Bioinformatics Scientist/Senior Bioinformatics Scientist at MaxCyte, Inc – Waltham, Massachusetts

We are seeking a highly motivated Bioinformatics Scientist to join our interdisciplinary R&D team focused on developing innovative analytical tools and assays that assess the off-target safety profiles of CRISPR-based gene editing systems. The successful candidate will bring deep expertise in bioinformatics, genomics, and next-generation sequencing (NGS) analysis, coupled with strong programming and analytical skills.

This role centers on the development, optimization, and support of bioinformatics workflows and computational pipelines that drive MaxCyte’s assay development and data interpretation efforts. The Bioinformatics Scientist will collaborate closely with colleagues across R&D, Data Science, Product Development, and Operations to translate complex genomic data into actionable scientific and product insights.

• Design, develop, and deploy scalable, validated bioinformatics pipelines for NGS data analysis, ensuring reproducibility and compliance with relevant standards (e.g., GLP).
• Perform comprehensive genomic data processing (e.g., read alignment, variant calling), enforce strict quality control standards, and evaluate emerging algorithms and databases to optimize analysis pipelines
• Partner with cross-functional teams to integrate biological and computational data for off-target assessment.
• Translate complex bioinformatics results into clear visualizations and actionable insights to guide experimental design and product development.
• Maintain thorough documentation of all code, analyses, and validation procedures to support regulatory transparency and scientific rigor.
• Stay current with emerging bioinformatics tools, genome editing technologies, and NGS analysis methodologies.
• Effectively present assay offerings and results externally via conference posters and presentations.

• Ph.D., or M.S. +3 years, or BS +6 years in Bioinformatics, Computational Biology, Genomics, or a related discipline (or equivalent professional experience).
• Proven expertise in NGS data analysis, combining strong foundational skills in both common genomics tasks (alignment, variant calling, annotation, etc.) and downstream data interpretation and visualization.
• Hands-on experience with commonly used bioinformatics tools and packages (ex. Samtools, BWA, GATK, Picard, BEDTools, or equivalent).
• Familiarity with CRISPR-based gene editing and related off-target assessment methods.
• Strong programming skills in Python and R, with experience developing and maintaining computational pipelines.
• Proficiency in Linux environments, version control (ex. GitHub), and workflow management systems (ex. NextFlow, CI/CD).
• Experience with cloud computing environments (ex. AWS, GCP) for large-scale data processing and pipeline infrastructure.
• Hands-on experience building Docker containers and orchestrating batch processing workflows using AWS Batch and Elastic Container Registry (ECR), or similar.
• Strong organizational, communication, and documentation skills, with the ability to work effectively in a collaborative, interdisciplinary setting.

Preferred Skills

• Experience in industry preferred.
• Experience integrating multi-omics datasets (transcriptomics, epigenomics, proteomics) to support biological insight.
• Familiarity with regulatory and quality system standards (e.g., GLP, GxP) for bioinformatics data management.
• Working knowledge of statistical and computational approaches for data interpretation, visualization, and reproducibility.
• Familiarity with infrastructure-as-code frameworks (AWS CDK, Terraform).

MaxCyte also offers a comprehensive base salary, annual bonus, and equity. Benefits package include health, dental, vision, life, and disability insurance and generous time off.

MaxCyte is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, sex, sexual orientation, gender identity, religion, national origin, disability, veteran status, age, marital status, pregnancy, genetic information, or other legally protected status.