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.

u^{⋆} = ar g u \in U min [D (F (P_{S}, u), P_{T}) + λ R (u)]

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 C2 · Proxy inverse design

This page records Class C2 and the 10 indexed methods placed in this explicitness class. Search the corpus below; the class equation and definition follow.

Class equation

u^{⋆} = ar g u min D (\hat{F}_{proxy} (P_{S}, u), P_{T}) + λ R (u)

Canonical objective for this explicitness class.

Definition

Uses an empirical or learned proxy response map (signature reversal, latent displacement, drug-response prediction, or network propagation) rather than a mechanistic model.

Find a method in Class C2

10 methods

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

OncoTreat

C2

Alvarez et al. · 2018 · Cancer Discovery

Classical Level 2 proxy method. Estimates master-regulator activity with VIPER and ranks compounds by their ability to reverse that activity profile against perturbation atlases.

P

Code Repro 3/4 FAIR 3/5

OCSANA+

C2

Marazzi L et al. · 2020 · Bioinformatics (Oxford, England)

SUMMARY: OCSANA+ is a Cytoscape app for identifying nodes to drive the system toward a desired long-term behavior, prioritizing combinations of interventions in large-scale complex networks, and estimating the effects…

D P

Code Repro 4/4 FAIR 2/5

DECCODE

C2

Napolitano F et al. · 2021 · Stem cell reports

Controlling cell fate has great potential for regenerative medicine, drug discovery, and basic research.

I

Code Repro 2/4 FAIR 3/5

scREMOTE

C2

Tran A et al. · 2022 · NAR genomics and bioinformatics

Cell reprogramming offers a potential treatment to many diseases, by regenerating specialized somatic cells.

D

Code Repro 2/4 FAIR 0/5

PC3T

C2

Han L et al. · 2023 · Communications biology

Cellular transitions hold great promise in translational medicine research.

I D T

Code Repro N/A FAIR N/A

SiPER

C2

Zheng M et al. · 2023 · Stem cell reports

Cellular conversion can be induced by perturbing a handful of key transcription factors (TFs).

I D T P

Code Repro 4/4 FAIR 1/5

DIRECTEUR

C2

Hamano M et al. · 2024 · Bioinformatics (Oxford, England)

MOTIVATION: Direct reprogramming (DR) is a process that directly converts somatic cells to target cells.

T

Code Repro 2/4 FAIR 0/5

Transfer Learning (Wytock & Motter)

C2

Wytock TP et al. · 2024 · Proceedings of the National Academy of Sciences of the United States of America

Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene…

I T P

Code Repro 4/4 FAIR 1/5

DrugReflector

C2

DeMeo B et al. · 2025 · Science (New York, N.Y.)

Phenotypic drug screening remains constrained by the vastness of chemical space and the technical challenges of scaling experimental workflows.

D P

Code Repro 4/4 FAIR 3/5

REVIVE

C2

Jung S et al. · 2025 · Aging

Great efforts have been devoted to discovering rejuvenation strategies that counteract age-related functional decline and improve cellular functions in humans.

P

Code Repro 2/4 FAIR 1/5