Senior Scientific Program Manager, ML - Guided Protein Design Evaluation
About The Position
Profluent is an AI-first protein design company founded in 2022, focused on developing deep generative models for novel, functional proteins to revolutionize biomedicine. We are backed by leading investors and have raised over $150M. We are expanding our ML Design Evaluation (MDE) program, a cross-functional initiative that runs structured design campaigns to generate high-quality experimental data for our protein design models. The MDE program operates through internal labs and external Contract Research Organizations (CROs), requiring strong program execution, effective vendor management, and meticulous documentation. This role will focus on the operational and external-partnership aspects of the MDE program, managing campaigns end-to-end, overseeing CRO relationships, and ensuring program documentation and timelines are maintained so the scientific team can focus on research.
Requirements
- 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
Nice To Haves
- Prior experience managing CRO relationships in protein production, biochemical/biophysical assays, NGS-based screens, or gene editing workflows
- Experience running cross-functional programs that span ML/computational and wet-lab teams
- Familiarity with LIMS or design-management systems (Benchling, PIMS, or equivalent) and with how experimental data flows into a data warehouse
- Background or degree in life sciences, bioengineering, or a related field
- Experience standing up new programs (processes, templates, cadences) from scratch, not just running existing ones
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
Benefits
- Competitive compensation package with equity participation
- Comprehensive benefits including health/dental/vision insurance
- Generous PTO policy and commitment to work-life balance
- Professional development opportunities in a cutting-edge field at the intersection of AI and biology
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What This Job Offers
Job Type
Full-time
Career Level
Senior
Education Level
Ph.D. or professional degree
