Senior Bioinformatics Scientist – Transcriptomics

About Somite

is a venture-backed company aiming to become the OpenAI of stem cell biology, developing AI foundation models for human stem cells to drive novel cell therapies at scale.

We take a full-stack approach - generating data at 1,000x lower cost, training large-scale models with unmatched predictive power, and using these models to discover, refine, and optimize high-impact applications in cell therapy.

Our founding team includes repeat AI entrepreneur Dr. Micha Breakstone , acquired for $575M), the Head of the Fundamental AI Group at MIT (pioneered the foundational research on scaling laws), and three Harvard Medical School professors and National Academy of Sciences/Medicine members, including the Chair of the Genetics Department at HMS. Based in Boston and launching operations in January 2024, Somite has raised close to $60M to date (Forbes).

Somite's 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 (onsite, full-time)

About the Role:

We seek a skilled Bioinformatician to lead the design and execution of analysis pipelines for large-scale transcriptomic datasets. You'll be responsible for preprocessing, quality control, and biological interpretation of sequencing data, contributing to the development of novel sequencing protocols and technologies in close collaboration with wet lab scientists, computational biologists and machine learning researchers to support Somite's therapeutic programs.

This is a hands-on, data-centric role ideal for someone who thrives in a fast-paced, interdisciplinary environment and wants to help build transformative cell therapy technologies from the ground up.

Responsibilities:

• Build, maintain, and run robust, reproducible pipelines for single-cell and bulk RNA-seq data (QC, alignment, quantification, normalization, clustering, annotation, etc.).

• Apply standard and advanced analyses using tools like Scanpy, Seurat, and R/Bioconductor packages.

• Process and interpret data from state-of-the-art single-cell transcriptomic and multiomic platforms, alongside new in-house protocols being developed to enable innovative microbiological sequencing workflows.

• Collaborate with wet lab scientists to support experimental design and data interpretation.

• Mentor and foster collaboration and knowledge sharing across disciplines.

• Help design and validate cutting-edge protocols for novel transcriptomic technologies, integrating new experimental modalities with bioinformatics pipeline.

Qualifications:

• PhD in Bioinformatics, Genomics, Computational Biology, or a related field. Equivalent industry experience is also welcome

• 3+ years of hands-on experience analyzing large-scale single-cell or bulk transcriptomic datasets

• Proficiency with common genomics tools: SAMtools, STAR/STARsolo, Bowtie, Tophat, HTSeq, Clustal, bash scripting, etc.

• Strong command of Scanpy or Seurat

• Demonstrated fluency in Nextflow/Snakemake and workflow reproducibility principles.

• Strong R and/or Python programming skills

• Excellent organizational and documentation habits

Preferred Qualifications:

• Experience working in a quantitative lab or with biotech/pharma pipelines

• Experience working in a fast-paced startup or interdisciplinary team

• The opportunity to contribute to platform technologies with real-world therapeutic impact

• Experience working at the interface of technology development and data analysis, particularly involving novel molecular biology or sequencing techniques

What We Offer

• A mission-driven team reshaping healthcare through innovation in AI and cellular engineering

• The opportunity to contribute to platform technologies with real-world therapeutic impact

• Competitive compensation and equity in a high-growth company

• Flexible work arrangements, generous benefits, and a collaborative environment

Exceptional candidates who demonstrate outstanding capabilities and potential will be considered, even if they do not meet every qualification listed.

Join us and help unlock the full potential of AI for the benefit of human health

Somite is committed to equal employment opportunity and non-discrimination for all employees and applicants regardless of race, color, ancestry, sex, sexual orientation, age, religion, national origin, ancestry, genetic information, disability, veteran status, marital status, citizenship status, or any characteristic protected under applicable law.