← Cellular intervention design framework

Four reprogramming modalities

Pluripotency induction, directed differentiation, transdifferentiation, and phenotype reprogramming are not four unrelated computational questions. They are four constraint regimes on the same intervention design syntax: each modality fixes how source state, target state, admissible interventions, and feasibility penalties enter the template. Select a modality for its definition and indexed methods.

Reprogramming modality

Directed differentiation

This page records Directed differentiation and the 25 indexed methods for this reprogramming modality. Search the corpus below; the modality definition follows.

Definition

Trajectory guidance from a pluripotent or progenitor state toward a defined lineage endpoint, usually with waypoint constraints.

Find a method for differentiation

25 methods

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

DEPCs (Crespo et al. 2013)

Crespo I et al. · 2013 · BMC systems biology

BACKGROUND: Cellular differentiation and reprogramming are processes that are carefully orchestrated by the activation and repression of specific sets of genes.

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No code Repro N/A FAIR N/A

FVS (Mochizuki et al.)

Mochizuki A et al. · 2013 · Journal of theoretical biology

Modern biology provides many networks describing regulations between many species of molecules.

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No code Repro N/A FAIR N/A

CellNet

Cahan et al. · 2014 · Cell

Canonical Level 1 method. Reconstructs cell-type-specific GRNs from expression data and prioritizes regulators whose perturbation is expected to restore the target network.

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Code Repro 4/4 FAIR 3/5

Hopfield Neural Networks (Lang et al.)

Lang AH et al. · 2014 · PLoS computational biology

A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network.

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Stable Motifs

Zañudo JG et al. · 2015 · PLoS computational biology

Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming.

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Code Repro 4/4 FAIR 0/5

Toggle Switches (Okawa et al.)

Okawa S et al. · 2016 · Stem cell reports

Identification of cell-fate determinants for directing stem cell differentiation remains a challenge.

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Del Vecchio et al.

Del Vecchio D et al. · 2017 · Cell systems

To artificially reprogram cell fate, experimentalists manipulate the gene regulatory networks (GRNs) that maintain a cell's phenotype.

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Zañudo et al. (FVS control)

Zañudo JGT et al. · 2017 · Proceedings of the National Academy of Sciences of the United States of America

What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that…

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Code Repro 4/4 FAIR 0/5

SeesawPred

Hartmann A et al. · 2018 · Scientific reports

Cellular differentiation is a complex process where a less specialized cell evolves into a more specialized cell.

Code Repro 4/4 FAIR 1/5

BoolIFFNN

Choo SM et al. · 2020 · Frontiers in physiology

The molecular regulatory network (MRN) within a cell determines cellular states and transitions between them.

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OCSANA+

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…

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Code Repro 4/4 FAIR 2/5

TransSynW

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

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

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Code Repro 4/4 FAIR 0/5

IRENE

Jung S et al. · 2021 · Nature communications

Human cell conversion technology has become an important tool for devising new cell transplantation therapies, generating disease models and testing gene therapies.

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Code Repro 4/4 FAIR 0/5

NETISCE

Marazzi L et al. · 2022 · NPJ systems biology and applications

The search for effective therapeutic targets in fields like regenerative medicine and cancer research has generated interest in cell fate reprogramming.

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Code Repro 4/4 FAIR 3/5

scREMOTE

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

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

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CellOracle

Kamimoto K et al. · 2023 · Nature

Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks1.

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PC3T

Han L et al. · 2023 · Communications biology

Cellular transitions hold great promise in translational medicine research.

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scANANSE

Smits JGA et al. · 2023 · F1000Research

The recent development of single-cell techniques is essential to unravel complex biological systems.

Code Repro 4/4 FAIR 3/5

SiPER

Zheng M et al. · 2023 · Stem cell reports

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

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Code Repro 4/4 FAIR 1/5

CAESAR

Kim N et al. · 2024 · Briefings in bioinformatics

The tendency for cell fate to be robust to most perturbations, yet sensitive to certain perturbations raises intriguing questions about the existence of a key path within the underlying molecular network that…

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Code Repro 3/4 FAIR 0/5

BoNesis + CABEAN

Chevalier S et al. · 2025 · NPJ systems biology and applications

Boolean networks provide robust, explainable, and predictive models of cellular dynamics, especially for cellular differentiation and fate decision processes.

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Code Repro 4/4 FAIR 3/5

CellCartographer

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.

Code Repro 3/4 FAIR 0/5

DrugReflector

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.

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Code Repro 4/4 FAIR 3/5

SwitchTFI

Martini P et al. · 2025 · Genome biology

Many methods exist that infer cell differentiation trajectories from single-cell RNA sequencing data, but only few determine which mechanisms drive the inferred differentiation dynamics.

Code Repro 4/4 FAIR 4/5

TFcomb

Li C et al. · 2025 · Genome research

Reprogramming cell state transitions provides the potential for cell engineering and regenerative therapy.

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Code Repro 4/4 FAIR 3/5