Senior/Principal Scientist, Bioinformatics

Acrivon Therapeutics • Watertown, MA

20h • Hybrid

About The Position

Acrivon (NASDAQ: ACRV) is a clinical stage biopharmaceutical company discovering and developing precision medicines utilizing its proprietary Generative Phosphoproteomics AP3 platform. The platform allows the company to interpret and quantify compound specific, drug-regulated pathway activity levels inside the intact cell in an unbiased manner, yielding terabytes of proprietary data and delivering rapid, actionable insights. The Generative Phosphoproteomics AP3 platform is comprised of a growing suite of powerful, internally-developed tools, including the AP3 Data Portal, converting multimodal data into structured data for generative AI analyses, the AP3 Kinase Substrate Relationship Predictor and the AP3 Interactome. These distinctive capabilities enable the company to go beyond the limitations of traditional drug discovery, as well as current AI-based target-centric drug discovery, and rapidly design highly differentiated compounds with desirable pathway effects through intracellular protein network analyses and advance these agents into the clinic for streamlined development.
Acrivon is currently advancing its lead program, ACR-368 (also known as prexasertib), a selective small molecule inhibitor targeting CHK1 and CHK2 in a potentially registrational Phase 2b trial for endometrial cancer. The company has received Fast Track designation from the Food and Drug Administration, or FDA, for the investigation of ACR-368 as a monotherapy based on OncoSignature-predicted sensitivity in patients with endometrial cancer. The FDA has granted a Breakthrough Device designation for the ACR-368 OncoSignature assay for the identification of patients with endometrial cancer who may benefit from ACR-368 treatment.
In addition to ACR-368, Acrivon is also leveraging its proprietary Generative Phosphoproteomics AP3 platform for developing its co-crystallography-driven, internally discovered pipeline programs. These include ACR-2316, the company’s second clinical stage asset, a novel, potent, selective WEE1/PKMYT1 inhibitor designed for superior single-agent activity through strong activation of not only CDK1 and CDK2, but also of PLK1 to drive pro-apoptotic cell death, as observed in preclinical studies against benchmark inhibitors. The Phase 1 trial of ACR-2316 is advancing with enrollment in the first three dose-escalation cohorts completed. Drug target engagement was observed at DL1 and 2 using the company’s clinical mass-spectrometry-based AP3 profiling, with evidence of approximate dose proportionality based on plasma pharmacokinetic analyses, and initial clinical activity with tumor shrinkage observed at DL3. In addition, the company is advancing a preclinical program directed against an undisclosed cell cycle regulatory target.
Our global team operates out of two leading life science clusters, Watertown, MA and Medicon Village in Lund, Sweden.

The Senior Scientist/Principal Scientist, Bioinformatics, within the Data Science team will play a central role in developing and applying advanced computational approaches to support drug discovery and development, leveraging Acrivon’s generative phosphoproteomics AP3 platform.
We are seeking a highly accomplished scientist with expertise in building scalable analytical workflows, applying rigorous quantitative methods, and extracting actionable biological insights from large-scale omics data. The successful candidate will lead analyses across proteomics, phosphoproteomics, transcriptomics, and other high-dimensional datasets, integrating these data with systems biology and AI/ML approaches to inform target discovery, mechanism-of-action studies, indication selection, and biomarker identification. Experience in proteomics-driven pathway analysis and network biology will be highly valued.
This individual will work closely within a multidisciplinary environment that includes proteomics, biology, and biomarker teams to maximize the scientific and translational value of Acrivon’s AP3 platform.
This role is based in Watertown, MA.

Requirements

• D. or M.S. in Bioinformatics, Computational Biology, Computer Science, Engineering, or a related quantitative discipline, with 5+ years of industry experience in a biotechnology or pharmaceutical setting.
• Expertise in the computational analysis, integration, and visualization of large-scale omics datasets, with a particular emphasis on mass spectrometry-based proteomics.
• Proven track record of designing and implementing scalable computational workflows for large-scale omics datasets and translating analytical findings into actionable biological insights.
• Strong programming skills in R and Python, encompassing scripting, data wrangling, statistical analysis, and visualization.
• Experience building interactive analytical tools, visualizations, and enterprise-level web applications using frameworks such as R Shiny, Streamlit, Flask, or Django.
• Experience with cloud computing environments and scalable data infrastructure, including workflow orchestration and data management on cloud platforms.
• Experience with data integration strategies and biological database design, including systems for managing, storing, and retrieving large-scale omics datasets.
• Strong scientific knowledge of oncology, including cancer biology, signaling pathways, biomarkers, and therapeutic modalities.

Nice To Haves

• Experience with single-cell and/or spatial omics data analysis is preferred.
• Experience applying AI/ML approaches, such as generative AI, agentic workflows, knowledge graphs, large language models, or foundation models, to biological data interpretation or hypothesis generation is preferred.

Responsibilities

• Lead computational analysis and interpretation of large-scale proteomics and other multi-omics datasets to support mechanism-of-action studies, indication prioritization, target identification and validation, and biomarker discovery.
• Design, develop, and optimize robust, scalable, and secure computational pipelines for proteomics and multi-omics data analysis.
• Develop and maintain interactive web-based applications and data visualization tools that enable robust analytics within a cloud-based environment.
• Evaluate and incorporate emerging bioinformatics, mass spectrometry proteomics, and AI/ML technologies into data science workflows and analytical pipelines.
• Apply advanced AI/ML approaches, including generative and agentic AI, to enhance biological interpretation, hypothesis generation, and data-driven decision-making.
• Partner closely with proteomics, biology, biomarker, and other cross-functional teams to deliver tailored analyses and actionable biological insights.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Number of Employees: 11-50 employees