ArticleProceedings of the National Academy of Sciences of the United States of America2012
On a fundamental structure of gene networks in living cells.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed.
- Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer.Nature communications · 2026Article
- SurprisalAnalysis: an open-source software for information-theoretic analysis of gene expression.Bioinformatics advances · 2025Article
- SCA: recovering single-cell heterogeneity through information-based dimensionality reduction.Genome biology · 2023Article
- Overexpressed kinetochore genes are used by cancer cells as genome destabilizers and transformation catalysts.Translational oncology · 2023Article
- Density Matrix via Few Dominant Observables for the Ultrafast Non-Radiative Decay in Pyrazine.Journal of chemical theory and computation · 2023Article
- Article
- A novel estimator of the interaction matrix in Graphical Gaussian Model of omics data using the entropy of non-equilibrium systems.Bioinformatics (Oxford, England) · 2021Article
- Explant Modeling of the Immune Environment of Head and Neck Cancer.Frontiers in oncology · 2021Article
- Thermodynamic energetics underlying genomic instability and whole-genome doubling in cancer.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Translational Components Contribute to Acclimation Responses to High Light, Heat, and Cold in Arabidopsis.iScience · 2020Article
- Exploring Alzheimer's Disease Molecular Variability via Calculation of Personalized Transcriptional Signatures.Biomolecules · 2020Article
- Metabolic, Physiological, and Transcriptomics Analysis of Batch Cultures of the Green MicroalgaCells · 2019Article
- Intracellular redox potential is correlated with miRNA expression in MCF7 cells under hypoxic conditions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance.PLoS computational biology · 2019Article
- Personalized disease signatures through information-theoretic compaction of big cancer data.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis.Proteomics · 2017Review
- A Thermodynamic-Based Interpretation of Protein Expression Heterogeneity in Different Glioblastoma Multiforme Tumors Identifies Tumor-Specific Unbalanced Processes.The journal of physical chemistry. B · 2016Article
- Genome-wide association studies and gene expression profiles of rheumatoid arthritis: An analysis.Bone & joint research · 2016Article
- Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like transcripts vary greatly, even among tumors of the same type from different individuals. Two distinguishable classes could be identified within the hardware-like component: those transcripts that are highly expressed and stable and an adaptable subset with lower expression that respond to external stimuli. Importantly, we demonstrate that this structure is conserved across organisms. Deletions of transcripts from the highly stable core are predicted to result in cell mortality. The approach provides a conceptual thermodynamic-like framework for the analysis of gene-expression levels and networks and their variations in diseased cells.
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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.