ArticleNPJ systems biology and applications2016
A Method to Identify and Analyze Biological Programs through Automated Reasoning.
Article in NPJ systems biology and applications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- Control-guided refinement of partially specified Boolean networks: applications to RTK signaling.Bioinformatics (Oxford, England) · 2026Article
- Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data.PLoS computational biology · 2026Article
- Sketchbook: logical model inference from Boolean network sketches.Bioinformatics advances · 2026Article
- Esrrb guides naive pluripotent cells through the formative transcriptional programme.Nature cell biology · 2023Article
- Boolean network sketches: a unifying framework for logical model inference.Bioinformatics (Oxford, England) · 2023Article
- Automatic mechanistic inference from large families of Boolean models generated by Monte Carlo tree search.Frontiers in cell and developmental biology · 2023Article
- Modeling the C. elegans germline stem cell genetic network using automated reasoning.Bio Systems · 2022Article
- IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.PLoS computational biology · 2022Article
- Computational Stem Cell Biology: Open Questions and Guiding Principles.Cell stem cell · 2021Review
- Robust network inference using response logic.Bioinformatics (Oxford, England) · 2019Article
- Let it RE:IN: integrating experimental observations to predict pluripotency network behaviour.The EMBO journal · 2019Article
- A common molecular logic determines embryonic stem cell self-renewal and reprogramming.The EMBO journal · 2019Article
- Kinetic models of hematopoietic differentiation.Wiley interdisciplinary reviews. Systems biology and medicine · 2019Review
- Stem cell bioengineering: building from stem cell biology.Nature reviews. Genetics · 2018Review
- Synthesizing and tuning stochastic chemical reaction networks with specified behaviours.Journal of the Royal Society, Interface · 2018Article
- Article
- Computational dynamic approaches for temporal omics data with applications to systems medicine.BioData mining · 2017Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Predictive biology is elusive because rigorous, data-constrained, mechanistic models of complex biological systems are difficult to derive and validate. Current approaches tend to construct and examine static interaction network models, which are descriptively rich but often lack explanatory and predictive power, or dynamic models that can be simulated to reproduce known behavior. However, in such approaches implicit assumptions are introduced as typically only one mechanism is considered, and exhaustively investigating all scenarios is impractical using simulation. To address these limitations, we present a methodology based on automated formal reasoning, which permits the synthesis and analysis of the complete set of logical models consistent with experimental observations. We test hypotheses against all candidate models, and remove the need for simulation by characterizing and simultaneously analyzing all mechanistic explanations of observed behavior. Our methodology transforms knowledge of complex biological processes from sets of possible interactions and experimental observations to precise, predictive biological programs governing cell function.
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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.