Senior Bioinformatics Scientist

Cellular Intelligence; 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

About Cellular Intelligence

Cellular Intelligence (CI) is an AI‑native TechBio and clinical‑stage BioTech company building a universal foundation model of cell signaling to understand, predict, and ultimately control cellular behavior, transforming biology from trial‑and‑error into an engineering discipline. We take a full‑stack approach, generating perturbation data at over 1,000x the efficiency of conventional methods, capturing millions of time‑resolved treatment combinations per experiment, and training large‑scale models that generalize across contexts to enable rational protocol design for regenerative medicine, context‑specific drug effect prediction, and systematic disease modeling. Our founding team includes repeat AI entrepreneur Dr. Micha Breakstone (Chorus.ai, acquired for $575M), the Head of the Fundamental AI Group at MIT, and four professors from Harvard Medical School and the University of Washington, including the Chair of Genetics at Harvard, collectively holding five National Academy memberships. Based in Boston, CI has raised over $60M to date from Khosla Ventures, CZI, SciFi VC, and AMD Ventures, and is rapidly scaling its world‑class team.

Core Values

• We show up – fully accountable, all‑in, doing whatever it takes.
• We act with urgency – swift, decisive, proactive.
• We support one another – collaborative, helpful, empathetic.

Location: Boston, MA
Reports to: Director of Bioinformatics

About the Role

We seek a Senior Bioinformatics Scientist to own and develop the methods and pipelines that power our proprietary capsule platform and feed our Universal Virtual Cell‑Signaling Model. Working across single‑cell, spatial, and bulk RNA‑seq, you'll build reproducible pipelines, develop new bioinformatics methods, and apply them to our data. You'll collaborate closely with wet‑lab scientists, software engineers, and machine learning researchers to advance novel sequencing protocols and our therapeutic programs. This is a hands‑on role spanning single‑cell and spatial omics, ideal for someone who thrives in a fast‑paced, interdisciplinary environment and wants to help build our cell‑replacement therapy platform from the ground up.

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.

Qualifications

• PhD in Bioinformatics, Genomics, Computational Biology, Computer Science, or a related field. Equivalent industry experience is also welcome.
• 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.
• Experience applying state‑of‑the‑art large language models (LLMs) to bioinformatics projects.
• Excellent organizational and documentation habits.

Preferred Qualifications

• Experience with spatial transcriptomics data analysis and visualization.
• Experience applying and improving automated cell type annotation methods (e.g., marker‑based and reference‑based methods).
• Experience working at the interface of technology development and data analysis, particularly involving novel molecular biology or sequencing techniques.
• Strong domain knowledge in developmental biology or stem cell research.
• Experience mentoring scientists or reviewing scientific code.
• Prior experience in a startup or fast‑paced, interdisciplinary environment.

Cellular Intelligence is committed to creating a diverse and inclusive workplace. We welcome and encourage applicants from all backgrounds, regardless of race, ethnicity, gender, sexual orientation, religion, disability, or age. We embrace differences and believe that a diverse workforce enhances our creativity, innovation, and overall success.