ArticleBioinformatics (Oxford, England)2012
A comprehensive computational model of facilitated diffusion in prokaryotes.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.Computational and structural biotechnology journal · 2020Article
- Transcription factor target site search and gene regulation in a background of unspecific binding sites.Journal of theoretical biology · 2018Article
- Reliable scaling of position weight matrices for binding strength comparisons between transcription factors.BMC bioinformatics · 2015Article
- Real sequence effects on the search dynamics of transcription factors on DNA.Scientific reports · 2015Article
- Estimating binding properties of transcription factors from genome-wide binding profiles.Nucleic acids research · 2015Article
- Facilitated diffusion buffers noise in gene expression.Physical review. E, Statistical, nonlinear, and soft matter physics · 2014Article
- Physical constraints determine the logic of bacterial promoter architectures.Nucleic acids research · 2014Article
- The effects of transcription factor competition on gene regulation.Frontiers in genetics · 2013Article
- The influence of transcription factor competition on the relationship between occupancy and affinity.PloS one · 2013Article
- Computational models for large-scale simulations of facilitated diffusion.Molecular bioSystems · 2012Review
- System size reduction in stochastic simulations of the facilitated diffusion mechanism.BMC systems biology · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
motivationGene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed.
resultsWe present a comprehensive computational model of the search process of TF for their genomic target site(s). The computational model considers: the DNA sequence, various TF species and the interaction of the individual molecules with the DNA or between themselves. We also demonstrate a systematic approach how to parametrize the system using available experimental data.
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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.