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DINGO

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

Cancer progression and development are initiated by aberrations in various molecular networks through coordinated changes across multiple genes and pathways. It is important to understand how these networks change under different stress conditions and/or patient-specific groups to infer differential patterns of activation and inhibition. Existing methods are limited to correlation networks that are independently estimated from separate group-specific data and without due consideration of relationships that are conserved across multiple groups.

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4
Average: 4 (4 votes)

miRNA-Analyzer

Submitted by ChenLiang on Mon, 01/09/2017 - 11:41

MicroRNAs (miRNAs) are small biological molecules that play an important role during the mechanisms of protein formation. Recent findings have demonstrated that they act as both positive and negative regulators of protein formation. Thus, the investigation of miRNAs, i.e., the determination of their level of expression, has developed a huge interest in the scientific community. One of the leading technologies for extracting miRNA data from biological samples is the miRNA Affymetrix platform.

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Average: 5 (1 vote)

MLSeq

Submitted by ChenLiang on Sun, 09/10/2017 - 17:14

RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of gene-expression data are either based on a continuous scale (eg. microarray data) or require a normal distribution assumption.

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Average: 4 (1 vote)

mirSTP

Submitted by ChenLiang on Sun, 09/10/2017 - 20:30

The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nascent transcriptomes generated by global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq).

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Average: 5 (1 vote)

ARTS

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

A fast growing number of non-coding RNAs have recently been discovered to play essential roles in many cellular processes. Similar to proteins, understanding the functions of these active RNAs requires methods for analyzing their tertiary structures. However, in contrast to the wide range of structure-based approaches available for proteins, there is still a lack of methods for studying RNA structures.

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Average: 5 (1 vote)

NanoStringNorm

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

The NanoString nCounter Platform is a new and promising technology for measuring nucleic acid abundances. It has several advantages over PCR-based techniques, including avoidance of amplification, direct sequence interrogation and digital detection for absolute quantification. These features minimize aspects of experimental error and hold promise for dealing with challenging experimental conditions such as archival formalin-fixed paraffin-embedded samples.

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Average: 5 (1 vote)

MSbind

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

We study microRNA (miRNA) bindings to metastable RNA secondary structures close to minimum free energy conformations in the context of single nucleotide polymorphisms (SNPs) and messenger RNA (mRNA) concentration levels, i.e. whether features of miRNA bindings to metastable conformations could provide additional information supporting the differences in expression levels of the two sequences defined by a SNP.

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Average: 5 (1 vote)

YamiPred

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

MicroRNAs (miRNAs) are small non-coding RNAs, which play a significant role in gene regulation. Predicting miRNA genes is a challenging bioinformatics problem and existing experimental and computational methods fail to deal with it effectively. We developed YamiPred, an embedded classification method that combines the efficiency and robustness of support vector machines (SVM) with genetic algorithms (GA) for feature selection and parameters optimization.

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Average: 5 (1 vote)

miRNAfe

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

miRNAfe is a comprehensive tool to extract features from RNA sequences. It is freely available as a web service, allowing a single access point to almost all state-of-the-art feature extraction methods used today in a variety of works from different authors. It has a very simple user interface, where the user only needs to load a file containing the input sequences and select the features to extract. As a result, the user obtains a text file with the features extracted, which can be used to analyze the sequences or as input to a miRNA prediction software.

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Average: 5 (1 vote)

GRNMF

Submitted by ChenLiang on Tue, 01/09/2018 - 17:03

MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulations and various cellular processes. The identification of disease-related miRNAs provides great insights into the underlying pathogenesis of diseases at a system level. However, most existing computational approaches are biased towards known miRNA-disease associations, which is inappropriate for those new diseases or miRNAs without any known association information.

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Average: 5 (1 vote)

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