Companion to the review
Computational cell reprogramming: a classification of published methods.
Computational Cell Reprogramming: A Cross-Modality Framework for Cellular Intervention Design · Paola Vera-Licona · Under submission, 2026
The Atlas is a maintained, curated index of published computational methods for cell reprogramming. It launches with the 57 methods audited in the companion review and is expanded as new peer-reviewed methods appear. Each entry is classified by inverse-intervention explicitness (C0-C3) and mapped across all four reprogramming modalities.
The classification
Four explicitness classes (C0-C3)
The classes rank methods by how completely they instantiate the shared inverse-design objective, from feature ranking with no intervention model, to explicit forward simulation of each candidate.
Four typed problems
The reprogramming modalities
The four modalities are not four unrelated algorithmic problems; they are four typed versions of the same intervention-design question. Each constrains source state, target geometry, admissible interventions, timescale, and feasibility penalty differently.
Field-level audit
Code, reproducibility, and dataset reuse
Audit figures below refer to the 57-method review corpus frozen at publication. Less than half can be independently rerun; validation data are almost entirely siloed (121 of 129 datasets used by exactly one method). Live audit scores appear on each method page.
57
Review corpus (frozen)
57
Methods indexed on site
43
Review corpus with public code
27
Review corpus rerunnable (4/4)
Curated, not crowdsourced
Authors of new methods are invited to contact the maintainer
The Atlas is curated by Paola Vera-Licona. Each method is placed in the taxonomy with a written rationale; authors of new methods are invited to propose additions and corrections directly.
Propose a method →Maintained index
Site status
Release v0.1.2. 57 methods indexed and updated as new peer-reviewed methods are curated in. Audit scores are refreshed periodically. See the changelog.
Vera-Licona P. Computational Cell Reprogramming: A Cross-Modality Framework for Cellular Intervention Design. Under submission, 2026. Full citation →