Author

Jose A. Bird

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Preprint Aug 2026

Orchestra: Corroboration-Based Regulatory Candidate Discovery via Composed Bioinformatics MCP Agents

Orchestra composes two independently built bioinformatics MCP servers -- RegNetAgents, which infers gene regulatory network topology from ARACNe networks, and CASCADE, which supplies four independent evidence sources (LINCS knockdown, DepMap essentiality, super-enhancer status, DoRothEA transcription-factor confidence)...

Jose A. Bird · 0 citations

#artificial intelligence Preprint Aug 2026

CASCADE: An Agentic Regulatory Network Framework for Patient-Data-Validated Downstream Perturbation Prediction

CASCADE is an agentic framework that predicts downstream transcriptional effects of gene perturbation from precomputed ARACNe regulatory networks, exposed via MCP. Prior work validates such tools by checking whether predicted genes are known cancer genes (membership); we instead test whether the predicted direction of...

Jose A. Bird · 1 citation