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PACRAT

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

Analysis of intergenic sequences for purposes such as the investigation of transcriptional signals or the identification of small RNA genes is frequently complicated by traditional biological database structures. Genome data is commonly treated as chromosome-length sequence records, detailed by gene calls demarcating subsequences of the chromosomes. Given this model, the determination of non-called subsequences between any gene and its nearest neighbors requires an exhaustive search of all gene calls associated with the chromosome.

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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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DynaMod

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

A comprehensive analysis of enriched functional categories in differentially expressed genes is important to extract the underlying biological processes of genome-wide expression profiles. Moreover, identification of the network of significant functional modules in these dynamic processes is an interesting challenge. This study introduces DynaMod, a web-based application that identifies significant functional modules reflecting the change of modularity and differential expressions that are correlated with gene expression profiles under different conditions.

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ShrinkBayes

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

Complex designs are common in (observational) clinical studies. Sequencing data for such studies are produced more and more often, implying challenges for the analysis, such as excess of zeros, presence of random effects and multi-parameter inference. Moreover, when sample sizes are small, inference is likely to be too liberal when, in a Bayesian setting, applying a non-appropriate prior or to lack power when not carefully borrowing information across features.

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Director

Submitted by ChenLiang on Tue, 01/09/2018 - 17:47

High-throughput measurement technologies have triggered a rise in large-scale cancer studies containing multiple levels of molecular data. While there are a number of efficient methods to analyze individual data types, there are far less that enhance data interpretation after analysis. We present the R package Director, a dynamic visualization approach to linking and interrogating multiple levels of molecular data after analysis for clinically meaningful, actionable insights.

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Tools4miRs

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

MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods.

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miRNAmeConverter

Submitted by ChenLiang on Mon, 01/09/2017 - 10:23

The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone.

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ICG

Submitted by ChenLiang on Tue, 01/09/2018 - 18:32

Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions.

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miRCarta

Submitted by ChenLiang on Tue, 01/09/2018 - 18:46

The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014.

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sRNATarget

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

Accurate prediction of sRNA targets plays a key role in determining sRNA functions. Here we introduced two mathematical models, sRNATargetNB and sRNATargetSVM, for prediction of sRNA targets using Nai ve Bayes method and support vector machines (SVM), respectively. The training dataset was composed of 46 positive samples (real sRNA-targets interaction) and 86 negative samples (no interaction between sRNA and targets). The leave-one-out cross-validation (LOOCV) classification accuracy was 91.67% for sRNATargetNB, and 100.00% for sRNATargetSVM.

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