← 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

Pluripotency induction

This page records Pluripotency induction and the 14 indexed methods for this reprogramming modality. Search the corpus below; the modality definition follows.

Definition

Global reset of a somatic distribution toward a distant pluripotent attractor.

Find a method for induction

14 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.

I D T P

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.

I D T

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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No code Repro N/A FAIR N/A

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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No code Repro N/A FAIR N/A

DGC (Data Guided Control)

Ronquist S et al. · 2017 · Proceedings of the National Academy of Sciences of the United States of America

The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away.

I T

No code Repro N/A FAIR N/A

ANANSE

Xu Q et al. · 2021 · Nucleic acids research

Proper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors.

I T

Code Repro 4/4 FAIR 3/5

DECCODE

Napolitano F et al. · 2021 · Stem cell reports

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

Code Repro 2/4 FAIR 3/5

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.

I D T

Code Repro 4/4 FAIR 0/5

Taiji-reprogram

Wang J et al. · 2021 · NAR genomics and bioinformatics

Cellular reprogramming is a promising technology to develop disease models and cell-based therapies.

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Code Repro 2/4 FAIR 0/5

CELLoGeNe

Andersson E et al. · 2022 · iScience

Experimental and computational efforts are constantly made to elucidate mechanisms controlling cell fate decisions during development and reprogramming.

Code Repro 3/4 FAIR 0/5

PC3T

Han L et al. · 2023 · Communications biology

Cellular transitions hold great promise in translational medicine research.

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Code Repro N/A FAIR N/A

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

Transfer Learning (Wytock & Motter)

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…

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Code Repro 4/4 FAIR 1/5

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