Senior Bioinformatics Scientist

Fapon

Pleasanton, CA, United States permanent

Posted: December 17, 2025

Job Description

PromptBio, established in 2023 in Pleasanton, California, is a biotechnology company dedicated to developing AI-driven workflows that automate the discovery of novel biomarkers from multi-omics data, translating them into clinical diagnostic applications.

We seek a motivated Senior Bioinformatics Scientist to join our interdisciplinary team, focusing on integrating AI solutions within the life sciences domain. The role will have significant customer facing responsibilities.

Key Responsibilities

• Work closely with the Business Development team and serve as the primary scientific point of contact for enterprise customers, building deep technical relationships and helping customers derive biological insights.
• Design and implement custom multi-omics analysis workflows (genomics, transcriptomics, proteomics, metabolomics, epigenomics) tailored to customer use cases
• Evaluate and incorporate new bioinformatics tools, algorithms, and computational methods to stay at the forefront of the field.
• Author and contribute to scientific publications, presentations, and IP filings.

• Minimum of 3 years of industry experience in processing and analyzing mutli-omics datasets (e.g., genomics, transcriptomics, proteomics, metabolomics, epigenomics) and deriving meaningful insights
• Hands-on experience with applying advanced statistical methods and machine learning techniques to analyze omics data and identify novel biomarkers, therapeutic targets, and molecular mechanisms.
• Excellent publication record and communication skills with ability to explain concepts to diverse audiences.
• Fluency in programming languages like Python, R, and bioinformatics workflows (e.g., using Nextflow, Snakemake, or similar).
• Familiarity with software engineering best practices, including testing, code reviews, version control (e.g., Git), and containerization.
• Experience with cloud computing environments and AI technologies is a significant plus.
• PhD in Bioinformatics, Computational Biology, Genomics, or related field

Desired Attributes

• Entrepreneurial mindset with comfort in ambiguous, fast-paced environments.
• Proactive, results-oriented, and driven with a "get things done" mindset.
• Strong problem-solving skills and adaptability to evolving project requirements.
• Intellectual curiosity about emerging AI technologies and their biological applications.
• Collaborative team player who thrives in dynamic environments.

• Financial security through competitive compensation, incentives, and retirement plan
• Healthcare and well-being programs including competitive medical, dental, and vision  benefits
• Generous paid time-off including vacation, sick time, holidays, and discretionary winter shutdown
• 401(k) retirement savings with a generous company match
• Other comprehensive voluntary benefits include but are not limited to pet insurance, life insurance, employee assistance program (EAP), discount programs, and many more
• We continue to optimize our benefits & wellness programs as we grow our organization to make sure they meet our diverse workforce needs
• Hybrid work opportunities.

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