Passionate about building a future powered by science?
Check out the opportunities in our portfolio companies.

Scientist I, Antibody Discovery

A-Alpha Bio

A-Alpha Bio

Seattle, WA, USA
Posted on Friday, May 3, 2024

A-Alpha Bio is an early-stage and rapidly growing drug discovery company headquartered in Seattle, WA. We are enabling the next generation of high-impact therapeutics by combining high-throughput synthetic biology to measure protein-protein interactions at scale with state-of-the-art machine learning to predict how proteins bind. We partner with leading pharmaceutical and biotechnology companies to enable the discovery of antibodies, molecular glues, and other protein interaction-related drugs. In parallel, we use our wet-lab and computational platforms to discover and develop an internal pipeline of biologics and molecular glues to improve human health.

This role is not open to remote applicants and would require relocation to Seattle, WA.

Starting Salary Range: $122,000 - $138,000 annually

Exemption Status: Exempt

Location Expectations: Onsite

Role Description

At A-Alpha Bio, we’re on a mission to improve human health by unlocking the potential of protein-protein interactions – and we’re now seeking a highly motivated Scientist to execute and optimize multiple antibody discovery and assay development initiatives.

  • As a scientist, you’ll be an integral member of a highly collaborative and cross-functional team, executing experiments that support phage display, AlphaSeq, and machine learning optimization platforms.
  • As a strategist, you’ll collaborate closely with other team members in R&D and Data Science to create and optimize antibody discovery and computational workflows.
  • As an analyst, you’ll play an integral role in identifying and optimizing antibody candidates to advance both internal and external therapeutic antibody projects.

The ideal candidate will possess extensive experience in molecular biology and phage panning, coupled with proficiency in data analysis and computational biology. This position will involve actively engaging in troubleshooting and optimizing workflows, presenting findings at cross-functional program meetings, and providing valuable scientific input and guidance to the team beyond designated responsibilities.

Key Responsibilities

  • Perform selections from company ML-derived antibody libraries against targets of interest using standard phage display techniques.
  • Execute and refine custom data analysis workflows to identify optimal candidates from a discovery or optimization campaign.
  • Design and conduct ELISA screening of phage outputs.
  • Coordinate the transfer of phage output sequences to AlphaSeq and perform downstream data analysis.
  • Coordinate ML-based antibody optimization campaigns in AlphaSeq and perform downstream data analysis.
  • Develop and implement new high-throughput workflows to characterize antibody hits from discovery campaigns, including methods for batch cloning of phage outputs into mammalian expression vectors.
  • Collaborate with Data Science team to implement and optimize bioinformatic workflows for downselection of antibody candidates.
  • Utilize bioinformatics workflows and ELN systems for experiment design, molecule registration, sample tracking, and analysis of results.
  • Present findings at group meetings to support program-level, data-driven decisions.
  • Apply scientific rigor to all aspects of the job, including experimental design, execution, analysis, and interpretation.
  • Remain current with scientific literature and present to the team on relevant topics.
  • Maintain a strong and creative team culture with a clear understanding of project timelines, deliverables, and priorities.
  • Perform other duties as assigned or special projects as needed.

Qualifications & Experience


  • PhD in a relevant field; or Bachelor's degree in a relevant field and 8+ years of relevant laboratory experience, including 4+ years of specialized antibody experience in the biotechnology industry; or an equivalent combination of education and experience.
  • Expertise with phage panning techniques and optimization strategies, with the ability to implement new phage or alternative selection capabilities.
  • Expertise with general molecular biology techniques and advanced methods such as library design and build, with the ability to implement new molecular biology capabilities.
  • Expertise performing and troubleshooting ELISAs and other common binding assays, with the ability to implement new screening capabilities.
  • Experience performing and troubleshooting high-throughput phage panning with Kingfisher or other similar instruments, with the ability to implement new throughput capabilities.
  • Deep understanding of antibody structure and nomenclature.
  • Experience with the computational analysis of large antibody sequence datasets.
  • Experience with Python and R or other relevant coding languages.
  • Understanding of next-generation sequencing.
  • Strong written and oral communication skills, with a demonstrated ability to organize and describe complex datasets to cross-functional team members.
  • Self-motivated with strong organizational, time management, and problem-solving skills and the ability to recognize project timelines, priorities, and deliverables.
  • Scientific rigor in the planning and execution of experiments.


  • Experience with performing developability and manufacturability assessments for selection and optimization of antibody candidates.
  • Proficiency in biolayer interferometry assays utilizing Octet/Gator BLI systems.
  • Background in the areas of oncology and/or immunology.
  • Interest and/or experience with structural modeling, machine learning approaches for antibody optimization, computational library design, or use of in silico prediction methods.
  • Understanding of yeast biology.

We offer competitive compensation, including benefits, flexible time off, and equity in a fast-growing start-up. Applicants must have legal authorization to work in the United States. At this time, A-Alpha Bio is unable to offer visa sponsorship in any form.

About A-Alpha Bio

A-Alpha Bio is a biotechnology company that leverages synthetic biology and machine learning to measure, predict, and engineer protein-protein interactions. Our AlphaSeq platform applies synthetic biology to experimentally measure millions of protein interaction affinities simultaneously. Protein binding data is incorporated into our AlphaBind platform to train machine learning models that predict binding from sequence. We use both platforms to discover and optimize high-impact therapeutics for our pipeline and in partnership with leading pharmaceutical and biotechnology companies.

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 focused on an oncology-centered internal pipeline along with pharma and biotech partnerships to collaboratively train predictive machine learning models and discover and optimize drugs for therapeutic areas ranging from infectious disease to neurodegeneration. 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. While the startup lifestyle occasionally requires grueling hours, we strongly value the need for a work-life balance. 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!