Atlas of Computational Cell Reprogramming
A maintained companion to the review paper: a curated catalog of peer reviewed computational methods for cell reprogramming. The index launched with the 57 methods audited in the review and now lists 57, updated as new peer reviewed methods are added. Methods are classified by explicitness class (C0, C1, C2, C3) and reprogramming modality; reproducibility and validation evidence are recorded under uniform rubrics.
Computational Cell Reprogramming: A Cross-Modality Framework for Cellular Intervention Design · Paola Vera-Licona · 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 catalog of indexed methods, search by name or class, and open any entry for placement rationale, reproducibility scores, and links to the primary paper and source code. Open the methods catalog.
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.
Release v0.1.2. Updates are logged on the changelog. About · Propose a method