You are here

Home

Linux/Unix

Mirnacle

Submitted by ChenLiang on Thu, 04/06/2017 - 19:26

MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs).

Rating: 
Average: 5 (1 vote)

Tiresias

Submitted by ChenLiang on Tue, 01/09/2018 - 19:08

MicroRNAs (miRNAs) are short non-coding RNAs that regulate expression of target messenger RNAs (mRNAs) post-transcriptionally. Understanding the precise regulatory role of miRNAs is of great interest since miRNAs have been shown to play an important role in development, diseases, and other biological processes. Early work on miRNA target prediction has focused on static sequence-driven miRNA-mRNA complementarity. However, recent research also utilizes expression-level data to study context-dependent regulation effects in a more dynamic, physiologically-relevant setting.

Rating: 
Average: 5 (1 vote)

COGERE

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

Understanding how regulatory networks globally coordinate the response of a cell to changing conditions, such as perturbations by shifting environments, is an elementary challenge in systems biology which has yet to be met. Genome-wide gene expression measurements are high dimensional as these are reflecting the condition-specific interplay of thousands of cellular components.

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)

iSubgraph

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

The high tumor heterogeneity makes it very challenging to identify key tumorigenic pathways as therapeutic targets. The integration of multiple omics data is a promising approach to identify driving regulatory networks in patient subgroups. Here, we propose a novel conceptual framework to discover patterns of miRNA-gene networks, observed frequently up- or down-regulated in a group of patients and to use such networks for patient stratification in hepatocellular carcinoma (HCC).

Rating: 
Average: 5 (1 vote)

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)

nRC

Submitted by ChenLiang on Tue, 01/09/2018 - 17:25

Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes.

Rating: 
Average: 5 (1 vote)

Centratliy-based Pathway Enrichment

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

Biological pathways are important for understanding biological mechanisms. Thus, finding important pathways that underlie biological problems helps researchers to focus on the most relevant sets of genes. Pathways resemble networks with complicated structures, but most of the existing pathway enrichment tools ignore topological information embedded within pathways, which limits their applicability.

Rating: 
Average: 5 (1 vote)

MixMir

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

microRNAs (miRNAs) are a class of ~22nt non-coding RNAs that potentially regulate over 60% of human protein-coding genes. miRNA activity is highly specific, differing between cell types, developmental stages and environmental conditions, so the identification of active miRNAs in a given sample is of great interest. Here we present a novel computational approach for analyzing both mRNA sequence and gene expression data, called MixMir.

Rating: 
Average: 5 (1 vote)

LeARN

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

In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs) in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to Linux/Unix