Surveying computational algorithms for identification of miRNA–mRNA regulatory modules

Ray, Rishav; Pandey, Priyanka

doi:10.1007/s13237-017-0208-5

Cited by 7 publications

(3 citation statements)

References 34 publications

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“…Vaccine developers use computational algorithms in the creation of mRNA vaccines. Such algorithms aid in the identification of microRNAs (miRNAs) that "target gene expression at post-transcriptional level" (Ray & Pandey, 2017). Critical to this process is the use of computational algorithms and other research tools that have been identified as essential to understanding the virus and its structure (Waltz, 2020).…”

Section: Algorithms For Mrna Vaccinesmentioning

confidence: 99%

International Copyright Flexibilities for Prevention, Treatment and Containment of COVID-19

Flynn

Nkrumah

Schirru

2022

Afr. j. inf. commun. (Online)

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Most policymaking attention with respect to intellectual property barriers toCOVID-19 prevention, treatment and containment has been focused on patents.This focus is reflected in the World Trade Organisation (WTO) Ministerial Decisionon the TRIPS Agreement, adopted on 17 June 2022, which provides a limited waiverof TRIPS rules on compulsory licences for production of COVID-19 vaccines. Theoriginal WTO proposal for a TRIPS waiver, however, explicitly applied to all formsof intellectual property, including copyright. This article outlines the numerous waysin which copyright can create barriers to addressing COVID-19. It also provides adescription of international copyright treaty provisions that permit uses of copyrightmaterials in response to the barriers identified, despite the exclusion of copyrightfrom the final TRIPS waiver.

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Section: Algorithms For Mrna Vaccinesmentioning

confidence: 99%

International Copyright Flexibilities for Prevention, Treatment and Containment of COVID-19

Flynn

Nkrumah

Schirru

2022

Afr. j. inf. commun. (Online)

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“…The method presented in this paper is based on dynamic changes of mRNA expression, as opposed to previous studies that mostly considered single time point measurements (see the summary of the most popular methods in ref. [29]).…”

Section: Introductionmentioning

confidence: 99%

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes

et al. 2019

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BackgroundRapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation, since the amounts of miRNAs in cells also vary upon irradiation. To address this possibility, we designed experiments using cancer-derived cell lines transfected with luciferase reporter gene containing sequences targeted by different miRNA species in its 3′- untranslated region. We focus on the early time-course response (1 h past irradiation) to eliminate secondary mRNA expression waves.ResultsExperiments revealed that the irradiation-induced changes in the mRNA expression depend on the miRNAs which interact with mRNA. To identify the strongest interactions, we propose a mathematical model which predicts the mRNA fold expression changes, caused by perturbation of microRNA-mRNA interactions. Model was applied to experimental data including various cell lines, irradiation doses and observation times, both ours and literature-based. Comparison of modelled and experimental mRNA expression levels given miRNA level changes allows estimating how many and which miRNAs play a significant role in transcriptome response to stress conditions in different cell types. As an example, in the human melanoma cell line the comparison suggests that, globally, a major part of the irradiation-induced changes of mRNA expression can be explained by perturbed miRNA-mRNA interactions. A subset of about 30 out of a few hundred miRNAs expressed in these cells appears to account for the changes. These miRNAs play crucial roles in regulatory mechanisms observed after irradiation. In addition, these miRNAs have a higher average content of GC and a higher number of targeted transcripts, and many have been reported to play a role in the development of cancer.ConclusionsOur proposed mathematical modeling approach may be used to identify miRNAs which participate in responses of cells to ionizing radiation, and other stress factors such as extremes of temperature, exposure to toxins, and drugs.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5464-0) contains supplementary material, which is available to authorized users.

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“…Commonly LncRNAs epigenetically remodel the genome, but an interesting feature of HOTAIR, LncRNA is that it not only plays key roles in development and body axis patterning but also promotes cancer progression when dysregulated in the adult [2]. In another article several computational algorithms and tools widely used discovering miRNA-mRNA regulatory modules have been collated that utilize sequence based predictions [11].…”

mentioning

confidence: 99%

Editorial

Sharma

2017

Nucleus

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Surveying computational algorithms for identification of miRNA–mRNA regulatory modules

Cited by 7 publications

References 34 publications

International Copyright Flexibilities for Prevention, Treatment and Containment of COVID-19

International Copyright Flexibilities for Prevention, Treatment and Containment of COVID-19

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes

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