ArticleProceedings of the National Academy of Sciences of the United States of America2018
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 128 citations in OpenAlex.
- Gaugefixer: overcoming parameter non-identifiability in models of sequence-function relationships.BMC bioinformatics · 2026Article
- Disentangling factors affecting bacterial transcriptional regulatory network inference.iScience · 2026Article
- The adaptive landscapes of three globaleLife · 2026Article
- De novo promoters emerge more readily from random DNA than from genomic DNA.Science advances · 2026Article
- Informational blueprints reveal condition-dependent gene regulatory architectures.bioRxiv : the preprint server for biology · 2026Article
- GaugeFixer: overcoming parameter non-identifiability in models of sequence-function relationships.bioRxiv : the preprint server for biology · 2026Article
- Predictive modeling of gene expression and localization of DNA binding site using deep convolutional neural networks.PLoS computational biology · 2026Article
- Model-guided design of regulatable promoters for synthetic biology.Current opinion in microbiology · 2026Review
- Unraveling the start element and regulatory divergence of core promoters across the domain bacteria.Nucleic acids research · 2025Article
- Computational Pipeline for Targeted Integration and Variable Payload Expression in Bacteriophage Engineering.ACS synthetic biology · 2025Article
- The latent cis-regulatory potential of mobile DNA in Escherichia coli.Nature communications · 2025Article
- The Environment-Dependent Regulatory Landscape of thebioRxiv : the preprint server for biology · 2025Article
- Article
- Tailoring Escherichia coli BL21 (DE3) for preferential xylose utilization via metabolic and regulatory engineering.Applied microbiology and biotechnology · 2025Article
- Gauge fixing for sequence-function relationships.PLoS computational biology · 2025Article
- The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR.Nature communications · 2024Article
- The emergence and evolution of gene expression in genome regions replete with regulatory motifs.eLife · 2024Article
- MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data.Genome biology · 2024Article
- Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns.PLoS computational biology · 2024Article
- Limits on inferring T cell specificity from partial information.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Gene regulation is one of the most ubiquitous processes in biology. However, while the catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in these genomes are regulated. At present, characterizing the molecular mechanisms by which individual regulatory sequences operate requires focused efforts using low-throughput methods. Here, we take a first step toward multipromoter dissection and show how a combination of massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect multiple bacterial promoters in a systematic way. We show this approach on both well-studied and previously uncharacterized promoters in the enteric bacterium
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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.