Sr. Bioinformatics Scientist San Diego, CA

Singular Genomics Systems, Inc.; San Diego (CA); Hybrid; USD 132,000 - 155,000; Full time

Benefits offered by this job

Equity

Job summary

Singular Genomics seeks a Senior Scientist on the Bioinformatics team to expand spatial biology offerings. You will work at the intersection of computation, assay development, and software, with initial focus on designing targeted in situ panels for tissue and disease contexts.

You will build automated workflows, collaborate across R&D, and contribute novel analysis methods for spatial multiomics. Remote or hybrid work is possible, with quarterly travel to San Diego.

Qualifications

• PhD in a related field or MS with industry experience.
• Experience analyzing spatial transcriptomics or single-cell data.
• Proficiency in Python and scripting for pipelines.

Responsibilities

• Support design and optimization of spatial transcriptomics panels.
• Define panel content for cell type annotation and state characterization.
• Develop automated tools for panel design and evaluation.
• Collaborate with molecular biology and assay teams to improve panels.
• Evaluate panel performance using internal and external references.
• Develop and maintain spatial bioinformatics workflows and pipelines.
• Stay current with spatial biology and single-cell methods.

Skills

Python

Spatial biology

Bioinformatics

Linux

Communication

Education

PhD in Bioinformatics

MS with industry experience

Tools

Docker

Nextflow

Scanpy

Seurat

Squidpy

Job description

ABOUT SINGULAR GENOMICS

Singular Genomics is inventing at the forefront of genomics, one of the world’s fastest-growing industries. The commercially available G4® Sequencing Platform is a powerful, highly versatile benchtop genomic sequencer designed to produce fast and accurate results. In addition, the company is currently developing the G4X™ Spatial Sequencer, an upgrade to the G4, which will leverage Singular’s proprietary sequencing technology, applying it as an in situ readout for transcriptomics, proteomics and fluorescent H&E in tissue, with spatial context. Singular Genomics’ mission is to empower researchers and clinicians to advance science and medicine.

We foster a culture of creativity and technical excellence, both catalysts for innovation. We celebrate diversity, emphasize collaboration and, as we rapidly mature, we are constantly looking at ways we can do better for our people.

Our Headquarters are located on the Torrey Pines Mesa, in La Jolla, California at the center of the biotech hub. Our Manufacturing facility is in Sorrento Valley.

Position Summary:

As a Senior Scientist on the Bioinformatics team, you will play a key role in expanding Singular Genomics' spatial biology platform and service offerings. This position sits at the intersection of computational biology, assay development, and hands-on scientific computing. You will report into the Bioinformatics functional group and, initially, be matrixed into the Panel Design team to focus on its most pressing needs. Your initial focus will be supporting the design and optimization of targeted in situ transcriptomics panels for tissue- and disease-specific applications. This includes selecting biologically informative genes for cell type identification, defining pathway-focused content that enables cell-state interpretation, and developing computational tools to automate and improve panel design. As the platform and services continue to evolve, you will contribute to the development of spatial bioinformatics workflows, analysis pipelines, and computational methods that enable customers to generate meaningful biological insight from spatial multiomics data. This is an ideal role for someone who enjoys applying computational approaches to challenging biological problems while building software that directly impacts cutting-edge products and services. This position can be remote or hybrid/on-site. If remote, travel to the headquarters in San Diego, CA will be required at least quarterly.

Responsibilities

Primary Responsibilities

• Support the computational design and optimization of targeted spatial transcriptomics panels for tissue- and disease-specific applications.
• Define biologically relevant panel content by integrating current literature, public datasets, and pathway knowledge to support cell type annotation and cell state characterization.
• Develop computational methods and software tools for automated panel design, probe evaluation, and panel optimization.
• Collaborate closely with molecular biology, chemistry, and assay development teams to iteratively improve probe performance and panel quality.
• Evaluate panel performance using internal datasets and external spatial and single-cell reference atlases.

Spatial Bioinformatics

• Develop and maintain analysis pipelines for spatial transcriptomics and spatial multiomics datasets.
• Apply modern spatial bioinformatics methods to support sequencer / assay development and biological interpretation, including cell typing, differential expression, pathway analysis, spatial neighborhood analysis, and cell-state characterization.
• Work with scientists across R&D to develop new analysis capabilities that support expanding service offerings.
• Stay current with advances in spatial biology, single-cell genomics, and computational biology, incorporating new approaches where appropriate.

Scientific Software & Automation

• Write clear, workable code (primarily Python) to automate panel design, analysis, and other repetitive scientific tasks.
• Build and maintain automated analysis workflows that make routine spatial and single-cell analyses repeatable and easy to run.

Qualifications

• PhD in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related discipline. Candidates with an MS plus industry experience will also be considered.
• Experience analyzing spatial transcriptomics, single-cell sequencing, or related genomics datasets.
• Strong understanding of tissue biology, cell type annotation, and pathway-based biological interpretation.
• Proficiency writing analysis code in Python; able to produce clear, workable code without requiring production-software polish.
• Experience building automated analysis workflows or pipelines. Working knowledge of Linux-based computational environments.
• Excellent written and verbal communication skills

Preferred Qualifications

• Experience designing targeted sequencing or hybridization-based panels.
• Experience with probe design, oligonucleotide design, or molecular assay development.
• Experience with single-cell analysis frameworks such as Scanpy, Squidpy, Seurat, or similar.
• Knowledge of cancer biology, immunology, or tissue-specific biology.
• Experience developing workflow pipelines using Nextflow.
• Familiarity with containerization (e.g., Docker) and reproducible-environment tooling.
• Software-engineering rigor (testing, CI/CD, packaging) is welcome but not expected at this level.
• Experience with cloud computing environments (AWS preferred). Familiarity with image-based spatial technologies or microscopy data.
• Experience with primary analysis methods such as image processing, feature detection, registration, or sequencing base calling is a plus but not required..

The estimated base salary range for this role based in the United States of America is: $131,600 - $154,800. Additionally, this role is eligible for to receive equity as part of the compensation package. Compensation decisions are dependent on several factors including, but not limited to, an individual’s qualifications, location where the role is to be performed, internal equity, and alignment with market data. Should the level of the role change during the hiring process, the applicable salary range may be updated accordingly.

Singular Genomics is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees.

Singular Genomics is committed to working with and providing reasonable accommodations to job applicants with physical or mental disabilities. Applicants with a disability who require a reasonable accommodation for any part of the application or hiring process can provide their name and contact information to our Accommodations team at [e-mail]. Your request will be responded to as soon as possible.