Inverse design fidelity
Candidate interventions enter an explicit model with intervention semantics and the predicted outcome of each candidate is simulated forward.
Methods at this level
Sorted by publication year, oldest first.
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.
Other levels