Atlas of Computational Cell Reprogramming
A maintained compendium of peer reviewed computational methods for cell reprogramming, intended as a durable reference for the field. Entries are classified by inverse intervention explicitness class (C0, C1, C2, C3) and cell reprogramming modality, with reproducibility assessed in a uniform audit of code availability, practical rerunnability, and FAIR4RS compliance.
Computational Cell Reprogramming: A Cross-Modality Framework for Cellular Intervention Design · Under submission, 2026
Inverse intervention explicitness
The taxonomy sorts reviewed methods by how completely they instantiate the shared inverse design objective below. Explicitness refers to which mathematical objects enter the formulation (source and target states, admissible interventions, forward map, mismatch functional, and feasibility penalty), not biological accuracy or held-out performance.
The reprogramming modalities
The four reprogramming modalities are typed versions of the same intervention design question. Select a modality below to read its definition and browse indexed methods.
Indexed methods
Browse the full compendium, search by name or class, and open any entry for placement rationale, reproducibility scores, and links to the primary paper and source code. Browse the compendium.
Reproducibility audit
A uniform audit of code availability, practical rerunnability, and FAIR4RS compliance across the indexed methods. Filter and sort the corpus on the reproducibility page. Open the audit explorer.
Benchmarking
Cross method benchmark suites are in preparation. Until assessments are published, validation evidence for each method appears on its method page. View benchmarking status.
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