Associate Director, Functional Genomics, Data Science

Job Description

Our company is a global health care leader committed to being the world’s premier research intensive biopharmaceutical company. Our Research Laboratories will take our leading discovery capabilities and world class small molecule and biologics research and development expertise to create breakthrough science that radically changes how we approach serious diseases.

The Data, AI and Genome Sciences (DAGS) department seeks a talented computational biologist to join our Translational Genome Analytics (TGA) team in Cambridge, MA. In this role, you will lead the functional genomics analytics function, owning the computational infrastructure, hit calling frameworks, and analytical tooling that underpin our CRISPR screening programs. You will serve as a technical and scientific leader, shaping how functional genomics evidence is generated, interpreted, and integrated with orthogonal data sources to inform early discovery decisions and support our discovery portfolio. You will also oversee and directly contribute to the computational analysis of optical CRISPR screens and high throughput imaging datasets, bridging morphological phenotypes with our functional genomics capabilities.

In This Exciting Role You Will

• Lead the design, development, and maintenance of scalable computational analytics frameworks for pooled, arrayed, single cell, and optical CRISPR screens, including QC pipelines, library design, and longitudinal readout analysis.

• Oversee and actively contribute to image analysis pipelines for high content and optical CRISPR screens, extracting biologically meaningful morphological features to support target prioritization.

• Integrate functional genomics and imaging derived results with high throughput transcriptomics and proteomics datasets to build multi evidence target prioritization packages for multiple stages of drug discovery.

• Leverage cutting edge AI and ML approaches, including LLM powered agentic workflows and network based methods, to accelerate target triage and automate biological evidence synthesis.

• Manage and mentor PhD level scientists, set the technical direction for the analytics sub team, and drive standards for reproducible research and FAIR data infrastructure.

• Collaborate across disciplines with experimental scientists, software engineers, and external partners to advance shared analytical platforms and support Therapeutic Area target identification.

Education Minimum Requirement

• Ph.D. in Bioinformatics, Biostatistics, Computational Biology, Statistics, Computer Science, Mathematics, Genetics/Genomics, or a related STEM field.

Required Experience and Skills

• A minimum of 4+ years of industry or applied academic experience.

• A passion for solving biological problems through computational methods with a proactive focus on details and execution.

• Experience with the computational analysis, algorithm development, and biological interpretation of large scale NGS and functional genomics datasets.

• A proven track record of applying machine learning to analyze single cell RNA sequencing data to identify novel patterns and functional insights.

• Previous experience with experimental design of biological assays, statistical hypothesis testing, and integrating results from multiple omics data sources.

• Proficiency in at least one statistical programming language such as R or Python, along with experience using version control environments like Git.

• Familiarity with public data repositories like The Cancer Genome Atlas, Dependency Map, Cancer Cell Line Encyclopedia, and Clinical Proteomic Tumor Analysis Consortium.

• Experience with AWS cloud computing infrastructure and Linux environments.

• Excellent oral and written communication skills.

Preferred Experience and Skills

• A strong background with post doctoral or relevant industry experience, including prior experience leading an analytics team and mentoring scientists.

• Substantial computational experience specifically with functional genomics data, including CRISPR screen hit calling frameworks and library design interpretation.

• Experience with optical pooled CRISPR screening image analysis pipelines and integrating morphological readouts with genomic datasets.

• Expertise applying deep learning approaches to image based phenotypic profiling and cell classification for target identification.

• Deep understanding of general disease biology and immunology, with knowledge of the latest functional genomics research.

• Expertise in utilizing network based analysis frameworks or transfer learning techniques to infer gene regulatory patterns from NGS datasets.

• Hands on experience building or deploying LLM powered systems or AI tools for biological data interrogation.

• Experience developing interactive data visualization tools, for example R Shiny, for multiomics readouts.

Travel

• Up to 10% travel is required.

#EligibleforERP

Required Skills

Amazon Web Services (AWS), Bioinformatics, Biostatistics, Computer Science, CRISPR-Cas System, Data Engineering, Data Modeling, Data Science, Data Visualization, Genome, Genomics, Hypothesis Testing, Linux Environments, Machine Learning (ML), Model Fine-Tuning, Omics, Single-Cell Genomics, Software Development, Stakeholder Relationship Management, Statistical Design of Experiments (DOE), Statistical Programming

Preferred Skills

Current Employees apply HERE

Current Contingent Workers apply HERE

US and Puerto Rico Residents Only

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.

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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We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.

Learn more about your rights, including under California, Colorado and other US State Acts

The salary range for this role is

$176,200.00 - $277,300.00

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

Search Firm Representatives Please Read Carefully

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

10%

Flexible Work Arrangements

Hybrid

Shift

Not Indicated

Valid Driving License

No

Hazardous Material(s)

n/a

Job Posting End Date

08/14/2026*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.