<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ewing, Adam D</style></author><author><style face="normal" font="default" size="100%">Houlahan, Kathleen E</style></author><author><style face="normal" font="default" size="100%">Hu, Yin</style></author><author><style face="normal" font="default" size="100%">Ellrott, Kyle</style></author><author><style face="normal" font="default" size="100%">Caloian, Cristian</style></author><author><style face="normal" font="default" size="100%">Yamaguchi, Takafumi N</style></author><author><style face="normal" font="default" size="100%">Bare, J Christopher</style></author><author><style face="normal" font="default" size="100%">P’ng, Christine</style></author><author><style face="normal" font="default" size="100%">Waggott, Daryl</style></author><author><style face="normal" font="default" size="100%">Sabelnykova, Veronica Y</style></author><author><style face="normal" font="default" size="100%">Kellen, Michael R</style></author><author><style face="normal" font="default" size="100%">Norman, Thea C</style></author><author><style face="normal" font="default" size="100%">Haussler, David</style></author><author><style face="normal" font="default" size="100%">Friend, Stephen H</style></author><author><style face="normal" font="default" size="100%">Stolovitzky, Gustavo</style></author><author><style face="normal" font="default" size="100%">Margolin, Adam A</style></author><author><style face="normal" font="default" size="100%">Stuart, Joshua M</style></author><author><style face="normal" font="default" size="100%">Boutros, Paul C</style></author></authors><secondary-authors><author><style face="normal" font="default" size="100%">ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants</style></author><author><style face="normal" font="default" size="100%">Liu Xi</style></author><author><style face="normal" font="default" size="100%">Ninad Dewal</style></author><author><style face="normal" font="default" size="100%">Yu Fan</style></author><author><style face="normal" font="default" size="100%">Wenyi Wang</style></author><author><style face="normal" font="default" size="100%">David Wheeler</style></author><author><style face="normal" font="default" size="100%">Andreas Wilm</style></author><author><style face="normal" font="default" size="100%">Grace Hui Ting</style></author><author><style face="normal" font="default" size="100%">Chenhao Li</style></author><author><style face="normal" font="default" size="100%">Denis Bertrand</style></author><author><style face="normal" font="default" size="100%">Niranjan Nagarajan</style></author><author><style face="normal" font="default" size="100%">Qing-Rong Chen</style></author><author><style face="normal" font="default" size="100%">Chih-Hao Hsu</style></author><author><style face="normal" font="default" size="100%">Ying Hu</style></author><author><style face="normal" font="default" size="100%">Chunhua Yan</style></author><author><style face="normal" font="default" size="100%">Warren Kibbe</style></author><author><style face="normal" font="default" size="100%">Daoud Meerzaman</style></author><author><style face="normal" font="default" size="100%">Kristian Cibulskis</style></author><author><style face="normal" font="default" size="100%">Mara Rosenberg</style></author><author><style face="normal" font="default" size="100%">Louis Bergelson</style></author><author><style face="normal" font="default" size="100%">Adam Kiezun</style></author><author><style face="normal" font="default" size="100%">Amie Radenbaugh</style></author><author><style face="normal" font="default" size="100%">Anne-Sophie Sertier</style></author><author><style face="normal" font="default" size="100%">Anthony Ferrari</style></author><author><style face="normal" font="default" size="100%">Laurie Tonton</style></author><author><style face="normal" font="default" size="100%">Kunal Bhutani</style></author><author><style face="normal" font="default" size="100%">Nancy F Hansen</style></author><author><style face="normal" font="default" size="100%">Difei Wang</style></author><author><style face="normal" font="default" size="100%">Lei Song</style></author><author><style face="normal" font="default" size="100%">Zhongwu Lai</style></author><author><style face="normal" font="default" size="100%">Liao, Yang</style></author><author><style face="normal" font="default" size="100%">Shi, Wei</style></author><author><style face="normal" font="default" size="100%">Carbonell-Caballero, José</style></author><author><style face="normal" font="default" size="100%">Joaquín Dopazo</style></author><author><style face="normal" font="default" size="100%">Cheryl C K Lau</style></author><author><style face="normal" font="default" size="100%">Justin Guinney</style></author></secondary-authors></contributors><titles><title><style face="normal" font="default" size="100%">Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature methods</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">cancer</style></keyword><keyword><style  face="normal" font="default" size="100%">NGS</style></keyword><keyword><style  face="normal" font="default" size="100%">variant calling</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 May 18</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3407.html</style></url></web-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Eduati, Federica</style></author><author><style face="normal" font="default" size="100%">Mangravite, Lara M</style></author><author><style face="normal" font="default" size="100%">Wang, Tao</style></author><author><style face="normal" font="default" size="100%">Tang, Hao</style></author><author><style face="normal" font="default" size="100%">Bare, J Christopher</style></author><author><style face="normal" font="default" size="100%">Huang, Ruili</style></author><author><style face="normal" font="default" size="100%">Norman, Thea</style></author><author><style face="normal" font="default" size="100%">Kellen, Mike</style></author><author><style face="normal" font="default" size="100%">Menden, Michael P</style></author><author><style face="normal" font="default" size="100%">Yang, Jichen</style></author><author><style face="normal" font="default" size="100%">Zhan, Xiaowei</style></author><author><style face="normal" font="default" size="100%">Zhong, Rui</style></author><author><style face="normal" font="default" size="100%">Xiao, Guanghua</style></author><author><style face="normal" font="default" size="100%">Xia, Menghang</style></author><author><style face="normal" font="default" size="100%">Abdo, Nour</style></author><author><style face="normal" font="default" size="100%">Kosyk, Oksana</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Prediction of human population responses to toxic compounds by a collaborative competition.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature biotechnology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Aug 10</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3299.html</style></url></web-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The ability to computationally predict the effects of toxic compounds on humans could help address the deficiencies of current chemical safety testing. Here, we report the results from a community-based DREAM challenge to predict toxicities of environmental compounds with potential adverse health effects for human populations. We measured the cytotoxicity of 156 compounds in 884 lymphoblastoid cell lines for which genotype and transcriptional data are available as part of the Tox21 1000 Genomes Project. The challenge participants developed algorithms to predict interindividual variability of toxic response from genomic profiles and population-level cytotoxicity data from structural attributes of the compounds. 179 submitted predictions were evaluated against an experimental data set to which participants were blinded. Individual cytotoxicity predictions were better than random, with modest correlations (Pearson’s r &lt; 0.28), consistent with complex trait genomic prediction. In contrast, predictions of population-level response to different compounds were higher (r &lt; 0.66). The results highlight the possibility of predicting health risks associated with unknown compounds, although risk estimation accuracy remains suboptimal.</style></abstract></record></records></xml>