Rapid progresses in RNA-Seq and computational methods have assisted in quantifying A-to-I RNA editing and altered RNA editing sites have been widely observed in various diseases. Nevertheless, functional characterization of the altered RNA editing sites still remains a challenge. Here, we developed perturbations of RNA editing sites (PRES; http://bio-bigdata.hrbmu.edu.cn/PRES/) as the webserver for decoding functional perturbations of RNA editing sites based on editome profiling. After uploading an editome profile among samples of different groups, PRES will first annotate the editing sites to various genomic elements and detect differential editing sites under the user-selected method and thresholds. Next, the downstream functional perturbations of differential editing sites will be characterized from gain or loss miRNA/RNA binding protein regulation, RNA and protein structure changes, and the perturbed biological pathways. A prioritization module was developed to rank genes based on their functional consequences of RNA editing events. PRES provides user-friendly functionalities, ultra-efficient calculation, intuitive table and figure visualization interface to display the annotated RNA editing events, filtering options and elaborate application notebooks. We anticipate PRES will provide an opportunity for better understanding the regulatory mechanisms of RNA editing in human complex diseases.

Long non-coding RNAs (lncRNAs) have been revealed to play essential roles in the human cardiovascular system. However, information about their mechanisms is limited, and a comprehensive view of cardiac lncRNAs is lacking from a multiple tissues perspective to date. Here, the landscape of the lncRNA transcriptome in human heart was summarized. We summarized all lncRNA transcripts from publicly available human transcriptome resources (156 heart samples and 210 samples from 29 other tissues) and systematically analysed all annotated and novel lncRNAs expressed in heart. A total of 7485 lncRNAs whose expression was elevated in heart (HE lncRNAs) and 453 lncRNAs expressed in all 30 analysed tissues (EIA lncRNAs) were extracted. Using various bioinformatics resources, methods and tools, the features of these lncRNAs were discussed from various perspectives, including genomic structure, conservation, dynamic variation during heart development, cis-regulation, differential expression in cardiovascular diseases and cancers as well as regulation at transcriptional and post-transcriptional levels. Afterwards, all the features discussed above were integrated into a user-friendly resource named CARDIO-LNCRNAS (http://bio-bigdata.hrbmu.edu.cn/CARDIO-LNCRNAS/ or http://www.bio-bigdata.net/CARDIO-LNCRNAS/). This study represents the first global view of lncRNAs in the human cardiovascular system based on multiple tissues and sheds light on the role of lncRNAs in developments and heart disorders.

The discovery of microRNA (miRNA)-miRNA crosstalk has greatly improved our understanding of complex gene regulatory networks in normal and disease-specific physiological conditions. Numerous approaches have been proposed for modeling miRNA-miRNA networks based on genomic sequences, miRNA-mRNA regulation, functional information and phenomics alone, or by integrating heterogeneous data. In addition, it is expected that miRNA-miRNA crosstalk can be reprogrammed in different tissues or specific diseases. Thus, transcriptome data have also been integrated to construct context-specific miRNA-miRNA networks. In this review, we summarize the state-of-the-art miRNA-miRNA network modeling methods, which range from genomics to phenomics, where we focus on the need to integrate heterogeneous types of omics data. Finally, we suggest future directions for studies of crosstalk of noncoding RNAs. This comprehensive summarization and discussion elucidated in this work provide constructive insights into miRNA-miRNA crosstalk.

In this paper, a novel technique is proposed to address the joint sampling timing acquisition for baseband and broadband power-line communication (BB-PLC) systems using Orthogonal-Frequency-Division-Multiplexing (OFDM), including the sampling phase offset (SPO) and the sampling clock offset (SCO). Under pairwise correlation and joint Gaussian assumption of received signals in frequency domain, an approximated form of the log-likelihood function is derived. Instead of a high complexity two-dimension grid-search on the likelihood function, a five-step method is employed for accurate estimations. Several variants are presented in the same framework with different complexities. Unlike conventional pilot-assisted schemes using the extra phase rotations within one OFDM block, the proposed technique turns to the phase rotations between adjacent OFDM blocks. Analytical expressions of the variances and biases are derived. Extensive simulation results indicate significant performance improvements over conventional schemes. Additionally, effects of several noise models including non-Gaussianity, cyclo-stationarity, and temporal correlation are analyzed and simulated. Robustness of the proposed technique against violation of the joint Gaussian assumption is also verified by simulations.

In this paper, an improved algorithm of coarse synchronization in the downlink of 3GPP LTE system is presented. This new algorithm can reduce the MSE (mean square error) of detected fractional carrier frequency offset (FCFO) by an order of magnitude and improve the accuracy rate of start point estimation by near 80 percent when SNR equals 0 in contrast with conventional coarse synchronization algorithms, such as ML, MMSE, S&C and MC. The simulation result for the proposed algorithm is presented in comparison with the conventional algorithms.