ArticleMolecular systems biology2017
From word models to executable models of signaling networks using automated assembly.
Article in Molecular systems biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- Literature-derived, context-aware gene regulatory networks improve biological predictions and mathematical modeling.Bioinformatics (Oxford, England) · 2026Article
- Network methods for diagonal integration of unpaired single-cell multiomics data: a review.Bioinformatics (Oxford, England) · 2026Review
- Multiscale predictive cellular modeling: integrating hypothesis grammars, digital twins, and multi-omics for In silico oncology and precision theranostics.Functional & integrative genomics · 2026Review
- Transforming the cytokine literature into a resource for experimental analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Unveiling toxicological adverse outcomes: toward construction and simulation of large-scale networks.Toxicological sciences : an official journal of the Society of Toxicology · 2026Review
- VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs.bioRxiv : the preprint server for biology · 2026Article
- SIGNOR 4.0: the 2025 update with focus on phosphorylation data.Nucleic acids research · 2026Article
- Literature-driven extraction and computational prediction of causal statements linking genetic variants to biological processes, pathways and phenotypes.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2026Article
- Assembly and reasoning over semantic mappings at scale for biomedical data integration.Bioinformatics (Oxford, England) · 2025Article
- Adipocyte/Tumor cell crosstalk via IGF-1/TXNIP axis promotes malignancy and endocrine resistance in breast cancer.Cell communication and signaling : CCS · 2025Article
- Knowledge graph and its application in the study of neurological and mental disorders.Frontiers in psychiatry · 2025Review
- The Constrained Disorder Principle Overcomes the Challenges of Methods for Assessing Uncertainty in Biological Systems.Journal of personalized medicine · 2024Review
- The ENDOMIX perspective: how everyday chemical mixtures impact human health and reproduction by targeting the immune system†.Biology of reproduction · 2024Review
- Mathematical basis and toolchain for hierarchical optimization of biochemical networks.PLoS computational biology · 2024Article
- Illuminating the dark kinome: utilizing multiplex peptide activity arrays to functionally annotate understudied kinases.Cell communication and signaling : CCS · 2024Article
- Generating synthetic signaling networks for in silico modeling studies.Journal of theoretical biology · 2024Article
- A review of feature selection strategies utilizing graph data structures and Knowledge Graphs.Briefings in bioinformatics · 2024Review
- Nociceptor-immune interactomes reveal insult-specific immune signatures of pain.Nature immunology · 2024Article
- Context-aware knowledge selection and reliable model recommendation with ACCORDION.Frontiers in systems biology · 2024Article
28 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
Word models (natural language descriptions of molecular mechanisms) are a common currency in spoken and written communication in biomedicine but are of limited use in predicting the behavior of complex biological networks. We present an approach to building computational models directly from natural language using automated assembly. Molecular mechanisms described in simple English are read by natural language processing algorithms, converted into an intermediate representation, and assembled into executable or network models. We have implemented this approach in the Integrated Network and Dynamical Reasoning Assembler (INDRA), which draws on existing natural language processing systems as well as pathway information in Pathway Commons and other online resources. We demonstrate the use of INDRA and natural language to model three biological processes of increasing scope: (i) p53 dynamics in response to DNA damage, (ii) adaptive drug resistance in BRAF-V600E-mutant melanomas, and (iii) the RAS signaling pathway. The use of natural language makes the task of developing a model more efficient and it increases model transparency, thereby promoting collaboration with the broader biology community.
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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.