References

Abascal, Federico and, Reyes Acosta, Nicholas J. Addleman, et al. 2020. “Expanded Encyclopaedias of DNA Elements in the Human and Mouse Genomes.” Nature 583 (7818): 699–710. https://doi.org/10.1038/s41586-020-2493-4.
“Advanced Setup.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/setup.
“Agent Skills Overview.” n.d. Accessed September 23, 2026. https://agentskills.io/home.
“AGENTS.md.” n.d. Accessed September 23, 2026. https://agents.md/.
“All Settings.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/settings-reference.
Anthropic. 2026. Anthropics/Life-Sciences. Released September 23. https://github.com/anthropics/life-sciences.
“Appendix A — How This Book Was Made – AI in Medicine.” n.d. Accessed September 23, 2026. https://ai-in-medicine.seandavi.workers.dev/appendix/about.
“Appendix C — AI Ledger – AI in Medicine.” n.d. Accessed September 23, 2026. https://ai-in-medicine.seandavi.workers.dev/appendix/ai-ledger.
“Best Practices for Claude Code.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/best-practices.
Bourgon, Richard, Robert Gentleman, and Wolfgang Huber. 2010. “Independent Filtering Increases Detection Power for High-Throughput Experiments.” Proceedings of the National Academy of Sciences 107 (21): 9546–51. https://doi.org/10.1073/pnas.0914005107.
“Checkpointing.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/checkpointing.
“Choose a Permission Mode.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/permission-modes.
“Connect Claude Code to Tools via MCP.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/mcp.
“Desktop Application.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/desktop.
“Documenting Architecture Decisions.” 2011. November 15. https://www.cognitect.com/blog/2011/11/15/documenting-architecture-decisions.
“Extend Claude with Skills.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/skills.
“FAQ.” n.d. Accessed September 23, 2026. https://antigravity.google/docs/faq/.
“Feature Overview.” n.d. Accessed September 23, 2026. https://antigravity.google/docs/features/.
“Get Started with the Desktop App.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/desktop-quickstart.
“Getting Started.” n.d. Accessed September 23, 2026. https://antigravity.google/docs/getting-started/.
“How Claude Remembers Your Project.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/memory.
Howard, Jeremy. 2024. “The /Llms.txt File, V2.” September 3. https://llmstxt.org/.
Johnson, John L, Georgios Georgakilas, Jelena Petrovic, et al. 2018. “Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells.” Immunity 48 (2): 243–257.e10. https://doi.org/10.1016/j.immuni.2018.01.012.
Kassis, Timothy, Vinayak Agarwal, Yuhuan He, Darshil Patel, and Aubrey M. Brueckner. 2026. Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents. Version 2. arXiv. https://doi.org/10.48550/arxiv.2609.00065.
Lee, Benjamin D. 2018. “Ten Simple Rules for Documenting Scientific Software.” PLOS Computational Biology 14 (12): e1006561. https://doi.org/10.1371/journal.pcbi.1006561.
Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-seq Data with DESeq2.” Genome Biology 15 (12). https://doi.org/10.1186/s13059-014-0550-8.
“Migration.” n.d. Accessed September 23, 2026. https://antigravity.google/docs/cli/gcli-migration/.
Noble, William Stafford. 2009. “A Quick Guide to Organizing Computational Biology Projects.” PLoS Computational Biology 5 (7): e1000424. https://doi.org/10.1371/journal.pcbi.1000424.
Sandve, Geir Kjetil, Anton Nekrutenko, James Taylor, and Eivind Hovig. 2013. “Ten Simple Rules for Reproducible Computational Research.” PLoS Computational Biology 9 (10): e1003285. https://doi.org/10.1371/journal.pcbi.1003285.
Shan, Qiang, Xiang Li, Xia Chen, et al. 2021. “Tcf1 and Lef1 Provide Constant Supervision to mature CD8.” Nature Communications 12 (1): 5863. https://doi.org/10.1038/s41467-021-26159-1.
Shan, Qiang, Shaoqi Zhu, Xia Chen, et al. 2022. “Tcf1-CTCF Cooperativity Shapes Genomic Architecture to Promote CD8.” Nature Immunology 23 (8): 1222–35. https://doi.org/10.1038/s41590-022-01263-6.
“Terminal Guide for New Users.” n.d. Accessed September 23, 2026. https://code.claude.com/docs/en/terminal-guide.
“Use Claude Cowork on Web, Desktop, and Mobile Claude Help Center.” 2026. September 16. https://support.claude.com/en/articles/15520349-use-claude-cowork-on-web-desktop-and-mobile.
Walters, William H., and Esther Isabelle Wilder. 2023. “Fabrication and Errors in the Bibliographic Citations Generated by ChatGPT.” Scientific Reports 13 (1). https://doi.org/10.1038/s41598-023-41032-5.
Wang, Wenliang, Aditi Chandra, Naomi Goldman, et al. 2022. “TCF-1 Promotes Chromatin Interactions Across Topologically Associating Domains in T Cell Progenitors.” Nature Immunology 23 (7): 1052–62. https://doi.org/10.1038/s41590-022-01232-z.
“What Is the Model Context Protocol (MCP)?” n.d. Accessed September 23, 2026. https://modelcontextprotocol.io/docs/2026-07-28/getting-started/intro.
Wilson, Greg, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, and Tracy K. Teal. 2017. “Good Enough Practices in Scientific Computing.” PLOS Computational Biology 13 (6): e1005510. https://doi.org/10.1371/journal.pcbi.1005510.
Youngblut, Nicholas D., Christopher Carpenter, Arshia Nayebnazar, et al. 2026. “scBaseCount: An AI Agent-Curated, Standardized, Auto-Updated Single-Cell Data Repository.” Cell 189 (19): 5932–5944.e6. https://doi.org/10.1016/j.cell.2026.08.025.