Scientist II, Computational Biology (Single Cell & Spatial)

ABOUT eGENESIS eGenesis is a clinical-stage biotechnology company developing human-compatible engineered organs to address the severe global organ shortage. The Company’s proprietary genome engineering platform enables extensive, multiplex gene edits to remove key biological barriers, add protective human transgenes, and inactivate endogenous retroviruses. EGEN-2784, a genetically engineered porcine kidney, is the Company’s lead program and is currently being evaluated in a multi-patient Expanded Access study at MGH. eGenesis is headquartered in Cambridge, MA.

At eGenesis, our core values—innovation, collaboration, compassion, resilience, and passion—are at the center of how we work. We engineer hope and bring passion to everything we do. We collaborate and learn from one another, combining diverse expertise to tackle complex challenges. We innovate boldly, pushing boundaries and science to new heights. where no pig organ has gone before. With resilience, we navigate challenges and celebrate progress together. And in all we do, we lead with compassion—for our patients, our people, and our pigs.

POSITION SUMMARY We are seeking a highly skilled and motivated Scientist II with expertise in single cell and spatial genomics data analysis. The ideal candidate will play a key role in unraveling the cellular and spatial architecture of engineered organs and immune interactions in our translational research programs. This is a unique opportunity to drive high-impact research at the intersection of genomics, immunology, and synthetic biology.

PRIMARY RESPONSIBILITIES

• Identify and frame open biological questions across our programs, define the analytical strategy to address them, and set your own priorities with minimal day-to-day direction.
• Lead the design, analysis, and interpretation of single cell RNA-seq and spatial transcriptomics experiments.
• Integrate multimodal datasets, including spatial transcriptomics, scRNA-seq, proteomics, metabolomics, pathology and clinical metadata, to uncover insights into tissue remodeling and immune responses.
• Collaborate with cross-functional teams including wet lab scientists, immunologists, bioinformaticians, clinicians and translational scientists.
• Develop scalable pipelines for high-dimensional single cell and spatial datasets, and build new analytical approaches where existing tools fall short (e.g., cross-species cell mapping, sparse or incomplete reference annotations).
• Perform spatially resolved analyses of cell states, tissue architecture, cell-cell interactions, and molecular programs associated with graft injury, inflammation, remodeling, and repair.
• Translate biological and translational questions into computational analyses and testable hypotheses, with interpretation grounded in immunological mechanisms and xenotransplant biology.
• Present findings to internal stakeholders and contribute to publications and patents.

BASIC QUALIFICATIONS

• PhD in Computational Biology, Genomics, Bioinformatics, Immunology, or a related field.
• 3+ years of postdoctoral or industry experience analyzing single cell and spatial data, including scRNA-seq and spatial transcriptomics.
• Demonstrated experience leading computational projects from experimental design and data QC through biological interpretation and communication of results.
• Strong proficiency with R and/or Python for statistical computing and data visualization.
• Deep understanding of immune cell biology and ability to interpret immune-related transcriptional signatures.
• Hands-on experience analyzing spatial transcriptomics data from at least one sequencing-based or imaging-based platform (e.g., Visium/Visium HD, Xenium, Trekker, Seeker); experience integrating across platforms is a strong plus. Candidate should have an understanding of platform-specific strengths, limitations, and analytical considerations.
• Fluency with standard single cell and spatial analysis tools (e.g., Seurat, Scanpy, Cell Ranger, SpatialData, Squidpy).
• Practical experience using AI tools (e.g., LLM-based coding assistants and agents) to speed up analysis and software development, with the judgment to check AI-generated code and results critically.
• Track record of independently defining and answering open research questions, where the question, approach, or method was not set in advance, as shown by first-author publications, novel methods, or equivalent industry work.

135000 - 165000 USD a year