Senior/Principal Scientist, Single-Cell Transcriptomics

Research & Development Cambridge, Massachusetts


Company Overview

Repertoire Immune Medicines is a clinical-stage biotechnology company working to unlock and direct the remarkable power of the human immune system to prevent or treat cancer, as well as autoimmune and infectious disease.  The company is founded on the belief that the repertoire of T cell receptor (TCR)-antigen codes that drive health and disease represents one of the greatest opportunities for innovation in medical science.  Repertoire scientists created and developed the DECODE and DEPLOY suite of technologies, which allow in-depth characterization of TCR-antigen pairs, and the ability to rationally design and develop novel targeted immune medicines.

From its sites in Cambridge, Mass., and Zurich, Switzerland, Repertoire’s team of more than 120 is creating a new category of immune medicines enabled from its DECODE discovery platform.  The company’s first product in the clinic is a novel multiclonal T cell therapy consisting of T cells derived from the peripheral blood, activated against a curated set of antigens and armed with a proprietary cytokine.  Repertoire is in clinical-stage immuno-oncology development today, targeting metastatic solid tumors.  In the field of autoimmunity, Repertoire is currently using its proprietary platform to discover novel epitopes and TCRs from patients with type 1 diabetes.  We are currently expanding our remit into other autoimmune disorders.  The company is also using its DECODE platform to discover infectious disease antigens and responding T cell clones.

Role Overview

Repertoire Immune Medicines is seeking an experienced computational biologist to build cutting edge computational methods across a wide range of clinical indications.  The Senior/Principal Scientist of single-cell transcriptomics will be a member of the computational analytics team.  S/he will lead our single-cell transcriptomics efforts applying biological and computational insights to describe cellular phenotype and function serving various groups across the R&D organization including platform discovery and translational research.  This position may have one or more direct reports.

Repertoire has recently expanded the scope of its computational efforts and will be further integrating computational biology into all facets of the DECODE and DEPLOY platforms.  Given this expanding scope, the successful candidate will have the opportunity to further build out a team to serve the needs of the organization.  The computational analytics group will work side-by-side with the computational engineering group interfacing directly with our platform discovery, translational medicine, and clinical teams to scope, build, and implement computational solutions.  The ability to work in a fast-paced, highly collaborative environment will be critical to success.

Key Responsibilities

  • Provide leadership in single-cell analytics to scope, build, and deploy tools for phenotype characterization.
  • Contribute methods, models, and visualization tools for platform discovery and translational research.
  • Lead the development and deployment of computational methods for interpreting single-cell transcriptomics and proteomics data.
  • Develop and implement methods for dimensionality reduction, heterogenous cell population visualization, cell typing, and phenotypic feature identification.
  • Work across teams to integrate phenotype with TCR repertoire characterization.
  • Provide guidance to discovery projects around the application of single-cell phenotype data.
  • Ensure proper documentation of code, workflows, reports, and analyses.
  • Manage and execute multiple projects across matrixed teams working with leadership to meet short timelines while maintaining scientific rigor.
  • Provide transparency and regular communication on project status, setbacks, and modification of strategy.
  • Seek out external resource and expertise when required.


Basic Qualifications

  • Ph.D. in Computational Biology, Bioinformatics, Statistics, Computer Science with 6+ years’ experience in biotech/pharma industry.
  • Proven ability to manage people and projects.
  • Extensive experience analyzing single-cell data.
  • Experience with 10X Genomics Cell Ranger data outputs.
  • Extensive experience with dimensionality reduction techniques including UMAP, tSNE.
  • Deep biological knowledge in single-cell transcriptomics and proteomics.
  • Technical proficiency in Python and R.
  • Experience with computational methods for single-cell RNA expression analysis (eg. scanpy, SingleR, Seurat, etc.).
  • Proven ability to develop or apply new tools for the integrative analysis and visualization of multi-dimensional datasets.
  • Excellent verbal, written, analytical, and presentation communication skills.
  • Ability to meet critical timelines.

Preferred Qualifications

  • Experience with machine learning algorithms.
  • Experience in data analysis using cloud computing infrastructure.
  • Ability to showcase technologies with external partners to support business development activities.
  • Strong scientific publication record.
  • Experience in discovery research or translational medicine.


Repertoire is committed towards social responsibility and developing an inclusive culture.  Much as the power of the immune system lies in the diversity of T and B cells, we believe that our work requires the creativity and ingenuity of a diverse workforce, and we are committed to pursuing that in all facets of the work experience at Repertoire.  We will continue to educate ourselves about the inequities and barriers present in our society and act as a company where we can make a difference.

Repertoire is proud to be an Equal Opportunity Employer.