Position Summary:

Apellis seeking a highly motivated and collaborative Senior Scientist to join our Translational Development team to lead the development of innovative computational tools and models that accelerate biomarker discovery and enable precision medicine approaches in drug development. This position focuses on building end-to-end machine learning and computer vision pipelines using clinical, imaging, and multi-omics data to identify disease mechanisms, stratify patients, and predict therapeutic responses, especially in ophthalmology and neurodegenerative diseases.

This is an opportunity to drive the next generation of biomarker discovery and clinical development through cutting-edge AI/ML technologies, and close collaboration across R&D, clinical, and regulatory teams.

Key Responsibilities Include:

Design, implement, and optimize AI/ML models to solve complex and novel problems in clinical development, including patient stratification, disease progression modeling, and treatment effect prediction.
Develop algorithmic strategies tailored to translational research questions, including machine learning and deep learning architectures (e.g., CNNs, transformers, ODE-based models).
Analyze retinal imaging data (e.g., OCT, FAF, MRI) using computer vision and representation learning techniques to extract quantitative imaging biomarkers relevant to ophthalmology and neurodegenerative disease trials.
Drive integration of multimodal datasets - including imaging, clinical outcomes, and omics—to identify mechanistic insights and actionable biomarkers that inform clinical trial design and therapeutic strategy.
Navigate scientific ambiguity by working closely with clinical and research partners to understand high-level goals, formulate data-driven questions, and define fit-for-purpose ML solutions.
Lead development of end-to-end ML pipelines including data preprocessing, feature extraction, model training/validation, and deployment in GxP-aware environments, ensuring reproducibility and robustness.
Advocate for and help define the technical infrastructure: including compute resources, data access, and software tools required to successfully develop and deploy AI models at scale.
Collaborate cross-functionally with Clinical Development, Medical, Biostatistics, Regulatory, and external vendors to align modeling work with program priorities and ensure translational impact.
Communicate model rationale, design choices, assumptions, and results effectively to both technical and non-technical stakeholders, shaping data-driven decision-making across the organization.
Stay current with advances in AI/ML, contribute to internal innovation, and prepare for publication/presentations scientific findings in high-impact journals and conferences.
Support documentation of ML methodologies and biomarker strategies in clinical protocols, statistical analysis plans, regulatory submissions, and scientific publications.
Demonstrate excellent stakeholder management and deliver outstanding data that is meaningful and important for Apellis' goals.

Education, Registration & Certification:

Ph.D. in Computer Science, Biomedical Engineering, Computational Biology, Physics, Applied Mathematics.

Experience:

5+ years of hands-on experience in AI/ML and biomedical applications.

Skills, Knowledge & Abilities:

Algorithmic & Modeling Expertise: Deep understanding of classical and modern machine and deep learning methods - including Random Forests, gradient boosting, CNNs for segmentation, and temporal models, with the ability to match the right approach to the problem.
Scientific & Strategic Thinking: Strong ability to translate ambiguous scientific questions into well-defined modeling objectives and implement fit-for-purpose AI/ML solutions in translational and clinical settings.
Project Leadership: Ability to establish and maintain a leadership role, managing external vendors and collaborators to ensure timely and scientifically sound results.
Literature and Research: Strong capability to stay current with literature publications and congress presentations, synthesizing recent findings to guide project directions.
Stakeholder Management: Excellent skills in managing stakeholders and delivering data that aligns with and supports Apellis' goals.
Regulatory and Analytical Skills: Competence in overseeing data analysis, interpretation, and supporting regulatory submissions with original content and documentation.

Physical Demands and Work Environment:

This is largely a sedentary role; however, some filing is required. This would require the ability to lift files, open filing cabinets and bend or stand on a stool as necessary. This job operates in a professional office environment and routinely uses standard office equipment such as computers, phones, photocopiers, filing cabinets and fax machines.

Travel Requirements:

Up to 20% travel expected.

Benefits and Perks:

Apellis offers a comprehensive benefits package, including a 401(k) plan with company match, inclusive family building benefits, flexible time off, summer and winter shutdowns, paid family leave, disability and life insurance, and more! Visit https://apellis.com/careers/ to learn more.

Company Background:

Apellis Pharmaceuticals, Inc. is a global biopharmaceutical company that combines courageous science and compassion to develop life-changing therapies for some of the most challenging diseases patients face. We ushered in the first new class of complement medicine in 15 years and now have two approved medicines targeting C3. These include the first and only therapy for geographic atrophy, a leading cause of blindness around the world. With nearly a dozen clinical and pre-clinical programs underway, we believe we have only begun to unlock the potential of targeting C3 across many serious diseases.

For more information, please visit http://apellis.com or follow us on Twitter and LinkedIn

EEO Statement:

Apellis is an equal opportunity employer and complies with all applicable federal, state and local fair employment practices laws. Apellis strictly prohibits and does not tolerate discrimination against employees, applicants or any other covered persons because of race, color, religion, creed, national origin or ancestry, ethnicity, sex (including pregnancy), gender (including gender nonconformity and status as a transgender or transsexual individual), age, physical or mental disability, citizenship, past, current or prospective service in the uniformed services, genetic information, marital status, AIDS/HIV status, smoker/nonsmoker, and occupational pneumoconiosis or any other characteristic protected under applicable federal, state or local law.

For San Francisco postings: Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with arrest and conviction records.

Other Duties:

Please note this job description is not designed to cover or contain a comprehensive listing of activities, duties or responsibilities that are required of the employee for this job. Duties, responsibilities and activities may change at any time with or without notice.

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