Scientist, AI/ML - Antibody Developability

Ginkgo Bioworks; San Francisco (CA); On-site; 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

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.

Scientist, AI/ML - Antibody Developability

Datapoints Team | Ginkgo Bioworks | Boston, MA

About the Role

Datapoints, Ginkgo Bioworks' Bio O 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).

Location: Boston, MA (Hybrid).

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.