Computational Scientist for Protein Engineering

Manifold Bio•Boston, MA

20h•Onsite

About The Position

Manifold Bio is a platform biotechnology company pioneering AI-guided protein design and massively multiplexed in vivo screening to unlock tissue-targeted medicines and organism-scale models of living systems. Using proprietary molecular barcoding technology, we screen hundreds of thousands of protein designs simultaneously in living systems, producing in vivo-validated datasets at a scale no one else can match. The datasets power our computational models, which leads to better drug designs, creating a flywheel that gets stronger with every campaign. Our team of protein engineers, biologists, and computational scientists works across this full stack to pursue programs both internally and with leading pharma companies. Manifold Bio is seeking an exceptional Computational Scientist to join our growing Quantitative Biology team. You will work closely with experimental scientists to design and analyze highly multiplexed protein library experiments. You will specifically be working with traditional phage and yeast display readouts, as well as other proprietary display data. You will be expected to own and independently advance projects in areas related to your deep expertise such as protein design, DNA library design, or machine learning/biophysical modeling from MPRA data. You will work closely with our Head of Platform and our other computational scientists to onboard new capabilities that advance the M-Design platform for data-driven engineering of drugs with desired properties.

Requirements

PhD and/or 4+ years of equivalent experience in computational biology, bioinformatics, protein engineering, antibody engineering, or similar field working with biological sequences
Rich experience with Python, agentic coding, data pipeline development
Familiarity with version control, test-driven development, and Unix computing
Strong antibody engineering background with first-hand experience in antibody design, optimization, or discovery
Experience with massively parallel reporter assays (MPRAs) and high-throughput screening data analysis
Experience designing DNA libraries for binders, DMS, phage display, or equivalent high-throughput experiments
Experience working with Next Generation Sequencing (NGS) data from library-based experiments
Strong understanding of statistics fundamentals and data analysis methodologies
Outstanding written and verbal communication skills for cross-functional collaboration

Nice To Haves

Intuition or exposure to best practices in software/data engineering
Industry experience in antibody therapeutic development or biotechnology R&D
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

Responsibilities

Invent new quantitative protein engineering assays working with experimental scientists
Build robust data pipelines with rich metrics and statistics for real-time dataset analysis and reporting
Perform analysis and "hit calling" support, contributing new insights to active projects
Improve library design workflows to best co-optimize antibody libraries for enhanced performance
Write and contribute robust code in shared libraries for common protein design tasks
Collaborate on designing high-throughput experiments and analyze/interpret results from phage display (biopanning, phi-seq, in vivo) and yeast display platforms
Deliver high-quality data reporting through slides and documentation for cross-functional teams
Proactively share findings with colleagues through excellent documentation and discussions