Senior Data Scientist – Neuroscience Spatial Multi-omics

Job Description

Our Company’s Data, AI & Genome Sciences Department in Cambridge, MA is seeking a Senior Specialist (Senior Scientist), Data Science to join the Translational Neuroscience Analytics team and drive integrative analysis of spatial and single-nucleus multi-omics data from patients with neurodegenerative diseases. The qualified individual will be a motivated data scientist or computational biologist with a track record of developing and applying cutting-edge AI/ML methodologies to extract actionable insights from single-nucleus and spatial multi-omics data. In this role, they will leverage spatially resolved transcriptomics data with single-cell resolution to understand target pathway biology in relation to pathological hallmarks of neurodegenerative diseases, especially Alzheimer’s disease, and integrate this information with single-nucleus multi-omics data from large patient cohorts to enable causal modeling and prediction of target perturbation effects across cell populations of interest. Through these analyses, they will contribute to the evaluation of specific therapeutic hypotheses as well as the identification and placement of biomarkers along the causal cascade from therapeutic target to clinical outcome, ultimately shaping the translational strategies of our neurodegenerative therapeutic programs. They will work alongside with other data scientists and AI/ML scientists in the department to develop and apply innovative approaches to perform such analyses and further integration with clinical, genetic, and other omics data types. They will also be closely collaborating with cross-functional teams of data scientists, bench biologists, and clinical colleagues to drive our neuroscience biomarker and translational strategies.

Primary responsibilities:

• Build and deploy analytic workflows leveraging state-of-art computational methods to analyze spatial multi-omics datasets, with a specific focus on target MOA evaluation and biomarker discovery in neurodegenerative diseases. 

• Formulate and drive integration of spatial and single-nucleus multi-omics data to build unified predictive framework capturing the interactions among different CNS cell types (e.g., neurons and microglia).

• Lead data analytic projects to evaluate therapeutic hypothesis, drive precision biomarker discovery, inform translational strategies, and enable data-driven decision-making of multiple neuroscience drug discovery programs.  

• Collaborate with internal AI/ML teams to develop and incorporate new methodologies into existing frameworks to enhance data analysis capabilities.

• Work with experimental biologists, functional area experts, and clinical scientists to support drug discovery and development programs at various stages.

• Provide data science / computational biology input in research strategy, experimental design, provide data analytical input, and assist in interpreting results from both in-vitro and in-vivo studies.

• Communicate data analytic results effectively to project teams, key stakeholders, as well as the wider scientific community through written and verbal means, including proposals for further experiments, presentations at internal and external meetings, and publications in leading journals.

Required Qualifications:

• PhD in Data Science, Computational Biology, Computer Science, Genetics/Genomics, Biophysics, Bioinformatics, Statistics, Neuroscience, Neurology, or a related STEM discipline and 0+ years of experience, or an MS and 5+ years of experience.

• Deep understanding of computational methodologies for single-cell and spatial transcriptomics analysis and extensive experience in their applications, preferably in neurological disorders.

• Extensive experience in analyzing spatial transcriptomics data with single/sub-cell resolution (e.g., CosMx, Visium HD).

• Demonstrated expertise in leveraging advanced AI/ML models (e.g., transformers, foundation models) and in silico perturbation simulation.

• Ability to critically evaluate and apply novel data analysis methods in translational applications.

• Proficient in one or more programming languages (e.g., Python, R), HPC environments and/or cloud-based platforms, as well as version control systems (e.g., Github).

• Strong problem-solving skills, self-motivated, attention to detail, and ability to handle multiple projects.

• Extensive experience to conduct research in a collaborative environment and excellent ability to communicate scientific questions, methodologies, findings and insights.

• Proven track record (e.g., peer-reviewed publications) of extracting actionable insights from analysis of spatial/single-cell omics data.

Preferred Qualifications:

• Outstanding scientific caliber with strong capabilities to identify key analytic questions and formulate rigorous data analytic plans to address critical scientific needs of drug discovery programs.

• Good understanding of neurobiology, particularly neurodegenerative diseases.

• Familiarity with large public single-nucleus multi-omics datasets from neurodegenerative disease patient cohorts (e.g, ROSMAP, SEA-AD).

• Additional 2+ years of multi-omics data analytics experience post final degree is preferred.

#EligibleforERP

Required Skills:

Alzheimer's Disease, Computational Biology, Computer Science, Cross-Team Collaboration, Database Design, Data-Driven Decision Making, Data Engineering, Data Modeling, Data Science, Data Visualization, Machine Learning (ML), MultiModal AI, Neurodegenerative Diseases, Neuroscience, Omics, Programming Languages, Single Cell Analysis, Single-Cell Genomics, Spatial Data Analysis, Stakeholder Relationship Management, Teamwork, Transcriptomics

Preferred Skills:

Foundation Model Fine Tuning, Foundation Models, Transformer Model

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US and Puerto Rico Residents Only:

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As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.  As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

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The salary range for this role is

$144,800.00 - $227,900.00

This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits.  Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits.

You can apply for this role through https://jobs.merck.com/us/en (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.

San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance

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Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails. 

Employee Status:

Regular

Relocation:

Domestic

VISA Sponsorship:

Yes

Travel Requirements:

No Travel Required

Flexible Work Arrangements:

Hybrid

Shift:

Not Indicated

Valid Driving License:

No

Hazardous Material(s):

n/a

Job Posting End Date:

07/10/2026

*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.