ArticleNature communications2021
Quantifying information accumulation encoded in the dynamics of biochemical signaling.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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.
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Who cites it
21 citing papers in PubMed.
- Fundamental limits incorporating logical reasoning into Shannon's information theory.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A novel information-theoretic approach reveals loss of effective biomolecular communication in aging muscle cells.The journals of gerontology. Series A, Biological sciences and medical sciences · 2025Article
- Ligand discrimination in immune cells: Signal processing insights into immune dysfunction in ER+ breast cancer.PLoS computational biology · 2025Article
- Evolutionary Trajectories of Consciousness: From Biological Foundations to Technological Horizons.Brain sciences · 2025Review
- Why cellular computations challenge our design principles.Seminars in cell & developmental biology · 2025Review
- Frequency-Dependent Premature Differentiation of Pheochromocytoma Cells Exhibits Band-Pass Filter Behavior Correlation with Intracellular Enzyme Activation Kinetics.International journal of molecular sciences · 2025Article
- Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages.Molecular cell · 2024Article
- Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies.PLoS computational biology · 2024Article
- Co-imaging of RelA and c-Rel reveals features of NF-κB signaling for ligand discrimination.Cell reports · 2024Article
- A guide to ERK dynamics, part 2: downstream decoding.The Biochemical journal · 2023Article
- The MAPK/ERK channel capacity exceeds 6 bit/hour.PLoS computational biology · 2023Article
- An optimized reporter of the transcription factor hypoxia-inducible factor 1α reveals complex HIF-1α activation dynamics in single cells.The Journal of biological chemistry · 2023Article
- Quantifying stimulus-response specificity to probe the functional state of macrophages.Cell systems · 2023Article
- NF-κB dynamics in the language of immune cells.Trends in immunology · 2023Review
- Utility of monocyte HLA-DR and rationale for therapeutic GM-CSF in sepsis immunoparalysis.Frontiers in immunology · 2023Review
- NFκB signaling in T cell memory.Frontiers in immunology · 2023Review
- Efficient information coding and degeneracy in the nervous system.Current opinion in neurobiology · 2022Review
- Quantifying information of intracellular signaling: progress with machine learning.Reports on progress in physics. Physical Society (Great Britain) · 2022Review
- Universal antigen encoding of T cell activation from high-dimensional cytokine dynamics.Science (New York, N.Y.) · 2022Article
- Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Cellular responses to environmental changes are encoded in the complex temporal patterns of signaling proteins. However, quantifying the accumulation of information over time to direct cellular decision-making remains an unsolved challenge. This is, in part, due to the combinatorial explosion of possible configurations that need to be evaluated for information in time-course measurements. Here, we develop a quantitative framework, based on inferred trajectory probabilities, to calculate the mutual information encoded in signaling dynamics while accounting for cell-cell variability. We use it to understand NFκB transcriptional dynamics in response to different immune threats, and reveal that some threats are distinguished faster than others. Our analyses also suggest specific temporal phases during which information distinguishing threats becomes available to immune response genes; one specific phase could be mapped to the functionality of the IκBα negative feedback circuit. The framework is generally applicable to single-cell time series measurements, and enables understanding how temporal regulatory codes transmit information over time.
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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.