All methods

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.

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.

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.

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.

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.

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.

Hartmann A et al. · 2018 · Scientific reports

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

Xu Q et al. · 2021 · Nucleic acids research

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

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

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

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…

Smits JGA et al. · 2023 · F1000Research

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

Sinha S et al. · 2025 · Cell reports. Medicine

Reactivating lineage commitment to differentiate, and hence eliminate, cancer stem cells (CSCs) remains a therapeutic challenge.

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.

Zhang G et al. · 2025 · Nature communications

It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of…

Chung HK et al. · 2026 · Nature

CD8+ T cells differentiate into diverse states that shape immune outcomes in cancer and chronic infection1-4.

Alvarez et al. · 2018 · Cancer Discovery

Classical Level 2 proxy method. Estimates master-regulator activity with VIPER and ranks compounds by their ability to reverse that activity profile against perturbation atlases.

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…

Napolitano F et al. · 2021 · Stem cell reports

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

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

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

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).

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…

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.

Jung S et al. · 2025 · Aging

Great efforts have been devoted to discovering rejuvenation strategies that counteract age-related functional decline and improve cellular functions in humans.

Cornelius SP et al. · 2013 · Nature communications

The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response and cell reprogramming.

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.

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

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

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.

Murrugarra D et al. · 2016 · BMC systems biology

BACKGROUND: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a…

Okawa S et al. · 2016 · Stem cell reports

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

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.

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.

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…

Yang G et al. · 2018 · Frontiers in physiology

Dynamical models of biomolecular networks are successfully used to understand the mechanisms underlying complex diseases and to design therapeutic strategies.

Choo SM et al. · 2018 · BMC systems biology

BACKGROUND: Controlling complex molecular regulatory networks is getting a growing attention as it can provide a systematic way of driving any cellular state to a desired cell phenotypic state.

Choo SM et al. · 2019 · Scientific reports

A cell phenotype can be represented by an attractor state of the underlying molecular regulatory network, to which other network states eventually converge.

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.

Aguilar B et al. · 2020 · Letters in biomathematics

One of the ultimate goals in systems biology is to develop control strategies to find efficient medical treatments.

Choo SM et al. · 2020 · Frontiers in physiology

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

Sordo Vieira L et al. · 2020 · Bulletin of mathematical biology

Many problems in biology and medicine have a control component.

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

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

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.

Andersson E et al. · 2022 · iScience

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

Rukhlenko OS et al. · 2022 · Nature

Understanding cell state transitions and purposefully controlling them is a longstanding challenge in biology.

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.

Tercan B et al. · 2022 · iScience

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

Kamimoto K et al. · 2023 · Nature

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

An S et al. · 2023 · Bioinformatics (Oxford, England)

MOTIVATION: Cellular behavior is determined by complex non-linear interactions between numerous intracellular molecules that are often represented by Boolean network models.

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.

pbn-STAC · 2025

Method indexed in the Atlas. Editorial one-liner pending review.

Gonzalez et al. · 2025 · Nature Biotechnology

Recent Level 3 frontier. Graph neural network that predicts transcriptional responses to candidate interventions and ranks perturbations by predicted reconstruction of a target state.

Shin D et al. · 2025 · Advanced science (Weinheim, Baden-Wurttemberg, Germany)

A cell fate change such as tumorigenesis incurs critical transition.

Li C et al. · 2025 · Genome research

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