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Ebbie

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

DNA sequencing is used ubiquitously: from deciphering genomes to determining the primary sequence of small RNAs (smRNAs). The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products.

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CARD

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

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov).

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LimiTT

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

MicroRNAs (miRNAs) impact various biological processes within animals and plants. They complementarily bind target mRNAs, effecting a post-transcriptional negative regulation on mRNA level. The investigation of miRNA target interactions (MTIs) by high throughput screenings is challenging, as frequently used in silico target prediction tools are prone to emit false positives. This issue is aggravated for niche model organisms, where validated miRNAs and MTIs both have to be transferred from well described model organisms.

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5
Average: 4.5 (2 votes)

Automatic learning of pre-miRNAs from different species

Submitted by ChenLiang on Thu, 04/06/2017 - 17:26

Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower.

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Average: 5 (1 vote)

Mirnovo

Submitted by ChenLiang on Tue, 01/09/2018 - 19:25

The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large numbers of miRNAs that are expressed in very particular cell types and remain elusive. Sequencing allows us to quickly and accurately identify the expression of known miRNAs from small RNA-Seq data. The biogenesis of miRNAs leads to very specific characteristics observed in their sequences.

Rating: 
4
Average: 3.5 (2 votes)

si-shRNA Selector

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

Prediction of efficient oligonucleotides for RNA interference presents a serious challenge, especially for the development of genome-wide RNAi libraries which encounter difficulties and limitations due to ambiguities in the results and the requirement for significant computational resources. Here we present a fast and practical algorithm for shRNA design based on the thermodynamic parameters.

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Average: 5 (1 vote)

PmiRExAt

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

High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving.

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SAMMate

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

Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing this information.

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SMIRP

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

The prediction of novel pre-microRNA (miRNA) from genomic sequence has received considerable attention recently. However, the majority of studies have focused on the human genome. Previous studies have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained methods are applied to other species, however they have failed to report the dramatic drop in specificity (the ability to correctly reject non-miRNA sequences) in non-human genomes.

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OMICtools

Submitted by ChenLiang on Thu, 10/20/2016 - 20:44

Recent advances in 'omic' technologies have created unprecedented opportunities for biological research, but current software and database resources are extremely fragmented. OMICtools is a manually curated metadatabase that provides an overview of more than 4400 web-accessible tools related to genomics, transcriptomics, proteomics and metabolomics. All tools have been classified by omic technologies (next-generation sequencing, microarray, mass spectrometry and nuclear magnetic resonance) associated with published evaluations of tool performance.

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Average: 5 (1 vote)

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