Associate Director, Affinity Reagent Development and Characterization

At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome – one of the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing deep, hard science with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines.

We are seeking a visionary and execution-oriented Associate Director, Affinity Reagent Development and Characterization, to serve as a leader and scientist driving the affinity reagent development pipeline from initial candidate discovery through molecular characterization of binding interactions. This role is critical for expansion of the binders used in the Nautilus platform assay. The ideal candidate combines hands-on scientific expertise with leadership skills and strategic drive. The Associate Director will oversee teams focused on library panning, antibody production, affinity maturation, and bioanalytical chemistry. In addition, the candidate will be expected to work closely with other leaders to ensure that affinity reagents binding characteristics are well understood and are performant within our single-molecule proteomics assay.

Responsibilities

• Lead a high performing team with a mandate that spans from affinity reagent discovery and optimization to characterization of affinity reagent binding and epitope profiles

• Develop and apply in-silico design and ML/AI-driven methods to advance novel affinity reagents, combined with expert oversight of experimental approaches such as library panning and affinity maturation

• Continually refine the affinity reagent development strategy based on historical and on-going datasets, using quantitative approaches to identify key molecular characteristics that correlate with specificity, affinity and epitope recognition characteristics

• Prioritize and select new probe targets for development, based on proteome coverage and assay specifications

• Champion high levels of scientific rigor and exceptional standards in research, leading by example

• Partner with scientists to develop experimental designs which generate data suitable for rigorous downstream analysis, modeling, and decision-making

• Manage external vendors supporting antibody discovery, production, and characterization services

• Ensure a results-oriented, high-performance culture with metric-based accountability so that clear, quantitative metrics for scientific progress are defined and met across a range of timelines from one week to several years

• Mentor and develop scientists within their organization

• Collaborate with other teams throughout the company to optimize performance of the overall Nautilus platform assay. These teams include assay development, engineering, biochemistry, instrument integration, bioinformatics, and software.

• Define and drive team priorities with a clear strategic vision, ensuring alignment with company goals while rapidly adapting direction and building solutions that shape the organization’s future success.

• Expertly analyze complex information to craft effective strategies, establish actionable decision-making processes, and collaborate with leadership to uphold the company’s ethical standards.

Requirements

• PhD in biophysics, protein chemistry, structural biology, or similar field + 10 years experience (or postdoc + 5 years experience)

• 5+ years of management experience

• Demonstrated hands-on experience with affinity reagents, especially antibodies, including library panning (e.g. phase and/or ribosome-display) and affinity maturation

• Demonstrated experience using in silico and ML/AI tools to investigate and optimize affinity reagents

• Experience with interaction characterization tools such as SPR and BLI and high throughput protein-protein interaction / reactome characterization tools

• Exceptional communication, collaboration, and presentation skills

• Strong leadership, strategic planning, and decision-making capabilities

Preferred Requirements

• Experience leading fast paced discovery teams

• Background in launching products

• Experience with a variety of antibody discovery libraries

• Experience incorporating novel affinity reagents and antibodies into bioassays