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Briefings in Bioinformatics

Lidan Sun, Jing Wang, Xuli Zhu, Libo Jiang, Kirk Gosik, Mengmeng Sang, Fengsuo Sun, Tangren Cheng, Qixiang Zhang, Rongling Wu
No abstract text is available yet for this article.
February 15, 2017: Briefings in Bioinformatics
Lijun Lei, Siyu Xia, Dan Liu, Xiaoqing Li, Jing Feng, Yaqi Zhu, Jun Hu, Linjian Xia, Lieping Guo, Fei Chen, Hui Cheng, Ke Chen, Hanyang Hu, Xiaohua Chen, Feng Li, Shan Zhong, Nupur Mittal, Guohua Yang, Zhijian Qian, Leng Han, Chunjiang He
No abstract text is available yet for this article.
February 15, 2017: Briefings in Bioinformatics
Jifang Yan, Guohui Chuai, Chi Zhou, Chenyu Zhu, Jing Yang, Chao Zhang, Feng Gu, Han Xu, Jia Wei, Qi Liu
No abstract text is available yet for this article.
February 15, 2017: Briefings in Bioinformatics
Feng Bao, Yue Deng, Mulong Du, Zhiquan Ren, Qingzhao Zhang, Yanyu Zhao, Jinli Suo, Zhengdong Zhang, Meilin Wang, Qionghai Dai
No abstract text is available yet for this article.
February 15, 2017: Briefings in Bioinformatics
Khader Shameer, Benjamin S Glicksberg, Rachel Hodos, Kipp W Johnson, Marcus A Badgeley, Ben Readhead, Max S Tomlinson, Timothy O'Connor, Riccardo Miotto, Brian A Kidd, Rong Chen, Avi Ma'ayan, Joel T Dudley
No abstract text is available yet for this article.
February 15, 2017: Briefings in Bioinformatics
Guini Hong, Hongdong Li, Mengyao Li, Weicheng Zheng, Jing Li, Meirong Chi, Jun Cheng, Zheng Guo
No abstract text is available yet for this article.
February 14, 2017: Briefings in Bioinformatics
Xuefeng Wang, Hao Chen, Nancy R Zhang
No abstract text is available yet for this article.
February 4, 2017: Briefings in Bioinformatics
Yang-Jun Wen, Hanwen Zhang, Yuan-Li Ni, Bo Huang, Jin Zhang, Jian-Ying Feng, Shi-Bo Wang, Jim M Dunwell, Yuan-Ming Zhang, Rongling Wu
No abstract text is available yet for this article.
February 1, 2017: Briefings in Bioinformatics
Liyong Fu, Lidan Sun, Hao Han, Libo Jiang, Sheng Zhu, Meixia Ye, Shouzheng Tang, Minren Huang, Rongling Wu
No abstract text is available yet for this article.
February 1, 2017: Briefings in Bioinformatics
Yajing Hao, Lili Zhang, Yiwei Niu, Tanxi Cai, Jianjun Luo, Shunmin He, Bao Zhang, Dejiu Zhang, Yan Qin, Fuquan Yang, Runsheng Chen
Small proteins is the general term for proteins with length shorter than 100 amino acids. Identification and functional studies of small proteins have advanced rapidly in recent years, and several studies have shown that small proteins play important roles in diverse functions including development, muscle contraction and DNA repair. Identification and characterization of previously unrecognized small proteins may contribute in important ways to cell biology and human health. Current databases are generally somewhat deficient in that they have either not collected small proteins systematically, or contain only predictions of small proteins in a limited number of tissues and species...
January 29, 2017: Briefings in Bioinformatics
Alicia Poplawski, Harald Binder
Sample size calculation is a crucial step in study design but is not yet fully established for RNA sequencing (RNA-seq) analyses. To evaluate feasibility and provide guidance, we evaluated RNA-seq sample size tools identified from a systematic search. The focus was on whether real pilot data would be needed for reliable results and on identifying tools that would perform well in scenarios with different levels of biological heterogeneity and fold changes (FCs) between conditions. We used simulations based on real data for tool evaluation...
January 18, 2017: Briefings in Bioinformatics
Yunyan Gu, Ruiping Wang, Yue Han, Wenbin Zhou, Zhangxiang Zhao, Tingting Chen, Yuanyuan Zhang, Fuduan Peng, Haihai Liang, Lishuang Qi, Wenyuan Zhao, Da Yang, Zheng Guo
Synthetic viability, which is defined as the combination of gene alterations that can rescue the lethal effects of a single gene alteration, may represent a mechanism by which cancer cells resist targeted drugs. Approaches to detect synthetic viable (SV) interactions in cancer genome to investigate drug resistance are still scarce. Here, we present a computational method to detect synthetic viability-induced drug resistance (SVDR) by integrating the multidimensional data sets, including copy number alteration, whole-exome mutation, expression profile and clinical data...
January 17, 2017: Briefings in Bioinformatics
Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath
No abstract text is available yet for this article.
January 17, 2017: Briefings in Bioinformatics
Mehran Karimzadeh, Michael M Hoffman
Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others...
January 14, 2017: Briefings in Bioinformatics
Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands...
January 10, 2017: Briefings in Bioinformatics
James M Heather, Mazlina Ismail, Theres Oakes, Benny Chain
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information...
January 10, 2017: Briefings in Bioinformatics
Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes...
January 10, 2017: Briefings in Bioinformatics
Ping Zhang, Constantinos A Georgiou, Vladimir Brusic
Elemental metabolomics is quantification and characterization of total concentration of chemical elements in biological samples and monitoring of their changes. Recent advances in inductively coupled plasma mass spectrometry have enabled simultaneous measurement of concentrations of > 70 elements in biological samples. In living organisms, elements interact and compete with each other for absorption and molecular interactions. They also interact with proteins and nucleotide sequences. These interactions modulate enzymatic activities and are critical for many molecular and cellular functions...
January 10, 2017: Briefings in Bioinformatics
Hanyuan Zhang, Bruno Vieira Resende E Silva, Juan Cui
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes...
January 10, 2017: Briefings in Bioinformatics
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