Physically-Inspired Gaussian Process Models for Post-Transcriptional Regulation in Drosophila.

A new interesting article has been published in IEEE/ACM Trans Comput Biol Bioinform. 2019 May 27. doi: 10.1109/TCBB.2019.2918774. and titled:

Physically-Inspired Gaussian Process Models for Post-Transcriptional Regulation in Drosophila.

Authors of this article are:

Lopez-Lopera AF, Durrande N, Alvarez MA.

A summary of the article is shown below:

The regulatory process of Drosophila is thoroughly studied for understanding a great variety of biological principles. While pattern-forming gene networks are analysed in the transcription step, post-transcriptional events (e.g. translation, protein processing) play an important role in establishing protein expression patterns and levels. Since the post-transcriptional regulation of Drosophila depends on spatiotemporal interactions between mRNAs and gap proteins, proper physically-inspired stochastic models are required to study the link between both quantities. Previous research attempts have shown that using Gaussian processes (GPs) and differential equations lead to promising predictions when analysing regulatory networks. Here we aim at further investigating two types of physically-inspired GP models based on a reaction-diffusion equation where the main difference lies in where the prior is placed. While one of them has been studied previously using protein data only, the other is novel and yields a simple approach requiring only the differentiation of kernel functions. In contrast to other stochastic frameworks, discretising the spatial space is not required here. Both GP models are tested under different conditions depending on the availability of gap gene mRNA expression data. Finally, their performances are assessed on a high-resolution dataset describing the blastoderm stage of the early embryo of Drosophila melanogaster.

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