ArticleeLife2018
Measuring cis-regulatory energetics in living cells using allelic manifolds.
Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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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.
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Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
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- An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity.PLoS computational biology · 2024Article
- Specificity, synergy, and mechanisms of splice-modifying drugs.Nature communications · 2024Article
- Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli.Molecular systems biology · 2022Article
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- Quantifying the regulatory role of individual transcription factors in Escherichia coli.Cell reports · 2021Article
- Quantitative Control for Stoichiometric Protein Synthesis.Annual review of microbiology · 2021Article
- Nonequilibrium models of optimal enhancer function.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Deciphering the regulatory genome ofeLife · 2020Article
- Logomaker: beautiful sequence logos in Python.Bioinformatics (Oxford, England) · 2020Article
- Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems.Molecular systems biology · 2019Article
- How the avidity of polymerase binding to the -35/-10 promoter sites affects gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Gene expression in all organisms is controlled by cooperative interactions between DNA-bound transcription factors (TFs), but quantitatively measuring TF-DNA and TF-TF interactions remains difficult. Here we introduce a strategy for precisely measuring the Gibbs free energy of such interactions in living cells. This strategy centers on the measurement and modeling of 'allelic manifolds', a multidimensional generalization of the classical genetics concept of allelic series. Allelic manifolds are measured using reporter assays performed on strategically designed cis-regulatory sequences. Quantitative biophysical models are then fit to the resulting data. We used this strategy to study regulation by two Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that minor issues remain unresolved (see decision letter).
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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.