Showing papers by "Cheng Li published in 2016"

3Disease Browser: A Web server for integrating 3D genome and disease-associated chromosome rearrangement data

Abstract: Chromosomal rearrangement (CR) events have been implicated in many tumor and non-tumor human diseases. CR events lead to their associated diseases by disrupting gene and protein structures. Also, they can lead to diseases through changes in chromosomal 3D structure and gene expression. In this study, we search for CR-associated diseases potentially caused by chromosomal 3D structure alteration by integrating Hi-C and ChIP-seq data. Our algorithm rediscovers experimentally verified disease-associated CRs (polydactyly diseases) that alter gene expression by disrupting chromosome 3D structure. Interestingly, we find that intellectual disability may be a candidate disease caused by 3D chromosome structure alteration. We also develop a Web server (3Disease Browser, http://3dgb.cbi.pku.edu.cn/disease/) for integrating and visualizing disease-associated CR events and chromosomal 3D structure.

The exon junction complex regulates the splicing of cell polarity gene DLG1 to control Wingless signaling in development

Abstract: Wingless (Wg)/Wnt signaling is conserved in all metazoan animals and plays critical roles in development. The Wg/Wnt morphogen reception is essential for signal activation, whose activity is mediated through the receptor complex and a scaffold protein Dishevelled (Dsh). We report here that the exon junction complex (EJC) activity is indispensable for Wg signaling by maintaining an appropriate level of Dsh protein for Wg ligand reception in Drosophila. Transcriptome analyses in Drosophila wing imaginal discs indicate that the EJC controls the splicing of the cell polarity gene discs large 1 (dlg1), whose coding protein directly interacts with Dsh. Genetic and biochemical experiments demonstrate that Dlg1 protein acts independently from its role in cell polarity to protect Dsh protein from lysosomal degradation. More importantly, human orthologous Dlg protein is sufficient to promote Dvl protein stabilization and Wnt signaling activity, thus revealing a conserved regulatory mechanism of Wg/Wnt signaling by Dlg and EJC.

A graphical article-level metric for intuitive comparison of large-scale literatures

Abstract: With the advances of all research fields, the volume of scientific literature has grown exponentially over the past decades, and the management and exploration of scientific literature is becoming an increasingly complicated task. It calls for a tool that combines scientific impacts and social focuses to visualize relevant papers from a specific research area and time period, and to find important and interesting papers. Therefore, we propose a graphical article-level metric (gALM), which captures the impact and popularity of papers from scientific and social aspects. These two dimensions are combined and visualized graphically as a circular map. The map is divided into sectors of papers belonging to a publication year, and each block represents a paper's journal citations by block size and readerships in Mendeley by block color. In this graphical way, gALM provides a more intuitive comparison of large-scale literatures. In addition, we also design an online Web server, Science Navigation Map (SNM), which not only visualizes the gALM but provides it with interactive features. Through an interactive visualization map of article-level metrics on scientific impact and social popularity in Mendeley, users can intuitively make a comparison of papers as well as explore and filter important and relevant papers by these metrics. We take the journal PLoS Biology as an example and visualize all the papers published in PLoS Biology during 2003 and 2014 by SNM. From this map, one can easily and intuitively find basic statistics of papers, such as the most cited papers and the most popular papers in Mendeley during a time period. SNM on the journal PLoS Biology is publicly available at http://www.linkscholar.org/plosbiology/.