Senior Bioinformatics Scientist: Single-Cell & Spatial

PVH (Tommy Hilfiger/Calvin Klein); Boston (MA); On-site; USD 120,000 - 160,000; Full time

Job summary

Cellular Intelligence in Boston, MA seeks a Senior Bioinformatics Scientist to own and advance methods powering our capsule platform and the Universal Virtual Cell-Signaling Model.

You'll work across single-cell, spatial, and bulk RNA-seq, building reproducible pipelines, developing new methods, and collaborating with wet-lab, software, and ML researchers to push sequencing protocols and therapeutic programs forward.

Qualifications

• PhD in Bioinformatics, Genomics, Computational Biology, Computer Science, or a related field; Equivalent industry experience welcome.
• 3+ years developing and benchmarking bioinformatics methods and building reproducible pipelines for large-scale single-cell and/or spatial 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.
• Experience applying state-of-the-art large language models (LLMs) to bioinformatics projects.
• Excellent organizational and documentation habits.

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

Bioinformatics workflows

Nextflow/Snakemake

LLMs in bioinformatics

Documentation habits

Team mentorship

Education

PhD in Bioinformatics

Equivalent industry experience

Tools

Nextflow

Snakemake

Git

Containers

Job description

Cellular Intelligence in Boston, MA seeks a Senior Bioinformatics Scientist to own and advance methods powering our capsule platform and the Universal Virtual Cell-Signaling Model.

You'll work across single-cell, spatial, and bulk RNA-seq, building reproducible pipelines, developing new methods, and collaborating with wet-lab, software, and ML researchers to push sequencing protocols and therapeutic programs forward.