Associate Scientist, Computational Biology

Position Title: Associate Scientist, Computational Biology

Location: Hybrid/Philadelphia, PA

Reports to: Scientist, Computational Biology

Department: Research – Computational Biology

Cabaletta Bio (Nasdaq: CABA) is a late-stage clinical biotechnology company focused on developing and launching curative targeted cell therapies designed specifically for patients with autoimmune diseases. The CABA™ platform encompasses two complementary strategies which aim to advance the discovery and development of engineered T cell therapies with the potential to become deep and durable, perhaps curative, treatments for a broad range of autoimmune diseases. The lead CARTA (Chimeric Antigen Receptor T cells for Autoimmunity) strategy is prioritizing the development of rese-cel, a 4-1BB-containing fully human CD19-CAR T cell investigational therapy. Rese-cel is currently being evaluated in the RESET™ (REstoring SElf-Tolerance) clinical development program spanning multiple therapeutic areas, including rheumatology, neurology and dermatology. Cabaletta Bio’s headquarters and labs are located in Philadelphia, PA. For more information, please visit www.cabalettabio.com and connect with us on LinkedIn.

Uniquely Differentiated. Rapid. Elegant.

At Cabaletta, we are driven by the shared mission of developing cures, where a patients’ own cells are used to fight disease. We are building a culture grounded in the knowledge that successful cures can be achieved for patients if every member of the Cabaletta is focused on the success of the team. To nurture this, we make an active commitment to the well-being and continuous growth of each employee who joins the team. In this way, we are not only working to improve the lives of patients, but of everyone involved. #CabalettaCrew.

We’re proud to be a Great Place to Work-Certified™ company! #GPTWcertified Check out what our employees say makes working here so great: Working at Cabaletta Bio Inc | Great Place to Work®

About The Position

The Associate Scientist, Computational Biology will build and maintain programmatic and agentic workflows that clean, transform, and merge large, feature-rich datasets — primarily flow cytometry, MSD, and dPCR data — into analysis-ready information. Working under the guidance of senior computational biology staff, they will collaborate with Research, Translational, Manufacturing, and Clinical teams to visualize and correlate data across the organization, surface key scientific questions, and communicate clear summaries of their analyses to stakeholders.

Responsibilities

• Design, build, and maintain programmatic and agentic workflows to support recurring computational biology tasks, including cleaning, transforming, and merging large-scale biological datasets with many features.
• Mine public and internal databases for relevant biological and disease-related information.
• Develop and automate interactive data visualizations and dashboards.
• Perform correlative analyses and produce clear, intuitive summary reports of data exploration and analyses for scientific and non-scientific audiences.
• Communicate results and recommendations to stakeholders, including scientific colleagues and collaborators.
• Maintain thorough documentation of workflows and analytical methods in accordance with SOPs.

Required Qualifications

• MS in computational biology, bioinformatics, computer science, or a related field plus 1–2 years of relevant experience; or a BS with additional demonstrated experience in computational and programmatic analysis of biological data.
• Strong foundation in computer science, statistics, mathematics, and biology.
• Proficient in Python, with experience building automated scripts or pipelines.
• Demonstrated ability to integrate, mine, analyze, visualize, and interpret data using computational and statistical tools.
• Meticulous and detail-oriented, with the ability to follow complex operating procedures (SOPs) and thoroughly document work.
• Strong team orientation and a passion for continuous self-development.

Preferred Qualifications

• Experience designing agentic or LLM-driven workflows — whether through structured instructions/prompts, orchestration frameworks (e.g., LangChain, AutoGen), or direct API integrations.
• Familiarity with software engineering best practices (e.g., version control/Git, code review, testing).
• Familiarity with cloud computing environments (AWS, GCP, or Azure) and workflow orchestration tools (e.g., Airflow, Nextflow).
• Experience with data analysis and machine learning techniques.
• Experience with traditional bioinformatics analysis (e.g., genomic, transcriptomic, or proteomic data) and multi-omics data integration.
• Experience in an industry or startup setting is preferred.

Our name – Cabaletta – is derived from the operatic term that represents a rapid, repetitive, and technically challenging section of an operatic aria, designed to showcase the skills of the lead singer. Analogously, Cabaletta Bio strives to achieve rapid and repetitive product development, building on our indication prioritization and biologic platform that targets the driver of specific autoimmune diseases without the need for long-term immunosuppression.

For more information, please visit https://www.cabalettabio.com/join-our-crew

Our most important asset is our people, and we offer competitive benefits, PTO, and stock option plans.

Cabaletta Bio is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability, protected veteran status or any other basis protected by applicable law.

Cabaletta Bio, Inc. does not accept unsolicited resumes from recruiters, employment agencies, or staffing firms. To conduct business with Cabaletta, a Master Services Agreement (MSA) must be executed and confirmed prior to submitting any information relating to a potential candidate. Without a signed MSA, Cabaletta shall not be responsible to any individual or entity for any payment relating to any form of fee or compensation.

And, if a resume or candidate is submitted by a recruiter, an employment agency, or a staffing firm without a fully executed MSA, Cabaletta has the unrestricted right to pursue and hire any of those candidate(s) without any legal or financial responsibility to the recruiter, agency, and/or firm.