AI/ML Scientist, Antibody Developability & Design

Ginkgo Bioworks Inc.; California (MO); On-site; USD 131,000 - 184,000; Full time

Benefits offered by this job

Stock awards

Comprehensive benefits

401(k) with employer contribution

Unlimited Paid Time Off

Job summary

Ginkgo Bioworks Inc. in California seeks a Scientist to build and benchmark ML models predicting antibody developability, bridging the PROPHET-Ab platform with GDPa datasets. You will work with customer data and public datasets, focusing on timely, accurate modeling and rigorous evaluation.

The role requires a PhD with applied ML skills, experience with biological data, and interest in protein biophysics. Collaboration across teams and a strong emphasis on reproducible pipelines are essential.

Qualifications

• Ph.D. in Computational Biology, Bioinformatics, ML, Biophysics, or related field.
• Proficiency in Python and the scientific computing stack (NumPy, pandas, PyTorch/TensorFlow).
• Demonstrated experience in supervised learning on biological datasets, including cross-validation and bias mitigation.
• Knowledge of protein representations, including PLM embeddings (ESM, AbLang) and structural featurization.

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 and deploy data-efficient training strategies.
• Perform rigorous QC on biophysical assay data to identify outliers and maintain 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

data analysis

Education

PhD in Computational Biology/Bioinformatics/ML

Tools

Git

AlphaFold

ABodyBuilder

Job description

Ginkgo Bioworks Inc. in California seeks a Scientist to build and benchmark ML models predicting antibody developability, bridging the PROPHET-Ab platform with GDPa datasets. You will work with customer data and public datasets, focusing on timely, accurate modeling and rigorous evaluation.

The role requires a PhD with applied ML skills, experience with biological data, and interest in protein biophysics. Collaboration across teams and a strong emphasis on reproducible pipelines are essential.