Inverse design fidelity
Uses an empirical or learned proxy response map (signature reversal, latent displacement, drug-response prediction, or network propagation) rather than a mechanistic model.
Methods at this level
Sorted by publication year, oldest first.
Alvarez et al. · 2018 · Cancer Discovery
Classical Level 2 proxy method. Estimates master-regulator activity with VIPER and ranks compounds by their ability to reverse that activity profile against perturbation atlases.
Marazzi L et al. · 2020 · Bioinformatics (Oxford, England)
SUMMARY: OCSANA+ is a Cytoscape app for identifying nodes to drive the system toward a desired long-term behavior, prioritizing combinations of interventions in large-scale complex networks, and estimating the effects…
Napolitano F et al. · 2021 · Stem cell reports
Controlling cell fate has great potential for regenerative medicine, drug discovery, and basic research.
Tran A et al. · 2022 · NAR genomics and bioinformatics
Cell reprogramming offers a potential treatment to many diseases, by regenerating specialized somatic cells.
Han L et al. · 2023 · Communications biology
Cellular transitions hold great promise in translational medicine research.
Zheng M et al. · 2023 · Stem cell reports
Cellular conversion can be induced by perturbing a handful of key transcription factors (TFs).
Hamano M et al. · 2024 · Bioinformatics (Oxford, England)
MOTIVATION: Direct reprogramming (DR) is a process that directly converts somatic cells to target cells.
Wytock TP et al. · 2024 · Proceedings of the National Academy of Sciences of the United States of America
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene…
DeMeo B et al. · 2025 · Science (New York, N.Y.)
Phenotypic drug screening remains constrained by the vastness of chemical space and the technical challenges of scaling experimental workflows.
Jung S et al. · 2025 · Aging
Great efforts have been devoted to discovering rejuvenation strategies that counteract age-related functional decline and improve cellular functions in humans.
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