. We transform science into breakthrough, best-in-class and first-in-class medicines and vaccines. We believe in creating a diverse and inclusive workforce - and workplace - which brings together the collective brainpower of over 2,000 colleagues and provides you with an exciting place to grow and develop. We set the bar high, and we deliver.

Industry

Scientific research and development services

Company size

10,000+ Employees

Headquarters location

Bridgewater, NJ, US

Year founded

2004

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