Directed 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.

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

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

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.

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.

Okawa S et al. · 2016 · Stem cell reports

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

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…

Hartmann A et al. · 2018 · Scientific reports

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

Danter WR · 2019 · Orphanet journal of rare diseases

BACKGROUND: Conversion of human somatic cells into induced pluripotent stem cells (iPSCs) is often an inefficient, time consuming and expensive process.

Choo SM et al. · 2020 · Frontiers in physiology

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

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…

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

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

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.

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.

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

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

Kamimoto K et al. · 2023 · Nature

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

Han L et al. · 2023 · Communications biology

Cellular transitions hold great promise in translational medicine research.

Smits JGA et al. · 2023 · F1000Research

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

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…

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.

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.

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.

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.

Li C et al. · 2025 · Genome research

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