Bioinformatics Engineer

Manifold Bio is a dynamic biotech company building a pipeline of  targeted biologics using a novel in vivo-centric discovery approach. Our drug discovery engine is differentiated by massively parallel screening in vivo from the beginning of our discovery process. This unique platform is powered by a proprietary protein barcoding technology that allows multiplexed protein quantitation at unprecedented scale and sensitivity. We combine this and other high-throughput protein engineering approaches with computational design to create antibody-like drugs and other biologics. Our world-class team of protein engineers, biologists, and computational scientists are working together to aim the platform at therapeutic opportunities where precise targeting is the key to overcoming clinical challenges.

Position

Manifold Bio is seeking an exceptional Bioinformatics Engineer to join our growing team. In this role, you will work closely with computational and experimental scientists to build core infrastructure and extract insights from our Next Generation Sequencing readouts as part of our platform’s Compute team. Within the Compute team, you will engineer advanced DNA barcode sequence counting algorithms and associated infrastructure to support a wide variety of assay read-outs and modalities, including phage display, yeast display, and DNA barcode counting (“MPRAs”). Future projects may include RNA-seq, scRNA-seq, Whole Genome Sequence (WGS), and more, so familiarity with these is a plus. This position will also be responsible for refining and deploying the data pipelines as self-serve workflows for the wet lab scientists, so familiarity with workflow orchestrators/engines is additionally a plus. Library-based research is central to our research at Manifold, and this role will have a deep impact across our entire workflow.

Responsibilities

• Refine and improve central Python NGS infrastructure
• Implement advanced counting algorithms for Illumina and Oxford Nanopore sequencing readouts
• Support custom bioinformatics projects such as RNA-seq and scRNA-seq experiments
• Deploy bioinformatics data pipelines as self-serve workflows for wet lab scientists
• Support in NGS data management of dozens of terabytes of raw data

Required Qualifications

• PhD  in computational biology or bioinformatics, or B.S. with 7+ years of equivalent experience in computational biology or bioinformatics
• Experience working with Next Generation Sequencing (NGS) data from library-based experiments
• Strong Python development skills
• Experience with translating and scaling local workflows onto AWS
• Deep knowledge of version control, test-driven development, and cloud computing
• Experience working with workflow orchestrators/engines
• Strong understanding of statistics fundamentals and data analysis methodologies
• Outstanding written and verbal communication skills for cross-functional collaboration

Preferred Qualifications

• Industry experience in antibody therapeutic development or biotechnology R&D
• Experience building and supporting custom single cell sequencing workflows
• Experience with robust code package development, CI/CD
• Track record of developing computational tools or pipelines adopted by experimental teams
• Experience mentoring junior scientists or leading cross-functional project teams
• Publications or patents in antibody engineering, protein design, or high-throughput screening methods
• Familiarity with cloud computing platforms (AWS, GCP) and containerization technologies
• Experience with Tableau and other data visualization packages

This Role Might Be Perfect For You If

• You thrive in collaborative environments where computational insights directly guide experimental decisions
• You're energized by translating complex datasets into actionable recommendations for drug discovery teams
• You enjoy building robust, production-quality tools that others rely on for critical decisions
• You're passionate about the therapeutic potential of engineered antibodies and want to accelerate their development
• You love working at the intersection of cutting-edge computational methods and innovative experimental platforms

We value different experiences and ways of thinking and believe the most talented teams are built by bringing together people of diverse cultures, genders, and backgrounds.