Stanford researchers have developed a computational platform for analyzing the molecular behavior of individual cells in tissue samples,...
Read More »CREDO – disease-relevant A-to-I RNA-editing discovery in breast cancer
Adenosine-to-Inosine (A-to-I) RNA editing is the most prevalent post-transcriptional modification of RNA molecules. Researchers have attempted to find reliable RNA editing using next generation sequencing (NGS) data. However, most of these attempts suffered from a high rate of false positives, ...
Read More »PIRSitePredict – protein functional site prediction using position-specific rules
Methods focused on predicting 'global' annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage. Methods to provide fine-grained 'local' annotation...
Read More »Methods for annotation and validation of circular RNAs from RNA-Seq data
Circular RNAs are an emerging class of transcript isoforms created by unique back splicing of exons to form a closed covalent circular structure. While...
Read More »Ancestral transcriptome inference based on RNA-Seq data
With the help of high-throughput NGS (next-generation sequencing) technologies, ancestral transcriptome reconstruction is helpful to understand the complexity of transcriptional regulatory systems that underlies the evolution of multiple cellular metazoans with sophisticated functions and distinctive.,,
Read More »CisPi – a transcriptomic score for disclosing cis-acting disease-associated lincRNAs
Long intergenic noncoding RNAs (lincRNAs) have risen to prominence in cancer biology as new biomarkers of disease. Those lincRNAs transcribed from active cis-regulatory elements (enhancers) have provided mechanistic insight into cis-acting...
Read More »CRISPR Visualizer – rapid identification and visualization of CRISPR loci
A CRISPR locus, defined by an array of repeat and spacer elements, constitutes a genetic record of the ceaseless battle between bacteria and viruses, showcasing the genomic integration of spacers acquired from invasive DNA. In particular, iterative...
Read More »LncFinder – an integrated platform for long non-coding RNA identification
Discovering new long non-coding RNAs (lncRNAs) has been a fundamental step in lncRNA-related research. Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances ...
Read More »Researchers discover novel and valuable plant gene modules from large-scale RNA-seq samples
The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism. Using large-scale RNA-seq samples, ...
Read More »Identification of transcribed protein coding sequence remnants within lincRNAs
Long intergenic non-coding RNAs (lincRNAs) are non-coding transcripts >200 nucleotides long that do not overlap protein-coding sequences. Importantly, such elements are known to be tissue-specifically expressed and to play a widespread role in gene regulation...
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