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cyyuan2002

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[交流] RNA-seq相关论文征稿 (IF 1.17)

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2014年11月30日

本人作为Evolutionary Bioinformatics (https://www.la-press.com/journal-evolutionary-bioinformatics-j17)的guest editor，现在各位战友征集RNA-seq有关的论文稿件。稿件类型可以是研究论文，也可以是综述或者是会议摘要，研究计划等。投稿如果接收，将可享受25%的稿费减免。如果有投稿意向，或有其他问题，请尽快email与我联系(ychenbioinfo@gmail.com)。请在11月30日之前给我有关投稿意向，包括论文题目等信息，我将发送正式的约稿邀请，文章可以在接下来的几个月内完成。

以下是稿件征集有研究方向介绍：
Next generation sequencing (NGS) technologies have enabled unprecedentedly deep characterization of transcriptomes. Compared to the microarray technology, NGS has been a much more favorable method for transcriptome profiling, as it doesn’t require any pre-existing knowledge on the transcriptome of any given species. By sequencing transcriptomes to enough depth, several studies have reported a remarkably large number of novel RNA species and/or previously undetected splice forms. An inclusive identification of genes for organisms without genome information is also within reach. With intricate designs, it is even possible to specifically sequence the double- stranded portion of RNAs, such that the secondary structure of these RNAs could be inferred. Such comprehensive elucidation of transcriptomes has opened many new venues for studies on the function and evolution of the diverse RNA repertoire. Current supplement aims to serve as a portal to report original studies and summarize progress in this fast-moving area.
(1) Novel RNA species discovered by NGS and their unique evolutionary history

Genome-wide studies utilizing NGS technologies have uncovered novel types of RNAs, such as lncRNA, circular RNA and spliRNA. Many of these novel RNA species have been reported to play important regulatory roles. With the continuous advancement of sequencing technologies and experimental designs, it is expected that even more RNA species will be discovered. Surprisingly, many lincRNAs, including several lincRNAs with known functions, have low interspecific sequence conservation. Several studies have suggested that structural conversation in these lincRNAs may have been retained, despite the apparent lack of sequence conservation. These recently identified non-coding RNAs represent an evolutionary history different from that of the protein coding genes, which remains to be explored.
(2) The function and evolution of alternative splicing
Alternative splicing tremendously diversifies transcriptomes among organisms, even when their repertoires of protein coding genes are similar. The fast improvement on read length of NGS technologies will render a more thorough and unambiguous identification of alternative splice forms . Such resources could serve as the basis for exploring conservation and divergence of splicing events among organisms. They could also facilitate studies on the function of splicing events specific to certain organisms.
(3) RNA-seq of non-model organisms for phylogenomic studies
RNA-seq approachesenabled de novo identification of genes from organisms of no assembled genome sequences. Analyzing such extensive list of genes will result in better resolution of organism phylogeny. In addition, by comparing gene sequences among a wide range of organisms, many intriguing evolutionary questions may be addressed. For instance, how frequently genome duplication has happened in a certain taxon? How frequently horizontal gene transfer has happened between symbiotic organisms or parasites and hosts?
(4) RNA sequencing as an approach to study RNA secondary structure
Specific enrichment and sequencing of double-stranded portion of RNAs have been proven to be a useful measure to study RNA secondary structures. Comparison of RNA secondary structures among organisms will lead to identification of conserved structure motifs, and also may be used to infer their functions.

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