Applied AI Scientist (Pharma Partnerships)

Bioptimus; Berlin; Hybrid; EUR 80,000 - 120,000; Full time

Benefits offered by this job

Competitive salary

Equity package

Flexible work arrangements

Job summary

A cutting-edge biotech startup in Berlin seeks an Applied AI Scientist for pharmaceutical partnerships. This role involves bridging AI models with R&D pipelines of biopharma companies. Candidates should have a PhD in Computational Biology and experience in machine learning, alongside strong stakeholder management skills. The position offers a collaborative work environment, competitive salary, and opportunities for professional growth.

Qualifications

• PhD in Computational Biology, Machine Learning, Bioinformatics, Genomics, or a related field required.
• Deep understanding of biopharma R&D value chain.
• Strong fluency in biological data modalities.

Responsibilities

• Lead the post-sales journey for pharmaceutical partners.
• Orchestrate partner journey following contract execution.
• Consult with client R&D teams to diagnose challenges.

Skills

Computational biology

Machine learning

Stakeholder management

Python

Education

PhD in Computational Biology or related field

Tools

PyTorch

JAX

Job description

Bioptimus is building the first universal AI foundation model for biology to fuel breakthrough discoveries and accelerate innovation in biomedicine. With more than $75M in funding, Bioptimus is a fast‑growing start‑up headquartered in Paris, incorporated in October 2023. Backed by leading international venture capitalists, our world‑class team of scientists and engineers is redefining the frontiers of AI and life sciences.

Locations

• Europe: Paris / UK / Germany / Remote (EU)

About the role

We are looking for a scientifically credentialed strategist to lead the post‑sales journey for our pharmaceutical partners. In this role, you will be the bridge between our cutting‑edge foundational models and the R&D pipelines of the world’s leading biopharma companies. You will use your deep expertise in machine learning and computational biology to build credibility with stakeholders, identify new opportunities for model application within their pipelines, and translate customer feedback into our product roadmap.

What you’ll be doing

As our Applied AI Scientist (Pharma Partnerships) you are the primary architect of value for our most critical pharmaceutical partnerships. You will operate at the intersection of computational biology, ML and commercial scale across two strategic domains:

• Partnership Value Realisation & Growth
• Post‑Signature Leadership: Orchestrate the partner journey immediately following contract execution. You will act as the Project Manager for the deployment, ensuring seamless onboarding and integration of our foundational models.
• Scientific & technical thought‑leadership: Consult with client R&D teams (ranging from bench scientists and data science teams to Heads of R&D) to diagnose their specific therapeutic challenges. Identify key use cases where our AI foundation models can unlock high value to our customers research and therapeutic priorities.
• Commercial Adoption & Growth: Proactively identify opportunities to expand the scope of the partnership. Leverage your understanding of the client’s pipeline to suggest new use cases, therapeutic areas, or departments where our technology can drive value.
• Product Intelligence & Roadmap Influence
• Voice of the Customer: Synthesize technical feedback and performance metrics from the field. Translate complex biopharma user requirements into actionable technical specifications for our internal Research and Product teams. Identify high value opportunities to enrich our model capabilities and biology applications offering.
• Gap Analysis: Collaborate with our machine learning engineers to identify data modalities or functional gaps in our current offering, directly influencing future product iterations.

What you’ll bring

The successful candidate will have a ‘team‑first’ attitude; be independent, curious, and detail‑oriented; thrive in a dynamic, fast‑paced environment; and be fun to work with. We value individuals who bring deep domain expertise in computational biology, ML and pharmaceutical R&D alongside strong hands‑on business development skills.

Scientific & Technical Credibility

• Educational Background: PhD in Computational Biology, Machine Learning, Bioinformatics, Genomics, or a related field is required.
• Domain Expertise: Deep understanding of the biopharma R&D value chain (target discovery to clinical trials). You understand the specific pain points of drug developers and are able to translate ambiguous biopharma use cases into rigorous ML applications.
• Technical Fluency: Deep experience in biological data modalities, notably multi-omics (single-cell, transcriptomics, proteomics) and histopathology slides.
• Extensive knowledge in modern ML architectures and paradigms like Transformers (ViT), GNNs, foundation models with embedding‑based prediction heads (e.g., ABMIL), interpretability methods, and model evaluation & validation principles.
• Proven experience in designing end-to-end ML solutions for complex biological problems, including problem framing, data strategy and model design & evaluation.
• Strong fluency in Python and deep learning frameworks (PyTorch, JAX).

Relationship & Strategic Skills

• Stakeholder Management: Proven experience navigating complex, matrixed organizations (Big Pharma experience is a plus). You can present to a VP of R&D in the morning and troubleshoot with a bioinformatician in the afternoon.
• Consulting Mindset: You are not just a support agent; you are a trusted advisor. You have experience in roles such as Field Application Scientist (FAS), Solution Architecture, or Scientific Consulting.
• Feedback Synthesis: Ability to distill complex client complaints or requests into clear, prioritized product requirements.

How to stand out

• Experience in a startup or innovative environment, showing adaptability and proactiveness.
• A strong existing network within Global Top 20 Pharma R&D.
• Experience specifically with “Foundation Models” or Generative AI in a biological context.
• Track record of high‑impact publications (Nature, Cell, NeurIPS).

Candidate journey

To be considered, please submit your CV in English.

We believe in a transparent and collaborative interview process. We need to find a fit for both you and the company. Here is what you can expect after submitting your application:

• Screening: Once you have applied, the hiring team will review your application. If your experience and skills align with the role, you will be invited to a 30‑minute introductory call with the Hiring Manager to discuss your background, motivations, and the position in more detail.
• Interviews: Following a successful screening, you will be invited to a series of interviews:
  • Case Study (60 min): You will prepare a mock kick‑off document for a client engagement with us to evaluate the model on their desired use‑cases, including suggesting interesting use cases for our model and outlining the project plan. We want to see how well you understand the potential use cases for foundation models in the clinical stage of pharma development cycles, and how you would manage a key strategic partner through the deployment and delivery process.
  • Scientific Deep Dive Presentation (30 min): You will briefly present a piece of scientific work to a small panel of our researchers and engineers, led by a senior member of our technical team, and answer Q&S after (10‑15 min presentation, 15‑20 min Q&A). The content is up to you: it can be your own past research, a relevant paper in the field, or extra points if it’s a specific Bio‑AI use case you’ve worked on with a biopharma. The goal is to assess your technical fluency, your ability to facilitate scientific debate, and how you communicate complex concepts to experts.
  • Executive Interview (30 min): A comprehensive discussion with members of our Senior Leadership. This session moves beyond technical competency to focus on long‑term vision, values, and mutual potential. This is an opportunity for you to get to know the company better as well.
• Offer: Following the completion of all interviews, our hiring team will make a final decision and will be in touch to share the outcome. Please note that an offer is contingent upon the successful completion of a reference check.
• Onboarding: We are happy to have you joining the team! Once you have accepted and signed your offer, we will be in touch to begin the process of onboarding you.

Why this is a unique opportunity

• A collaborative and mission‑driven work environment.
• Competitive salary and equity package.
• Flexible work arrangements, including remote options.
• Opportunities for professional growth and leadership development.
• Shape the future of biology and AI by contributing to groundbreaking work.

We believe that the unique contributions of all Bioptimists create our success. To ensure that our culture continues to incorporate everyone’s perspectives and experience, we never discriminate based on race, religion, national origin, gender identity or expression, sexual orientation, age, or marital, or disability status. Decisions related to hiring are made fairly, and we provide equal employment opportunities to all qualified candidates. We take responsibility for always striving to create an inclusive environment that makes every employee and candidate feel welcome.