Associate Principal Scientist,… at Merck & Co. · Cambridge

Job Description

Our company is on a quest for cures and is committed to being the world’s premier, most research-intensive biopharmaceutical company. Today, we’re doubling down on this goal. Our company's Research Laboratories is a true scientific research facility of tomorrow and will take our company's leading discovery capabilities and world-class small molecule and biologics R&D expertise to create breakthrough science that radically changes the way we approach serious diseases. 

The Data, AI & Genome Sciences department is looking for a passionate and talented computational biologist with deep expertise in image analysis to join our Translational Genome Analytics research team. In this role, you will apply AI/ML-based analytics to analyze large multi-scale and multi-omics imaging- and functional genomics-based datasets and closely collaborate with a cross-functional team of computational biologists, data scientists, and stakeholders in Discovery Research to drive target and biomarker discovery and drug development efforts. This role will support multiple therapeutic areas with a strong emphasis on Oncology.

The successful candidate will be a scientifically curious team player, strong communicator, and self-motivated learner with previous demonstrated expertise in computational image analysis, experience with multi-omics data integration and functional genomics assays, and an interest in leveraging AI/ML strategies to aid in our interpretation of complex biological data.

This role is based at our company's Research Labs in Cambridge, MA.

In this exciting role, you will:

• Contribute to multiple stages of drug discovery by interrogating high-throughput functional genomics and cellular profiling assays, including high-content imaging-based screens (e.g., optical pooled screens, cell painting, arrayed CRISPR assays), large-scale NGS-based screens (e.g., pooled CRISPR screens, Perturb-seq), and proteomic datasets.

• Translate biological questions into computational solutions by performing quantitative and rigorous statistical analysis on large-scale in vitro imaging datasets and clinical histopathology images for novel biomarker and target discovery.

• Leverage machine-learning approaches to integrate multiparametric image-derived features with high-throughput phenotypic screens.

• Closely collaborate with a broad variety of stakeholders, including molecular biologists, pathologists, bioinformaticians, and software engineers, and act as a proactive bridge and translator in cross-disciplinary communications.

• Employ best reproducible research and FAIR data practices to generate reusable analysis frameworks and reports to support target identification and validation efforts across therapeutic areas.

• Characterize novel targets coming from genetics, translational and disease pathway exploration, explore target engagement, research mechanisms of action, and provide functional validation of novel drug targets.

• Work with large internal and public biological data sets including Next Generation Sequencing (NGS) data (e.g. RNA-Seq, single cell RNA-Seq, spatial transcriptomics, WGS, CRISPR).

Education Minimum Requirement: 

• Ph.D. in Bioinformatics, Computational Biology, Computer Science, Biostatistics, Genetics, Immunology, Mathematics, Molecular Biology, Statistics, or related field and 3+ years of experience.

• Master degree in areas mentioned above with 7+ years of experience.

• Bachelor degree in above areas with 11+ years of experience.

• Experience must be post-degree. Can be a mix of relevant academic or industry experience.

Required Experience and Skills: 

• In-depth experience with analyzing high-content cellular and/or tissue imaging assays (e.g., Cell Profiler, scikit‑image, OpenCV, etc.).

• Deep experience with computational analysis (e.g., stain normalization, WSI-level classification, segmentation, etc.) of histopathology imaging (e.g., H&E/IHC whole slide images).

• Advanced programming skills with application in imaging (Python) and statistical analysis (R, tidyverse packages).

• Demonstrated ability to distill complex data into interpretable visualizations (e.g., ggplot2, plotly).

• Demonstrated experience with computational analysis and biological interpretation of diverse large-scale experimental datasets from NGS and arrayed screening.

• Skilled at integrating results generated from multiple omics data sources, and biological knowledge bases to customize analytical approaches for discovery research.

• Experience with AWS cloud computing infrastructure (e.g., S3, EBS, EC2, etc) and HPC Linux environments.

• Experience with version control systems, such as Git, and the ability to collaborate on code bases and adapt to and work with existing analytic frameworks.

• Passion for problem solving and continuous learning; applied both to understanding biology and solving technical challenges.

• Self-motivated, proactive, detail-oriented, and independent phenotype supported by references.

• Excellent verbal and written communication skills for cross-disciplinary collaboration.

• Previous experience as full-time computational biologist.

Preferred Experience and Skills:

• Experience with optical pooled screening (OPS).

• Close familiarity with histology/microanatomy and microscopy readouts.

• Experience with digital pathology.

• Experience with using or developing pipelines with workflow orchestration tools such as Nextflow.

• Hands-on experience with applying AI/ML methods for analysis of image-based biological readouts.

• Interest in identifying novel applications of AI/ML strategies for biological target discovery.

• Experience with and understanding algorithms for DNA-seq, RNA-seq, single-cell RNA-seq and/or functional genomics data.

• Strong publication record.

#EligibleforERP

Required Skills:

Amazon Web Services (AWS), Cell Imaging, Computational Biology, High Content Image Analysis, High Content Imaging, High Performance Computing (HPC), Histology, NGS Data Analysis, Omics, Python (Programming Language), RNA Sequencing, Tissue Histology, Whole Slide Imaging

Preferred Skills:

Digital Pathology, Functional Genomics

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.

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U.S. Hybrid Work Model

Effective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as “remote”.

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

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:

No Travel Required

Flexible Work Arrangements:

Hybrid

Shift:

Not Indicated

Valid Driving License:

No

Hazardous Material(s):

n/a

Job Posting End Date:

05/15/2026

*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.