Publications
Dunn, C. W., Schultz, D. T., & Musser, J. M. (2026). Designing reproducible large-language-model-assisted scientific analyses. Patterns. https://doi.org/10.1016/j.patter.2026.101644
Wang, L., Davis, S., Quilitz, T., Beavis, T., Bonadonna, M., Lamprousi, M., Montanari, R., Ruperti, F., Stokkermans, A., Wiegand, T., Witte, V. A., Ortiz, A. G., Dorrity, M., Siemens, J., Musser, J., Arendt, D., Leisch, N., Vincent, F., Ikmi, A., Prevedel, R. (2026). A mobile optical coherence microscope for studying aquatic organisms in-and outside the laboratory. bioRxiv, 2026-07. https://doi.org/10.64898/2026.07.27.740915
Danladi, B., Al-Shaer, L., Jia, K., Havrilak, J. A., Faltine-Gonzalez, D., Forwood, W., DuBuc, T., Musser, J. M., & Layden, M. J. (2026). Lineage-specific elaboration of a conserved cnidogenic program drives cnidocyte diversification and illuminates cell type evolution. Research square, rs.3.rs-10009230. https://doi.org/10.21203/rs.3.rs-10009230/v1
Dehghannasiri, R., Kokot, M., Starr, A. L., Maziarz, J., Gordon, T., Tan, S. Y., Wang, P. L., Voskoboynik, A., Musser, J. M., Deorowicz, S., & Salzman, J. (2026). Reference-free discovery with barcoded single-cell sequencing. Nature Biotechnology. https://doi.org/10.1038/s41587-026-03084-6
Zang, R. X., Malaiwong, N., Wang, L., Maziarz, J. D., Jia, K., Drotleff, B., Frank S., Noor M., Roberts C. J., Rettel M., Schwarz J. J., Ikmi A., Watanabe S., Prevedel R., O'Donnell M. P., & Musser, J. M. (2026). An ancient monoaminergic signaling system coordinates contractility in a nerveless sponge. bioRxiv.
https://doi.org/10.64898/2026.02.14.704838
Oel A. P., Cros C., Christophe D. R., Pan L., Buglakova E., Haury P. S., Santangeli L., Gerber T., Papalopoulos N., Vergara H. M., Puga D., Disela V., Niederhaus L., Bertucci P. Y., Witte V., Bilgesu K. A., Quintana U. I., Acevedo J. M., Musser J. M., Kreshuk A., Arendt D. (2025). A whole-body cell type atlas mapped into an electron microscopy volume of an annelid worm. bioRxiv. https://doi.org/10.1101/2025.10.30.685666
Sebé-Pedrós A., Tanay A, Lawniczak M. K. N., Arendt D., Aerts S., Archibald J., Arnone M. I., Blaxter M. , Cleves P., Coelho S. M., Dias M., Dunn C., Elek A., Frazer J., Gabaldón T., Gillis J., Grau-Bové X., Guigó R., Hobert O., Huerta-Cepas J, Irimia M, Klein A, Lewin H, Lowe CJ, Marlow H., Musser J. M., Nagy LG, Najle S. R., Pachter P., Paez S., Papatheodorou I., Passalacqua M. J., Rajewsky N., Rhee S. Y., Richards T. A., Sauka-Spengler T., Saunders L. M., Seuntjens E., Solana J., Song Y., Technau U., Wang B. & Biodiversity Cell Atlas meeting participants (2025). The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution. Nature 645, 877–885. https://doi.org/10.1038/s41586-025-09312-4
Picciani N., Berger C. A., Nielsen S., Musser J., Oel A. P., Stoilova M. I., Arendt D., Garm A., Oakley T. H. (2025). Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes. Ecology and Evolution 15:e71784. https://doi.org/10.1002/ece3.71784
Musser, JM. (2024). Tripartite origin of the chordate brain. Nature Ecology & Evolution 8, 1782-1783.
Chicago. https://doi.org/10.1038/s41559-024-02528-z
Ruperti, F., Becher, I., Stokkermans, A., Wang, L., Marschlich, N., Potel, C., Maus, E., Stein, F., Drotleff, B., Schippers, K. J., Nickel, M., Prevedel, R., Musser, J. M., Savitski, M. M., & Arendt, D. (2024). Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response. Current biology 34, 361–375.e9. https://doi.org/10.1016/j.cub.2023.12.021
Piovani, L., Leite, D. J., Yañez Guerra, L. A., Simpson, F., Musser, J. M., Salvador-Martínez, I., Marlétaz, F., Jékely, G., & Telford, M. J. (2023). Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories. Science advances 9, eadg6034. https://doi.org/10.1126/sciadv.adg6034
Ruperti, F., Papadopoulos, N., Musser, J. M., Mirdita, M., Steinegger, M., & Arendt, D. (2023). Cross-phyla protein annotation by structural prediction and alignment. Genome biology 24, 113. https://doi.org/10.1186/s13059-023-02942-9
Almazán, A., Çevrim, Ç., Musser, J. M., Averof, M., & Paris, M. (2022). Crustacean leg regeneration restores complex microanatomy and cell diversity. Science advances 8, eabn9823. https://doi.org/10.1126/sciadv.abn9823
Tarashansky, A. J., Musser, J. M., Khariton, M., Li, P., Arendt, D., Quake, S. R., & Wang, B. (2021). Mapping single-cell atlases throughout Metazoa unravels cell type evolution. eLife 10, e66747. https://doi.org/10.7554/eLife.66747
Paganos, P., Voronov, D., Musser, J. M., Arendt, D., & Arnone, M. I. (2021). Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. eLife 10, e70416. https://doi.org/10.7554/eLife.70416
Musser, J. M., Schippers, K. J., Nickel, M., Mizzon, G., Kohn, A. B., Pape, C., Ronchi, P., Papadopoulos, N., Tarashansky, A. J., Hammel, J. U., Wolf, F., Liang, C., Hernández-Plaza, A., Cantalapiedra, C. P., Achim, K., Schieber, N. L., Pan, L., Ruperti, F., Francis, W. R., Vargas, S., … Arendt, D. (2021). Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science 374, 717–723. https://doi.org/10.1126/science.abj2949
Arendt, D., Bertucci, P. Y., Achim, K., & Musser, J. M. (2019). Evolution of neuronal types and families. Current opinion in neurobiology 56, 144–152. https://doi.org/10.1016/j.conb.2019.01.022
Liang, C., Musser, J. M., Cloutier, A., Prum, R. O., & Wagner, G. P. (2018). Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes. Genome biology and evolution, 10, 538–552. https://doi.org/10.1093/gbe/evy016
Arendt, D., Musser, J. M., Baker, C. V. H., Bergman, A., Cepko, C., Erwin, D. H., Pavlicev, M., Schlosser, G., Widder, S., Laubichler, M. D., & Wagner, G. P. (2016). The origin and evolution of cell types. Nature reviews. Genetics, 17(12), 744–757. https://doi.org/10.1038/nrg.2016.127