Phenotype reprogramming

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 · 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.

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…

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.

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.

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.

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.

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.

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…

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

Many problems in biology and medicine have a control component.

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.

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.

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…

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…

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

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

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.

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.

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.

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.