← Cellular intervention design framework

Four reprogramming settings

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 setting fixes how source state, target state, admissible interventions, and feasibility penalties enter the template. Select a setting for its definition and indexed methods.

Reprogramming setting

Transdifferentiation

This page records Transdifferentiation and the 24 indexed methods for this reprogramming setting. Search the corpus below; the setting definition follows.

Definition

Lateral movement across lineage barriers, often requiring chromatin opening or pioneer-factor-like access.

Find a method for transdifferentiation

24 methods

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

Crespo & Del Sol

Crespo I et al. · 2013 · Stem cells (Dayton, Ohio)

Transcription factor cross-repression is an important concept in cellular differentiation.

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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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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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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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D'Alessio et al.

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.

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Mogrify

Rackham OJ et al. · 2016 · Nature genetics

Transdifferentiation, the process of converting from one cell type to another without going through a pluripotent state, has great promise for regenerative medicine.

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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.

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Okawa & Del Sol (synergistic TF core)

Okawa S et al. · 2019 · Nucleic acids research

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

Code Repro 3/4 FAIR 0/5

Reprogram-Seq

Duan J et al. · 2019 · Cell reports

Ectopic expression of transcription factors (TFs) can reprogram cell state.

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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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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.

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CABEAN

Su C et al. · 2021 · Bioinformatics (Oxford, England)

SUMMARY: Direct cell reprogramming, also called transdifferentiation, has great potential for tissue engineering and regenerative medicine.

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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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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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Tercan / PBN

Tercan B et al. · 2022 · iScience

We developed a computational approach to find the best intervention to achieve transcription factor (TF) mediated transdifferentiation.

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TRANSDIRE

Eguchi R et al. · 2022 · Bioinformatics (Oxford, England)

MOTIVATION: Direct reprogramming involves the direct conversion of fully differentiated mature cell types into various other cell types while bypassing an intermediate pluripotent state (e.g. induced pluripotent stem…

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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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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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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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DIRECTEUR

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

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

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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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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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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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REPROcode

Kurochkin I et al. · 2026 · Cell systems

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

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