AI/ML Scientist for Antibody Developability

Ginkgo Bioworks; California (MO); Hybrid; USD 131,000 - 184,000; Full time

Job summary

Ginkgo Bioworks in Boston, MA is seeking a Scientist to build and benchmark ML models that predict antibody developability, sitting between PROPHET-Ab platform and datasets. This hybrid role focuses on rigorous modeling, data integrity, and cross-format transferability.

Ideal candidates are recent Ph.D. graduates with strong applied ML, experience in Python, PLM embeddings, and protein biophysics. Collaborative environment, opportunities for publication, and a competitive package await.

Qualifications

• Ph.D. in Computational Biology, Bioinformatics, ML, Biophysics, or related quantitative field with emphasis on applied ML.
• Proficiency in Python and the scientific computing stack (NumPy, pandas, PyTorch/TensorFlow).
• Experience with supervised learning on biological datasets, including cross-validation and bias mitigation.
• Knowledge of protein representations, PLM embeddings (ESM, AbLang) and structural featurization.
• Ability to analyze biophysical data with respect to signal-to-noise ratios and experimental dynamic range.
• Strong cross-disciplinary communication and ability to manage concurrent objectives.

Responsibilities

• Develop and validate predictive models for developability using PLM embeddings, structural features, and physicochemical descriptors.
• Implement leakage-aware evaluation frameworks for rigorous performance assessment of small-scale datasets.
• Evaluate cross-format transferability (IgG to VHH-Fc, bispecifics) and deploy data-efficient training strategies.
• Perform rigorous QC on biophysical assay data to identify outliers and maintain high data integrity for modeling.
• Maintain and develop automated pipelines to ensure reproducibility and facilitate technical reporting.
• Disseminate findings through technical reviews, peer-reviewed manuscripts, and external scientific presentations.

Skills

Python

NumPy

Pandas

PyTorch/TensorFlow

Supervised learning

Cross-validation

Bias mitigation

Communication

Education

Ph.D. in Computational Biology/Bioinformatics/ML/Biophysics

Tools

PLM embeddings (ESM, AbLang)

Protein representations

AlphaFold / ABodyBuilder

Job description

Ginkgo Bioworks in Boston, MA is seeking a Scientist to build and benchmark ML models that predict antibody developability, sitting between PROPHET-Ab platform and datasets. This hybrid role focuses on rigorous modeling, data integrity, and cross-format transferability.

Ideal candidates are recent Ph.D. graduates with strong applied ML, experience in Python, PLM embeddings, and protein biophysics. Collaborative environment, opportunities for publication, and a competitive package await.