Senior Bioinformatics Scientist, Single-Cell & Spatial Omics

Cellular-Intelligence; Boston (MA); On-site; USD 150,000 - 210,000; Full time

Job summary

Cellular Intelligence in Boston seeks a Senior Bioinformatics Scientist to own and develop methods powering our capsule platform and Universal Virtual Cell‑Signaling Model. You’ll work across single‑cell, spatial, and bulk RNA‑seq, building reproducible pipelines and new analysis methods.

Collaborating with wet‑lab, software, and ML teams, you’ll advance sequencing protocols and therapeutic programs, mentor colleagues, and help scale our cell‑replacement therapy platform from the ground up in a

Qualifications

• PhD in Bioinformatics, Genomics, Computational Biology, Computer Science, or a related field.
• 3+ years of experience developing, adapting, and benchmarking bioinformatics methods and building reproducible pipelines for large‑scale single‑cell and/or spatial transcriptomic data.
• Hands‑on experience with single‑cell transcriptomics analysis.
• Strong Python and/or R programming skills.
• Experience building reproducible workflows with a pipeline manager (e.g. Nextflow or Snakemake), containers, and version control.

Responsibilities

• Develop new bioinformatics methods for single‑cell, spatial, and bulk transcriptomics data, and adapt and benchmark existing ones.
• Build and maintain reproducible analysis pipelines for single‑cell, spatial, and bulk RNA‑seq, from QC and normalization through the downstream analysis appropriate to each modality (integration, clustering, annotation, differential expression).
• Analyze large‑scale single‑cell and spatial transcriptomics data, from raw output through to biological interpretation, including visualization of spatial data.
• Partner with wet‑lab scientists to bring novel multi‑omic assays online, developing the analysis methods and pipelines that new experimental modalities require.
• Collaborate with wet‑lab and computational scientists to design experiments and interpret results.
• Provide technical guidance and mentorship across the bioinformatics, ML, and engineering teams, including code and method reviews.

Skills

Python

R

Single-cell analysis

Spatial transcriptomics

LLMs in bioinformatics

Pipeline development

Mentorship

Education

PhD in Bioinformatics, Genomics, Computational Biology, Computer Science, or a related field

Tools

Nextflow

Snakemake

Docker

Git

Job description

Cellular Intelligence in Boston seeks a Senior Bioinformatics Scientist to own and develop methods powering our capsule platform and Universal Virtual Cell‑Signaling Model. You’ll work across single‑cell, spatial, and bulk RNA‑seq, building reproducible pipelines and new analysis methods.

Collaborating with wet‑lab, software, and ML teams, you’ll advance sequencing protocols and therapeutic programs, mentor colleagues, and help scale our cell‑replacement therapy platform from the ground up in a