Transdifferentiation

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

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

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.

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.

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.

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.

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.

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.

Okawa S et al. · 2019 · Nucleic acids research

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

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

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

Xu Q et al. · 2021 · Nucleic acids research

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

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

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

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

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

Tercan B et al. · 2022 · iScience

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

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…

Han L et al. · 2023 · Communications biology

Cellular transitions hold great promise in translational medicine research.

Zheng M et al. · 2023 · Stem cell reports

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

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…

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

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

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…

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.

Li C et al. · 2025 · Genome research

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

Kurochkin I et al. · 2026 · Cell systems

Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks.