We developed a robust computational statistical framework to identify RNA editing events from RNA-Seq data with high specificity. Our approach handles several outstanding challenges of genome-wide editing analyses, including the effect of editing on read alignment and the utilization of redundant reads. By applying this framework, we characterized the nuclear and cytosolic editomes of seven hum...

In higher plants, RNA editing is a posttranscriptional process that converts C to U in organelle mRNAs. Although RNA editing in mitochondria occurs much more frequently than in chloroplasts, editing of exogenously supplied RNA substrates in vitro and in organello has shown that editing in the two organelles shares some common features. In particular, the 20 nucleotides upstream of the editing s...

Post-transcriptional C-to-U RNA editing occurs at specific sites in plastid and plant mitochondrial transcripts. Members of the Arabidopsis pentatricopeptide repeat (PPR) motif-containing protein family and RNA-editing factor Interacting Protein (RIP, also known as MORF) family have been characterized as essential components of the RNA editing apparatus. Recent studies reveal that several organ...

We spell out a formal equivalence between the naive Laplacian editing and semi-supervised learning by bi-Laplacian Regularized Least Squares. This allows us to write the solution to Laplacian mesh editing in a closed form, based on which we introduce the Generalized Linear Editing (GLE). GLE has both naive Laplacian editing and gradient based editing as special cases. GLE allows using diffusion...

Despite consensus in focus on form (FOF) instruction over the facilitative role of noticing, controversy has not quelled over ways of directing EFL learners’ attention towards formal features via implicit techniques like input-enhancement or explicit metacognitive feedback and interactive peer-editing on the output they produce. This quasi-experimental study investigated the impact of input enh...

We present RADAR--a rigorously annotated database of A-to-I RNA editing (available at http://RNAedit.com). The identification of A-to-I RNA editing sites has been dramatically accelerated in the past few years by high-throughput RNA sequencing studies. RADAR includes a comprehensive collection of A-to-I RNA editing sites identified in humans (Homo sapiens), mice (Mus musculus) and flies (Drosop...

The serotonin 2C receptor (5-HT(2C)R)-a key regulator of diverse neurological processes-exhibits functional variability derived from editing of its pre-mRNA by site-specific adenosine deamination (A-to-I pre-mRNA editing) in five distinct sites. Here we describe a statistical technique that was developed for analysis of the dependencies among the editing states of the five sites. The statistica...

Enforcement of global cooperation urges the rapid growth of cooperative work. As a typical application of it, cooperative editing is widely used in many fields gradually, especially in knowledge intensive application. Workflow is a kind of automation technology by predefined process rules and tasks. It can bring us clarity in process control and management, which are two important facets in coo...

Alternative splicing and adenosine to inosine (A to I) RNA-editing are major factors leading to co- and post-transcriptional modification of genetic information. Both, A to I editing and splicing occur in the nucleus. As editing sites are frequently defined by exon-intron basepairing, mRNA splicing efficiency should affect editing levels. Moreover, splicing rates affect nuclear retention and wi...

RNA editing is a term describing a variety of novel mechanisms for the modification of nucleotide sequences of RNA transcripts in different organisms. These editing events include (a) the U-insertion and -deletion type of editing found in the mitochondrion of kinetoplastid protozoa, (b) the C-insertion editing found in the mitochondrion of Physarum, (c) the C-to-U substitution editing of the ma...