Senior Scientific Program Manager, ML - Guided Protein Design Evaluation

Profluent is an AI-first protein design company. Founded in 2022, we develop deep generative models to design and validate novel, functional proteins to revolutionize biomedicine. Based in Emeryville, CA, we are backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures, and have raised over $150M to date. We are expanding the ML Design Evaluation (MDE) program; the cross-functional program that runs dedicated, structured design campaigns to generate high-quality experimental data for Profluent’s protein design models. MDE runs campaigns across internal labs and external CROs, and its operating tempo depends on tight program execution, well-run vendor relationships, and clean documentation. We are looking for an experienced program manager to own the operational and external-partnership side of MDE. You will run campaigns end-to-end - tracking timelines across ML, Biology, Bioinformatics, and CROs - and you will own the CRO side of the program: sourcing vendors with suitable platforms, running technical and commercial evaluations, negotiating pricing and turnaround, and coordinating contracting with Legal and BD. You will keep the program documented, visible, and on schedule, so the scientific team can focus on the science. You will work closely with scientific stakeholders and need to be fluent enough in the language of assays, CROs, and data pipelines to ask sharp questions and push back when timelines or scope slip. Responsibilities Run MDE campaigns end-to-end as program manager: maintain campaign charters, Jira boards, timelines, meeting cadence, and post-campaign readouts across ML, Biology, and Bioinformatics Own CRO sourcing: identify vendors with suitable platforms for each campaign, run structured evaluations on cost, turnaround time, and quality, and make clear, documented recommendations Lead commercial negotiations with CROs for pricing, scope, TAT, T&C and coordinate contracting (CDA, T&C, MSA, SOWs, POs) with internal Legal and BD Serve as the primary day-to-day point of contact for CRO partners once engagements are active; manage scope changes, data delivery, and issue escalation Build and maintain a CRO landscape view - which vendors we have worked with, on what, with what outcomes, and which are candidates for future campaigns Keep the program documented: charters, SOPs, vendor playbooks, workflow diagrams, decision logs, and status updates to leadership Track program health metrics - cycle time, plan vs. actuals, CRO performance, data delivery against QC criteria - and surface bottlenecks early Partner with Finance and BD on budget forecasting and spend tracking for external MDE work Qualifications PhD in Molecular Biology, Biochemistry, Protein Engineering, Biophysics, Immunology, or a closely related field; or MS with equivalent industry experience 3+ years of program, project, or operations management experience in biotech, pharma services, or a closely related technical environment Demonstrated experience sourcing, evaluating, and negotiating with CROs or specialty service vendors, including comparing quotes and negotiating pricing and TAT Hands-on experience managing contracting workflows (CDA, MSA, SOW, PO) in partnership with Legal and BD teams Strong written communication and documentation - you produce clear charters, status updates, and decision records that stakeholders actually read Fluent with modern program tools/softwares: Jira (or equivalent), Confluence/Notion, Google Workspace, Slack Enough scientific literacy to read an assay protocol or quote, understand what is being offered, and ask the right follow-up questions Track record of running multiple complex workstreams in parallel and holding them to timelines without micromanaging the technical experts Preferences Prior experience managing CRO relationships in protein production, biochemical/biophysical assays, NGS-based screens, or g