Scientist, AI/ML — Antibody Developability

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

Scientist, AI/ML — Antibody Developability

California, United States

Our mission is to make biology easier to engineer. Ginkgo is constructing, editing, and redesigning the living world in order to answer the globe’s growing challenges in health, energy, food, materials, and more. Our bioengineers make use of an in-house automated foundry for designing and building new organisms.

Datapoints Team | Ginkgo Bioworks | Boston, MA

About the Role

Datapoints, Ginkgo Bioworks' Bio × AI data generation platform, is seeking a Scientist to build and benchmark machine learning models that predict and design antibody developability. You will sit between our PROPHET-Ab high-throughput biophysical platform and the models it enables, working with both newly generated customer datasets and the GDPa public dataset series (clinical IgGs, sequence-diverse natural IgGs, bispecifics, VHH-Fcs), cross-format prediction, and generative design campaigns.

This computational role requires deep understanding of biophysical assay measurements, noise characteristics, and rigorous evaluation strategies for small-scale datasets. Ideal candidates are recent Ph.D. graduates with strong applied ML proficiency and interest in protein biophysics, motivated by integrated experimental and computational design.

Key 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.

Qualifications

Required

• 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).
• Demonstrated experience in supervised learning on biological datasets, including expertise in cross-validation and bias mitigation.
• Knowledge of protein representations, including PLM embeddings (e.g., ESM, AbLang) and structural featurization.
• Ability to analyze biophysical data with respect to signal-to-noise ratios and experimental dynamic range.
• Effective communication across multidisciplinary teams and ability to manage concurrent technical objectives.

Preferred

• Familiarity with antibody formats (VHH, scFv), therapeutic developability liabilities, and relevant characterization assays.
• Experience with state of the art supervised techniques such as tabular foundation models.
• Exposure to generative sequence modeling, diffusion models, and reward-based steering.
• Experience with protein structure prediction (AlphaFold, ABodyBuilder) and surface patch analysis.
• Prior engagement with high-throughput experimental design and collaborative data generation.
• Record of scientific publication and software engineering fundamentals (Git, testing, cloud compute).

The base salary range for this role is $130,600 – $183,800. Actual pay within this range will depend on a candidate's skills, expertise, and experience. We also offer company stock awards, a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy.

Ginkgo has implemented a return to office policy effective October 1, 2025 with required in-office days 5x per week.This policy applies to all employees who live within 50 miles of Ginkgo’s offices in Boston, MA, Emeryville, CA and West Sacramento, CA.

It is the policy of Ginkgo Bioworks to provide equal employment opportunities to all employees, employment applicants, and EOE disability/vet.