In vivoandin vitroconsistency of thermodynamic models for transcription regulation
نویسندگان
چکیده
منابع مشابه
a study on thermodynamic models for simulation of 1,3 butadiene purification columns
attempts have been made to study the thermodynamic behavior of 1,3 butadiene purification columns with the aim of retrofitting those columns to more energy efficient separation schemes. 1,3 butadiene is purified in two columns in series through being separated from methyl acetylene and 1,2 butadiene in the first and second column respectively. comparisons have been made among different therm...
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation
Transcriptional control is central to many cellular processes, and, consequently, much effort has been devoted to understanding its underlying mechanisms. The organization of nucleosomes along promoter regions is important for this process, since most transcription factors cannot bind nucleosomal sequences and thus compete with nucleosomes for DNA access. This competition is governed by the rel...
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MOTIVATION Modeling transcriptional regulation using thermo-dynamic modeling approaches has become increasingly relevant as a way to gain a detailed understanding of transcriptional regulation. Thermodynamic models are able to model the interactions between transcription factors (TFs) and DNA that lead to a specific transcriptional output of the target gene. Such models can be 'trained' by fitt...
متن کاملThermodynamic State Ensemble Models of cis-Regulation
A major goal in computational biology is to develop models that accurately predict a gene's expression from its surrounding regulatory DNA. Here we present one class of such models, thermodynamic state ensemble models. We describe the biochemical derivation of the thermodynamic framework in simple terms, and lay out the mathematical components that comprise each model. These components include ...
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Many studies have identified binding preferences for transcription factors (TFs), but few have yielded predictive models of how combinations of transcription factor binding sites generate specific levels of gene expression. Synthetic promoters have emerged as powerful tools for generating quantitative data to parameterize models of combinatorial cis-regulation. We sought to improve the accuracy...
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ژورنال
عنوان ژورنال: Physical Review Research
سال: 2019
ISSN: 2643-1564
DOI: 10.1103/physrevresearch.1.033094