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Atlas of Computational Cell Reprogramming

← Cellular intervention design framework

Inverse intervention explicitness

Indexed methods are classified by how completely they instantiate the intervention design template above. Explicitness refers to which mathematical object is present in the formulation, not biological accuracy, causal identifiability, or held out performance. Not every method that outputs actionable perturbations is a formal inverse design method; higher class does not mean a better method.

Idealized intervention design template (Section 2 of the companion review). Classes C0, C1, C2, and C3 differ in how much of this objective each indexed method instantiates.

Class C0 · Target-feature discovery

This page records Class C0 and the 5 indexed methods placed in this explicitness class. Search the corpus below; the class equation and definition follow.

Class equation

Canonical objective for this explicitness class.

Definition

Uses the target state to identify characteristic factors or features; no source-to-target intervention model.

5 methods

Matches method names, authors, paper titles, journals, PMIDs/DOIs, explicitness class, modalities, frameworks, and audit scores.

D'Alessio et al.

C0

D'Alessio et al. · 2015 · Stem Cell Reports

Classical Level 0 exemplar. Identifies TFs specifically enriched in a target cell type against a broad background of other lineages.

T
No code Repro N/A FAIR N/A

Okawa & Del Sol (synergistic TF core)

C0

Okawa S et al. · 2019 · Nucleic acids research

Advances in single-cell RNA-sequencing techniques reveal the existence of distinct cell subpopulations.

T
Code Repro 3/4 FAIR 0/5

TransSynW

C0

Ribeiro MM et al. · 2020 · Stem cells translational medicine

Generation of desired cell types by cell conversion remains a challenge.

D T
Code Repro 4/4 FAIR 0/5

CellCartographer

C0

Appleton E et al. · 2025 · Cell reports

The creation of induced pluripotent stem cells (iPSCs) has enabled scientists to explore the function, mechanisms, and differentiation processes of many types of cells.

D
Code Repro 3/4 FAIR 0/5

REPROcode

C0

Kurochkin I et al. · 2026 · Cell systems

Combinatorial barcoded TF screening in HEFs with 3′ scRNA-seq readout to discover immune reprogramming cocktails.

T
Code Repro 4/4 FAIR 3/5