Bioinformatics Scientist, Panel and Probe Design

Location: Boston, MA

Department: Assay Research

Role Description

• The Bioinformatics Scientist, Panel and Probe Design is responsible for the end-to-end design, optimization, computational modeling, and validation of gene panels and oligonucleotide probe sets and high-plex STARmap and RIBOmap assay panels used in spatial biology.
• This role integrates molecular biology, oligonucleotide chemistry, and computational analytics.
• A key part of this role is partnering closely with software engineering teams to translate scientific workflows into robust, production-level software tools that automate probe and panel design, ensure quality, and support scaling of custom panel operations.
• Develop and generate standard and custom panels for internal R&D and customers.

Key Responsibilities

• Panel Design
• Probe Design
• Bioinformatics & Design Pipeline Integration
• Software Engineering Collaboration
• Cross-Functional Collaboration

What you'll do

• Panel Design

Lead the full lifecycle of panel design, from gene selection to final multiplex panel architecture.

Develop scoring frameworks for target ranking, sequence complexity, barcode compatibility, and tissue-relevant performance.

Create panel configurations for RUO products, custom customer-specific designs, FFPE optimization, 3D assays, and disease-specific discovery panels.

Maintain a validated library of targets, probe sets, and design rules.

• Probe Design

Design oligonucleotide probes optimized for specificity, thermodynamic stability, and balanced hybridization kinetics.

Use computational tools to ensure on-target performance and structural compatibility.

Collaborate with assay and engineering teams to match probe design to instrument capabilities.

• Bioinformatics & Design Pipeline Integration

Partner with computational biology to refine automated algorithms for probe tiling, panel scoring, and design rule enforcement.

Analyze transcriptomic datasets to identify biologically relevant genes and optimize panel balance.

Contribute to predictive modeling for hybridization success and imaging performance.

• Software Engineering Collaboration

Work closely with software engineers to develop, refine, and deploy production-grade software tools for probe and panel design.

Translate scientific requirements into technical specifications and software features.

Improve algorithms, workflow logic, and data-processing steps used in design pipelines.

Test, validate, and iterate software outputs to ensure accuracy, reproducibility, and scalability.

Collaborate on UI/UX design for tools supporting custom panel intake, QC review, and manufacturing readiness.

Ensure integration of sequence analysis engines, scoring systems, design rules, and QC metadata.

Participate in Agile processes and support code-quality reviews and documentation.

• Cross-Functional Collaboration

Partner with Reagent Manufacturing on oligo QC standards and pilot builds.

Support Field Applications and Customer Support by providing scientific rationale behind panel performance.

Contribute to stage-gate reviews, and design-transfer documentation.

Provide panel-design insights to Product Management for roadmap development.

Qualifications

• Ph.D. in Molecular Biology, Computational Biology, Bioengineering, Bioinformatics, or related field; or M.S.with 3–5+ years relevant experience.
• Experiences with analyzing scRNA-seq data.
• Experience designing probes or multiplexed panels for spatial transcriptomics or single cell assays.
• Strong sequence analysis skills (Python/R required). 
• Experience contributing to production or customer-facing scientific software tools.
• Familiarity with APIs, data models, automated QC pipelines, or algorithm integration.
• Background in probe scoring, or large-panel (>500 genes) design.

Why Stellaromics?

• Innovative Technology: Be part of a company at the cutting edge of spatial biology and genomics, revolutionizing the way researchers understand biology.
• Impactful Role: You will have a significant impact on the department and the future of the company.
• Collaborative Environment: Work with a talented, passionate team in a culture that values creativity, innovation, and teamwork.
• Career Growth: As a high-growth company, we offer significant opportunities for professional development and career advancement.

Compensation

An attractive compensation and benefits package based on market pay data will be commensurate with candidate skills, qualifications, and experience.

If you are interested in becoming part of a growing team energized by limitless possibilities, please submit your resume for consideration. To learn more about Stellaromics and our technology, please visit our website at www.stellaromics.com.

Stellaromics is an Equal Opportunity Employer striving to build an inclusive and diverse workplace culture.

About the Company

Spun out of Stanford and MIT, Stellaromics is an innovative biotech startup founded in 2022 and located in Boston, MA. Our pioneering proprietary technology helps researchers and clinicians create comprehensive cellular maps enhancing our understanding of various diseases, with our flagship product STARmap and upcoming Pyxa™ suite of products. We have a passionate management team and committed investors who believe in our patented technology and overall mission to profoundly advance biomedical research and accelerate the discovery of life-saving treatments.