We're the bioinformatics and computational team at the Tufts University Center for Cellular Agriculture (TUCCA), building open-source tools, libraries, and pipelines that accelerate cell-cultured-meat and alternative-protein research.

Bioinformatics pipelines — Production-quality workflows for the wet- and dry-lab work at TUCCA.

• tucca-rna-seq — RNA-Seq workflow for read quantification, differential expression, and pathway enrichment analysis. We're considering converting tucca-rna-seq into a custom Nextflow pipeline that handles downstream RNA-Seq analysis on top of nf-core/rnaseq as its upstream counterpart — potentially built as an extension or fork of nf-core/differentialabundance.

AI for cellular agriculture — Curated knowledge bases and computational frameworks at the intersection of AI/ML and cell-ag.

• caail — Cellular Agriculture AI Library. A curated, open-source library of papers, software, datasets, and educational resources for applying AI to cell-ag problems (CC-BY-4.0).

Additional research initiatives are in progress as private repositories and will be made public alongside their associated publications and challenge-phase completions.

Recent computational and bioinformatics publications from TUCCA and the Kaplan Lab:

• Contreras, E. J., Nagarajan, A., Bromberg, B. H., Villegas, M. P., & Kaplan, D. L. (2026). Comparative transcriptomics of adherent and suspension chicken fibroblast cell lines for the optimization of cultivated meat processes. Food Research International. https://doi.org/10.1016/j.foodres.2026.118368
• Lee, D. S., Park, B., Salgado, S., Dolgin, J., & Kaplan, D. L. (2026). Computational design of blue melanin with peptide motif scaffolding. bioRxiv. https://doi.org/10.64898/2026.02.02.703104
• Datta, B., Buehler, M. J., Chow, Y., Gligoric, K., Jurafsky, D., Kaplan, D. L., Ledesma-Amaro, R., Del Missier, G., Neidhardt, L., Pichara, K., Sanchez-Lengeling, B., Schlangen, M., St. Pierre, S. R., Tagkopoulos, I., Thomas, A., Watson, N. J., & Kuhl, E. (2025). Artificial Intelligence for Food Innovation. arXiv. https://doi.org/10.48550/arXiv.2509.21556
• McNulty, M. J., Stout, A. J., & Kaplan, D. L. (2025). Meating the moment. EMBO Reports. https://doi.org/10.1038/s44319-025-00492-8

The Tufts University Center for Cellular Agriculture (TUCCA) is an academic research center headquartered at Tufts University, working across cell biology, bioprocess engineering, scaffolding, tissue engineering, sensory science, and AI/ML for cellular agriculture.

• Website: https://cellularagriculture.tufts.edu/
• Twitter / X: @tuftscellag
• Bioinformatics contact: benjamin.bromberg@tufts.edu