m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome

N 6-Methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. It plays a pivotal role during various biological processes and disease pathogenesis. We present here a comprehensive knowledgebase, m6A-Atlas, for unraveling the m6A epitranscriptome. Compared to existing databases, m6A-Atlas features a high-confidence collection of 442 162 reliable m6A sites identified from seven base-resolution technologies and the quantitative (rather than binary) epitranscriptome profiles estimated from 1363 high-throughput sequencing samples. It also offers novel features, such as; the conservation of m6A sites among seven vertebrate species (including human, mouse and chimp), the m6A epitranscriptomes of 10 virus species (including HIV, KSHV and DENV), the putative biological functions of individual m6A sites predicted from epitranscriptome data, and the potential pathogenesis of m6A sites inferred from disease-associated genetic mutations that can directly destroy m6A directing sequence motifs. A user-friendly graphical user interface was constructed to support the query, visualization and sharing of the m6A epitranscriptomes annotated with sites specifying their interaction with post-transcriptional machinery (RBP-binding, microRNA interaction and splicing sites) and interactively display the landscape of multiple RNA modifications. These resources provide fresh opportunities for unraveling the m6A epitranscriptomes. m6A-Atlas is freely accessible at: www.xjtlu.edu.cn/biologicalsciences/atlas.

CFEA: a cell-free epigenome atlas in human diseases

Epigenetic alterations, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and nucleosome positioning (NP), in cell-free DNA (cfDNA) have been widely observed in human diseases, and many available cfDNA-based epigenome-wide profiles exhibit high sensitivity and specificity in disease detection and classification. However, due to the lack of efficient collection, standardized quality control, and analysis procedures, efficiently integrating and reusing these data remain considerable challenges. Here, we introduce CFEA (http://www.bio-data.cn/CFEA), a cell-free epigenome database dedicated to three types of widely adopted epigenetic modifications (5mC, 5hmC and NP) involved in 27 human diseases. We developed bioinformatic pipelines for quality control and standard data processing and an easy-to-use web interface to facilitate the query, visualization and download of these cell-free epigenome data. We also manually curated related biological and clinical information for each profile, allowing users to better browse and compare cfDNA epigenomes at a specific stage (such as early- or metastasis-stage) of cancer development. CFEA provides a comprehensive and timely resource to the scientific community and supports the development of liquid biopsy-based biomarkers for various human diseases.

A Visual Simulation Method for 2-D Complex Situation of Electromagnetic Environment

As the complex situation of electromagnetic environment is difficult to be analyzed and simulated visibly, interface program is developed based on the calculation module of Wireless Insite2.5 software. Equipments such as communication, radar, electronics resists and other radio devices are studied to build accurate theoretic models. Moreover, a method for creating software receivers quickly in MATLAB is proposed and other equipment models are created automatically just based on the parameters of equipments in the same way. Then, situations of time, frequency and energy-domain are calculated successfully with using Wireless Insite2.5. Complex 2-D situation of electromagnetic environment is displayed in the 2-D map by using MATLAB map display technology. At last, Display and query visualization for complex situation of electromagnetic environment is realized by designing a visual data query tool of mouse.

A Pool of Queries: Interactive Multidimensional Query Visualization for Information Seeking in Digital Libraries

In this article, I present a novel relational visualization that supports people at exploration of scientific literature in digital libraries. This visualization provides an integrated view of multiple dimensions concealed in the scientific literature. It displays, for example, authors and scientific organizations together with freely defined search queries and highlights the intersections between them. The proposed visual representation introduces interactive drag-and-drop operations for manipulation of queries in order to retrieve further results. These operations enable information seekers to employ efficient online search strategies that involve Boolean AND, OR and NOT operators. In doing so, an information seeker can refine (or relax) various search queries in an interactive way during a focusing or a defocusing phase. The intersections of queries are made explicitly visible to enable the information seeker to build an individual picture of the research area under investigation and to avoid frustrating ‘zero hit’ situations.