STREAM: Static Thermodynamic REgulAtory Model of transcription

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STREAM: Static Thermodynamic REgulAtory Model of transcription

MOTIVATION Understanding the transcriptional regulation of a gene in detail is a crucial step towards uncovering and ultimately utilizing the regulatory grammar of the genome. Modeling transcriptional regulation using thermodynamic equations has become an increasingly important approach towards this goal. Here, we present stream, the first publicly available framework for modeling, visualizing ...

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Organophosphate pesticides are considered as endocrine disruptors that interfere with reproductive functions. The corpus luteum (CL) is a transient endocrine gland that produces progesterone, a crucial hormone for a successful beginning and maintenance of pregnancy. Steroidogenic acute regulatory protein (StAR) facilitates the rate-limiting transfer of cholesterol from the outer mitochondrial m...

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Diazinon interrupts ovarian steroidogenic acute regulatory (StAR) gene transcription in gonadotropin-stimulated rat model

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Optimizing static thermodynamic models of transcriptional regulation

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...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2008

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/btn467