Welcome to the GitHub organization for the Musser Lab, led by Jacob M. Musser, Assistant Professor in the Department of Molecular, Cellular, and Developmental Biology at Yale University.
Our research focuses on understanding the origin, diversification, and evolution of animal cell types, with particular emphasis on early-branching animal lineages and comparative single-cell and multi-omics approaches.
🌐 Lab website: https://www.musserlab.org
A central goal of the Musser Lab is to reconstruct how novel cell types, tissues, and functional systems evolved over deep evolutionary time. We combine comparative genomics, single-cell transcriptomics, spatial and functional assays, and phylogenetic theory to address questions such as:
- How are cell types organized into evolutionary families and lineages?
- What molecular programs define conserved versus lineage-specific cell types?
- How do gene regulatory networks and signaling pathways evolve in differentiated cells?
- What can early-diverging animals tell us about the origins of nervous systems, contractile tissues, and epithelial organization?
Much of our work focuses on non-bilaterian animals, particularly:
- Sponges (Porifera) — e.g. Spongilla
- Cnidarians — e.g. Nematostella, Acropora
We also integrate data from bilaterians and vertebrates to place these findings in a broader evolutionary context.
This GitHub organization hosts code, workflows, and documentation associated with research conducted in the Musser Lab. Repositories may include:
- Analysis pipelines for single-cell RNA-seq, spatial transcriptomics, and comparative genomics
- Reproducible workflows for phylogenomics, cell type alignment, and evolutionary inference
- Data management schemas and tooling for large, multi-omic datasets
- Supplementary code and notebooks associated with published or in-preparation manuscripts
Many repositories are internal during active development and may be made public at the time of publication.
Please note:
- Some repositories represent work in progress and may change without notice.
- Code may prioritize clarity and reproducibility over optimization.
- Not all datasets referenced in code repositories are publicly available; access may depend on publication status or data-use agreements.
If you are interested in using or adapting code from this organization and have questions about scope or readiness, please reach out.
When associated with publications, data are typically deposited in appropriate public repositories (e.g. GEO, SRA, ENA) and linked from the relevant GitHub repository and/or manuscript.
GitHub repositories generally contain:
- Code
- Configuration files
- Documentation
- Lightweight metadata
Rather than raw sequencing data.
We welcome collaboration and scientific discussion.
If you are interested in:
- Reusing analysis pipelines
- Adapting methods for comparative cell type evolution
- Contributing improvements or extensions
please open an issue in the relevant repository or contact the lab directly via the website.
For current lab members, research projects, and contact information, please see:
If you use code or workflows from this organization in published work, please cite the associated manuscript (if available) or acknowledge the Musser Lab.
Specific citation instructions are provided in individual repositories where applicable.
© Musser