AI/ML Scientist, Antibody Developability (Hybrid, Boston)

Ginkgo Bioworks; San Francisco (CA); Hybrid; USD 131,000 - 184,000; Full time

Benefits offered by this job

Stock awards

Medical insurance

Dental insurance

Vision insurance

401(k) with employer contribution

Paid time off

Holiday shutdown

Unlimited PTO

Job summary

Ginkgo Bioworks in Boston, MA, is seeking a Scientist to build and benchmark ML models predicting antibody developability, sitting between the PROPHET-Ab platform and its data. You'll work with customer datasets and public datasets across IgGs, bispecifics, and VHH-Fcs.

Ideal candidates hold a PhD and have strong applied ML, experience with Python stack, and an interest in protein biophysics. This hybrid role offers collaboration across teams and opportunities to publish and present findings.

Qualifications

• Ph.D. in Computational Biology, Bioinformatics, ML, Biophysics, or related field.
• Strong applied ML experience with biological datasets and cross-validation.
• Familiarity with PLM embeddings (ESM) and protein representations.
• Ability to analyze biophysical data with respect to signal-to-noise and dynamic range.
• Excellent communication across multi-disciplinary teams.

Responsibilities

• Develop and validate predictive models for developability using embeddings and descriptors.
• Implement leakage-aware evaluation for small-scale datasets.
• Assess cross-format transferability (IgG to VHH-Fc, bispecifics) and data-efficient training.
• QC biophysical assay data to identify outliers and ensure data integrity.
• Maintain automated pipelines for reproducibility and reporting.
• Disseminate findings via technical reviews, manuscripts, and presentations.

Skills

Python & scientific computing stack

Applied ML in biology

Cross-validation & bias mitigation

Protein representations (PLM, ESM)

Signal-to-noise analysis in biophysics

Communication across multidisciplinary

Education

Ph.D. in Computational Biology or related

Tools

Git

Cloud compute

Bioware ML tooling

Job description

Ginkgo Bioworks in Boston, MA, is seeking a Scientist to build and benchmark ML models predicting antibody developability, sitting between the PROPHET-Ab platform and its data. You'll work with customer datasets and public datasets across IgGs, bispecifics, and VHH-Fcs.

Ideal candidates hold a PhD and have strong applied ML, experience with Python stack, and an interest in protein biophysics. This hybrid role offers collaboration across teams and opportunities to publish and present findings.