Showing papers by "Beifang Niu published in 2020"

Pan-cancer analysis of whole genomes

Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.

Red Blood Cells as Potential Repositories of MicroRNAs in the Circulatory System.

Abstract: The amount of erythrocyte-derived microRNAs (miRNAs) represents the majority of miRNAs expressed in whole blood. miR-451, miR-144, and miR-486, which are abundant in red blood cells (RBCs), are involved in the process of erythropoiesis and disease occurrence. Moreover, erythrocyte-derived miRNAs have been reported to be potential biomarkers of specific diseases. However, the function and underlying mechanisms of miRNAs derived from erythrocytes remain unclear. Based on a review of previously published literature, we discuss several possible pathways by which RBC miRNAs may function and propose that RBCs may serve as repositories of miRNAs in the circulatory system and participate in the regulation of gene expression mainly via the transfer of miRNAs from erythrocyte extracellular vesicles (EVs). In the whole blood, there are still other important cell types such as leukocytes and platelets harboring functional miRNAs, and hemolysis also exists, which limit the abundance of miRNAs as disease biomarkers, and thus, miRNA studies on RBCs may be impacted. In the future, the role of RBCs in the regulation of normal physiological functions of the body and the entire circulatory system under pathological states, if any, remains to be determined.

HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures.

Abstract: Motivation HotSpot3D is a widely used software for identifying mutation hotspots on the 3D structures of proteins. To further assist users, we developed a new HotSpot3D web server to make this software more versatile, convenient and interactive. Results The HotSpot3D web server performs data pre-processing, clustering, visualization and log-viewing on one stop. Users can interactively explore each cluster and easily re-visualize the mutational clusters within browsers. We also provide a database that allows users to search and visualize proximal mutations from 33 cancers in the Cancer Genome Atlas. Availability and implementation http://niulab.scgrid.cn/HotSpot3D/. Supplementary information Supplementary data are available at Bioinformatics online.

RabbitQC: high-speed scalable quality control for sequencing data.

Abstract: Motivation Modern sequencing technologies continue to revolutionize many areas of biology and medicine. Since the generated datasets are error-prone, downstream applications usually require quality control methods to pre-process FASTQ files. However, existing tools for this task are currently not able to fully exploit the capabilities of computing platforms leading to slow runtimes. Results We present RabbitQC, an extremely fast integrated quality control tool for FASTQ files, which can take full advantage of modern hardware. It includes a variety of operations and supports different sequencing technologies (Illumina, Oxford Nanopore and PacBio). RabbitQC achieves speedups between one and two orders-of-magnitude compared to other state-of-the-art tools. Availability and implementation C++ sources and binaries are available at https://github.com/ZekunYin/RabbitQC. Supplementary information Supplementary data are available at Bioinformatics online.

Change-Encryption: Encryption Using Spatiotemporal Information as a Function Model

Abstract: Change-Encryption is a distributed layer-by-layer symmetric encryption technology combined with blockchain technology and cryptography. The approach relies on the identity information of all the nodes in the blockchain, and the time, space, and other attributes are used as encryption parameters to enable repeated encryption. In this work, the identity information of the data sender and receiver is considered as the key, and the spatial and identity information values of the node are considered as dynamic encryption parameters to increase the uncertainty of decryption, thereby solving the data security problem of the blockchain technology during communication. In addition, the self-identification principle of the data receiver, reduction principle of the data sender, and two unique countermeasures employed in the Change-Encryption are introduced in detail. The findings demonstrate the value of the proposed approach.

Digital Currency Investment Strategy Framework Based on Ranking

Abstract: Quantitative research of digital currency is important in the financial sector. Existing quantitative research mainly focuses on pairs trade, multifactor models, and investment portfolios. Investment portfolios refer to the allocation of funds to different types of financial products to minimise investment risk when expected returns can be obtained, or maximise returns on investment when investment risks are controllable. Herein, we propose a ranking-based digital currency investment strategy framework for investment portfolios in the digital currency market. The framework mainly involves selecting digital currency attributes, pre-processing historical data, exporting the ranking model of the investment portfolio strategy, and parameter optimisation.