Key Responsibilities
Lead scientific analyses:Define and execute analysis plans for large-scale protein interaction datasets (often 1M PPIs), including evaluating binding affinity, specificity, and the performance of antibody and protein design methods.
Develop and evaluate ML models: Build, train, and apply models using experimental measurements, protein sequences, and structural information. Design rigorous benchmarks and assess model performance, uncertainty, and generalization.
Connect computation with experiments: Collaborate with experimental scientists to shape study designs, interpret results, investigate unexpected findings, and recommend follow-up experiments.
Deliver results to external partners: Serve as the computational lead for assigned projects, producing clear presentations, reports, and well-documented datasets for both internal teams and external collaborators. Many projects may have open-source elements, requiring a strong eye for detail and narrative.
Build reusable methods: Translate project-specific work into reliable analytical tools and workflows. Contribute maintainable Python code, review contributions, and document methods so others can use them.
Advance our scientific capabilities: Identify and develop new computational approaches that increase the value of AlphaSeq data for protein engineering.
Qualifications & Experience
Required
PhD in a relevant field with 2+ years of experience working on large-scale data analysis using biological sequence or structure data; or a bachelor’s degree with 10+ years of relevant experience, including 5+ years working onlarge-scale data analysis using biological sequence or structure data; or an equivalent education and experience.
Demonstrated expertise in Python for scientific computing, data analysis, visualization, and ML model development.
Experience analyzing large experimental datasets and making scientifically defensible decisions about data quality, statistical methods, and interpretation.
Strong understanding of model evaluation, including appropriate baselines, data leakage, and the limits of conclusions drawn from a benchmark.
Ability to translate an open-ended scientific question into an executable plan and deliver reproducible results with limited supervision.
Clear communication skills, including the ability to explain methods, findings, and limitations to computational and experimental audiences.
Experience contributing to a shared codebase through version control, code review, and documentation.
Preferred
Experience with antibody or protein engineering, particularly the relationship between sequence, structure, and binding.
Familiarity with the structural modeling of protein complexes and evaluation of structure prediction or generative design methods.
Use of modern ML frameworks such as PyTorch, TensorFlow, or Hugging Face.
Experience processing and analyzing next-generation sequencing data, (Illumina, Oxford Nanopore, etc.).
Experience developing analytical tools or workflows used by other scientists.
In 2018, A-Alpha Bio spun out of the University of Washington’s Institute for Protein Design and Center for Synthetic Biology – both communities filled with brilliant and highly entrepreneurial scientists. Since the company’s inception, we have built and scaled AlphaSeq, our high-throughput platform for quantitatively measuring protein-protein interactions at unprecedented scale. What began as a technology for generating large, standardized affinity datasets has grown into a broader data engine for AI-driven protein engineering. New members of the team should expect a fast-paced, highly dynamic, and interdisciplinary work environment. We are building a diverse, meritocratic, and supportive team that shares our values of speaking the truth, shooting for the moon, taking the reins, playing for the team, and improving the world.
A-Alpha Bio is headquartered in a custom designed lab and office space in downtown Seattle’s Belltown neighborhood. We are fortunate to be situated in a region that is renowned for its premier outdoor activities, including hiking, biking, climbing, skiing, kayaking, sailing, and more. At A-Alpha, you’ll find many who love the outdoors, but also gamers, amateur chefs, explorers, sports fans, bakers, crafters, photographers, brewers, jetsetters, animal lovers, and artists. Whatever your passions, you belong at A-Alpha Bio!
