ArticleMolecular systems biology2018
Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions.
Article in Molecular systems biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- OneSC: a computational platform for recapitulating cell state transitions.Bioinformatics (Oxford, England) · 2024Article
- Canalizing kernel for cell fate determination.Briefings in bioinformatics · 2024Article
- OneSC: A computational platform for recapitulating cell state transitions.bioRxiv : the preprint server for biology · 2024Article
- A gray box framework that optimizes a white box logical model using a black box optimizer for simulating cellular responses to perturbations.Cell reports methods · 2024Article
- Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response.NPJ systems biology and applications · 2023Article
- Modeling unveils sex differences of signaling networks in mouse embryonic stem cells.Molecular systems biology · 2023Article
- On the History of Ecosystem Dynamical Modeling: The Rise and Promises of Qualitative Models.Entropy (Basel, Switzerland) · 2023Article
- Virtual cells in a virtual microenvironment recapitulate early development-like patterns in human pluripotent stem cell colonies.Stem cell reports · 2023Article
- Human Stem Cells for Ophthalmology: Recent Advances in Diagnostic Image Analysis and Computational Modelling.Current stem cell reports · 2023Review
- Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.Frontiers in network physiology · 2023Review
- Organoid Cultures In Silico: Tools or Toys?Bioengineering (Basel, Switzerland) · 2022Review
- NETISCE: a network-based tool for cell fate reprogramming.NPJ systems biology and applications · 2022Article
- IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.PLoS computational biology · 2022Article
- Context-aware synthetic biology by controller design: Engineering the mammalian cell.Cell systems · 2021Review
- Unsupervised logic-based mechanism inference for network-driven biological processes.PLoS computational biology · 2021Article
- Computational Stem Cell Biology: Open Questions and Guiding Principles.Cell stem cell · 2021Review
- The Clinical Trials of Mesenchymal Stromal Cells Therapy.Stem cells international · 2021Review
- Evaluating totipotency using criteria of increasing stringency.Nature cell biology · 2021Article
- Identification of potential transcription factors that enhance human iPSC generation.Scientific reports · 2020Article
- Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The mechanisms that maintain pluripotency, or that cause its destabilization to initiate development, are complex and incompletely understood. We have developed a model to predict stabilized PSC gene regulatory network (GRN) states in response to input signals. Our strategy used random asynchronous Boolean simulations (R-ABS) to simulate single-cell fate transitions and strongly connected components (SCCs) strategy to represent population heterogeneity. This framework was applied to a reverse-engineered and curated core GRN for mouse embryonic stem cells (mESCs) and used to simulate cellular responses to combinations of five signaling pathways. Our simulations predicted experimentally verified cell population compositions and input signal combinations controlling specific cell fate transitions. Extending the model to PSC differentiation, we predicted a combination of signaling activators and inhibitors that efficiently and robustly generated a Cdx2
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.