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chimiRic

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

Recent technologies like AGO CLIP sequencing and CLASH enable direct transcriptome-wide identification of AGO binding and miRNA target sites, but the most widely used miRNA target prediction algorithms do not exploit these data. Here we use discriminative learning on AGO CLIP and CLASH interactions to train a novel miRNA target prediction model. Our method combines two SVM classifiers, one to predict miRNA-mRNA duplexes and a second to learn a binding model of AGO's local UTR sequence preferences and positional bias in 3'UTR isoforms.

Rating: 
5
Average: 4.5 (2 votes)

TargetExpress

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

Mammalian genomes encode for thousands of microRNAs, which can potentially regulate the majority of protein-coding genes. They have been implicated in development and disease, leading to great interest in understanding their function, with computational methods being widely used to predict their targets. Most computational methods rely on sequence features, thermodynamics, and conservation filters; essentially scanning the whole transcriptome to predict one set of targets for each microRNA.

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Average: 5 (1 vote)

miRMOD

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

In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications.

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Average: 5 (1 vote)

MMiRNA-Viewer

Submitted by ChenLiang on Mon, 01/09/2017 - 10:15

BACKGROUND: MicroRNAs (miRNA) are short nucleotides that interact with their target genes through 3' untranslated regions (UTRs). The Cancer Genome Atlas (TCGA) harbors an increasing amount of cancer genome data for both tumor and normal samples. However, there are few visualization tools focusing on concurrently displaying important relationships and attributes between miRNAs and mRNAs of both cancer tumor and normal samples.

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Average: 5 (1 vote)

miSTAR

Submitted by ChenLiang on Mon, 01/09/2017 - 11:43

In microRNA (miRNA) target prediction, typically two levels of information need to be modeled: the number of potential miRNA binding sites present in a target mRNA and the genomic context of each individual site. Single model structures insufficiently cope with this complex training data structure, consisting of feature vectors of unequal length as a consequence of the varying number of miRNA binding sites in different mRNAs. To circumvent this problem, we developed a two-layered, stacked model, in which the influence of binding site context is separately modeled.

Rating: 
Average: 5 (1 vote)

Exo-miRExplorer

Submitted by ChenLiang on Thu, 04/06/2017 - 19:38

MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms.

Rating: 
4
Average: 4 (2 votes)

miRBShunter

Submitted by ChenLiang on Sun, 09/10/2017 - 20:25

Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq).

Rating: 
Average: 5 (1 vote)

microRNAome

Submitted by ChenLiang on Tue, 01/09/2018 - 17:31

MicroRNAs are short RNAs that serve as regulators of gene expression and are essential components of normal development as well as modulators of disease. MicroRNAs generally act cell-autonomously, and thus their localization to specific cell types is needed to guide our understanding of microRNA activity. Current tissue-level data have caused considerable confusion, and comprehensive cell-level data do not yet exist. Here, we establish the landscape of human cell-specific microRNA expression.

Rating: 
Average: 5 (1 vote)

expmicro

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

MicroRNAs (miRNAs) are single-stranded non-coding RNAs shown to plays important regulatory roles in a wide range of biological processes and diseases. The functions and regulatory mechanisms of most of miRNAs are still poorly understood in part because of the difficulty in identifying the miRNA regulatory targets. To this end, computational methods have evolved as important tools for genome-wide target screening.

Rating: 
Average: 5 (1 vote)

IGDB.NSCLC

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

Lung cancer is the most common cause of cancer-related mortality with more than 1.4 million deaths per year worldwide. To search for significant somatic alterations in lung cancer, we analyzed, integrated and manually curated various data sets and literatures to present an integrated genomic database of non-small cell lung cancer (IGDB.NSCLC, http://igdb.nsclc.ibms.sinica.edu.tw).

Rating: 
Average: 5 (1 vote)

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