Associate Director, Data Science, Functional Genomics

MSD Malaysia; South San Francisco (CA); On-site; USD 176,000 - 277,000; Full time

Job summary

Merck & Co., Inc. is seeking an Associate Director of Data Science to lead Functional Genomics analytics within the Translational Genome Analytics division in Cambridge, MA.

The role focuses on building scalable computational frameworks for CRISPR and multi-omics data, guiding target prioritization and drug combinations using AI/ML approaches. You will mentor scientists, shape discovery strategies, and collaborate across disciplines to accelerate early discovery, including integration with

Qualifications

• MS in computational biology, bioinformatics, biostatistics, biophysics, mathematics, statistics, genetics/genomics, CS or related STEM with 8+ years of experience.
• Experience analyzing large scale NGS and functional genomics datasets.
• Experience applying ML to single-cell RNA-seq data and integrating multi-omics data.
• Proficiency in R or Python and Git; familiarity with public data repositories.

Responsibilities

• Lead design and build scalable computational analytics frameworks for CRISPR screens and related data.
• Invent scalable methods for single-cell perturbation screening and lineage tracing.
• Integrate genomics, imaging, transcriptomics and proteomics data for target prioritization.
• Apply modern AI/ML and LLM-powered workflows to triage targets and synthesize evidence.
• Mentor a team of scientists and set technical direction for functional genomics analytics.

Skills

AWS

Bioinformatics

Computational Biology

NGS

Machine Learning

Python/R

Linux

Git

Education

MS in computational biology or related field

Tools

Git

Job description

Associate Director of Data Science, Functional Genomics (R4) Translational Genome Analytics (TGA) / Data, AI and Genome Sciences (DAGS) Location Cambridge, MA

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 for our Translational Genome Analytics (TGA) team. In this role, you will lead our Functional Genomics & Predictive Modeling function, shaping how its evidence is generated, interpreted, and integrated across the discovery portfolio. You will own the computational and modeling frameworks that range from hit calling for our perturbational screens to multi-evidence integration to prioritize targets and/or drug combinations. You will serve as a technical and scientific leader who shapes early discovery direction, mentors a team of scientists, and applies cutting edge AI and ML to accelerate how we turn data into decisions. This is a rare opportunity to build and lead a functional genomics analytics capability from the ground up, where your team's calls directly shape which targets advance in our discovery portfolio, one of the most exciting frontiers in computational biology today.

In This Exciting Role You Will Lead the design and build of scalable computational analytics frameworks for pooled, arrayed, single cell, and optical CRISPR screens, from QC pipelines and library design to longitudinal readout analysis. Invent and scale computational methods for the next generation of functional genomics, spanning scalable single cell perturbation screening, cellular barcoding, and lineage tracing, to elucidate adaptive resistance mechanisms and drug combinations. Build image analysis pipelines for high content and optical CRISPR screens, turning morphological phenotypes into biological insight that guides 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. Bring modern AI and ML, including LLM powered agentic workflows and network based methods, to how we triage targets and synthesize biological evidence. Lead and mentor a team of scientists, set the technical direction for functional genomics analytics, 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.

Minimum Requirements

MS in computational biology, bioinformatics, biostatistics, biophysics, mathematics, statistics, genetics/genomics, computer science or a related STEM discipline and a minimum of 8 years of relevant professional experience, including hands on experience analyzing large scale NGS and functional genomics datasets. 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 Ph.D. in Bioinformatics, Biostatistics, Computational Biology, Statistics, Computer Science, Mathematics, Biophysics, Genetics/Genomics, or a related STEM field with 4+ years of professional experience. 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. A track record of developing novel functional genomics methods, demonstrated through first author publications or released tools.

Travel

Up to 10% travel is required.

#EligibleforERP

Required Skills: Amazon Web Services (AWS), Bioinformatics, Biological Data Analysis, Computational Biology, Computational Genomics, CRISPR-Cas System, Data Engineering, Data Modeling, Data Science, Data Visualization, Gene Expression Profiling, Genome, Genome Sequencing, Genomic Analysis, Genomics, Machine Learning (ML), Omics, RNA-Seq, Single-Cell Genomics, Software Development

Preferred Skills: 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. 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: EEOC Know Your Rights EEOC GINA Supplement 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

Employee Status

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

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

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.

Job Posting End Date

Job Posting End Date: 09/15/2026 *A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date.

Company Overview

Our company is a global health care leader with a diversified portfolio of prescription medicines, vaccines and animal health products. The difference between potential and achievement lies in the spark that fuels innovation and inventiveness; this is the space where we have codified our legacy for over a century. Our success is backed by ethical integrity, forward momentum, and an inspiring mission to achieve new milestones in global healthcare.

Salary

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.

Benefits

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.