About
A curated, classified, audited atlas
The Atlas is a continuously maintained companion to the review paper. It is intentionally curated rather than crowdsourced: every method is placed in the taxonomy with a written rationale, and authors are invited to discuss placements directly with the maintainer.
Scope
The Atlas indexes published computational methods that, given a source-cell distribution and a target identity or phenotype, predict an intervention designed to move the source toward the target. This is the same scope as the companion review: methods that explicitly produce an intervention $u$ for a source–target pair.
Closely related upstream tools — trajectory inference, optimal transport, RNA-velocity extensions, single-cell energy-landscape inference, quasi-potential analyses — are enabling tools rather than intervention-design methods and are not part of the indexed corpus.
Methodology
Each method receives:
- One level placement (L0, L1, L2, or L3) with a written rationale that ties the placement to the role the intervention $u$ plays in the method's objective.
- One representation family (signature / state-matching, regulatory-network influence, or executable intervention model).
- One or more modalities (I, D, T, P), taken from the original publication.
- An audit of code availability, reproducibility (0–4), and FAIR4RS compliance (0–5), refreshed periodically.
Maintainer
The Atlas is maintained by Paola Vera-Licona. Submissions and corrections from method authors are handled directly — see /submit.
Versioning & updates
Each release is tagged. Methods are re-audited periodically; their audit dates appear on every method page. A changelog records additions, re-placements, and re-audits across releases.
Citation
To cite this site:
Vera-Licona, P. (2026). Atlas of Computational Cell Reprogramming (companion site to "Computational Cell Reprogramming: Shared Principles, Distinct Constraints"), version v0.1.
A Zenodo DOI will be minted at publication of the companion review and added here.