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smiRNA-annotation

Submitted by ChenLiang on Tue, 01/09/2018 - 19:04

Cloning and sequencing is the method of choice for small regulatory RNA identification. Using deep sequencing technologies one can now obtain up to a billion nucleotides--and tens of millions of small RNAs--from a single library. Careful computational analyses of such libraries enabled the discovery of miRNAs, rasiRNAs, piRNAs, and 21U RNAs. Given the large number of sequences that can be obtained from each individual sample, deep sequencing may soon become an alternative to oligonucleotide microarray technology for mRNA expression profiling.

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sIR

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this report we describe a web-based computational tool, siRNA Information Resource (sIR), which consists of a new open source database that contains validation information about published siRNA sequences and also provides a user-friendly interface to design and analyze siRNA sequences against a chosen target sequence.

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isomiRex

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We present an open-access web platform isomiRex, to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. The open-access web-platform is not restricted only to NGS sequence dataset from animals and potentially analyzes a wider dataset for plants, animals and viral NGS dataset supporting miRBase (version 19 supporting 193 species). The platform can handle the bloated amount of the read counts and reports the annotated microRNAs from plant, animal and viral NGS datasets.

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MIR@NT@N

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

To understand biological processes and diseases, it is crucial to unravel the concerted interplay of transcription factors (TFs), microRNAs (miRNAs) and their targets within regulatory networks and fundamental sub-networks. An integrative computational resource generating a comprehensive view of these regulatory molecular interactions at a genome-wide scale would be of great interest to biologists, but is not available to date.

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LSD

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

By broad literature survey, we have developed a leaf senescence database (LSD, http://www.eplantsenescence.org/) that contains a total of 1145 senescence associated genes (SAGs) from 21 species. These SAGs were retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and were classified into different categories according to their functions in leaf senescence or morphological phenotypes when mutated.

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LoessM

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Microarray normalization is a fundamental step in removing systematic bias and noise variability caused by technical and experimental artefacts. Several approaches, suitable for large-scale genome arrays, have been proposed and shown to be effective in the reduction of systematic errors. Most of these methodologies are based on specific assumptions that are reasonable for whole-genome arrays, but possibly unsuitable for small microRNA (miRNA) platforms.

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A personalized microRNA microarray normalization method using a logistic regression model

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNA (miRNA) is a set of newly discovered non-coding small RNA molecules. Its significant effects have contributed to a number of critical biological events including cell proliferation, apoptosis development, as well as tumorigenesis. High-dimensional genomic discovery platforms (e.g. microarray) have been employed to evaluate the important roles of miRNAs by analyzing their expression profiling.

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miren

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Increasing studies have shown that the interactions between microRNAs (miRNAs) and environmental factors (EFs) play critical roles in determining phenotypes and diseases. In this study, we revealed a number of important biological insights by analyzing and modeling of miRNA-EF interactions and their relationships with human diseases. We demonstrated that the miRNA signatures of EFs could provide new information on EFs.

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SiDE

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity.

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rice_build

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper division of the plants is defined by the radiation of the angiosperms and gymnosperms, with the latter comprising the commercially important conifers. The conifers are expected to provide important information regarding the evolution of highly conserved small regulatory RNAs.

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