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| 1 | Identifying viruses from metagenomic data using deep learning显示文摘Background:The recent development of metagenomic sequencing makes it possible to massively sequence microbial genomes including viral genomes without the need for laboratory culture.Existing reference-based and gene homology-based methods are not efficient in identifying unknown viruses or short viral sequences from metagenomic data.Methods:Here we developed a reference-free and alignment-free machine learning method,DeepVirFinder,for identifying viral sequences in metagenomic data using deep learning.Results'.Trained based on sequences from viral RefSeq discovered before May 2015,and evaluated on those discovered after that date,DeepVirFinder outperformed the state-of-the-art method VirFinder at all contig lengths,achieving AUROC 0.93,0.95,0.97,and 0.98 for 300,500,1000,and 3000 bp sequences respectively.Enlarging the training data with additional millions of purified viral sequences from metavirome samples further improved the accuracy for identifying virus groups that are under-represented.Applying DeepVirFinder to real human gut metagenomic samples,we identified 51,138 viral sequences belonging to 175 bins in patients with colorectal carcinoma(CRC).Ten bins were found associated with the cancer status,suggesting viruses may play important roles in CRC.Conclusions:Powered by deep learning and high throughput sequencing metagenomic data,DeepVirFinder significantly improved the accuracy of viral identification and will assist the study of viruses in the era of metagenomics. | Jie Ren Kai Song Chao Deng Nathan AAhlgren Jed AFuhrman Yi Li Xiaohui Xie Ryan Poplin Fengzhu Sun | 2020 | Quantitative Biology2020，8，1： | 2 |
| 2 | Phase Ⅲ,randomized study of gemcitabine and oxaliplatin versus gemcitabine (fixed-dose rate infusion) compared with gemcitabine (SO-minute infusion) in patients with pancreatic carcinoma E6201:a trial of the Eastern Cooperative Oncology Group显示文摘 | Poplin E Feng Y Berlin J | 2009 | J Clin Oncol2009，27，23： | 1 |
| 3 | A framework for variation discovery and genotyping using next-generation DNA sequencing data显示文摘 | DePristo MA Banks E Poplin R | 2011 | Nat Genet2011，43，5： | 1 |
| 4 | Phase Ⅲ trial of gemcit- abine ( 30-minute infusion) versus gemcitabine ( fixed-dose-rate in- fusion (FDR) ) versus gemcitabine + oxaliplatin (GEMOX) in pa- tients with advanced pancreatic cancer显示文摘 | Poplin E Levy DE Berlin J | 2006 | J Clin Oncol2006，24，： | 1 |
| 5 | A hy- brid high integrity container for disposal of low- level radioactive wastes 显示文摘 | MCCOYSB POPLIN WM JUR T A | 1987 | Waste Manage1987，3，： | 1 |
| 6 | Randomized clinical trial of mitomyein-C with or without pretreatment with WR-2721 in patients with advanced colorectal cancer 显示文摘 | Poplin Ea Lorusso P Lokieh JJ | 1994 | Cancer Chemother Pharmaeol1994，33，5： | 1 |
| 7 | Mortality associated with irinotecan plus bolus fluorouracil/leucovorin: summary findings of an independent panel 显示文摘 | Rothenberg ML Meropol NJ Poplin EA | 2001 | J Clin Oncol2001，19，18： | 1 |
| 8 | Mortality associated with irinotecan plus bolus fluorouracil/leucovorin: summary findings of an independent panel显示文摘 | Rothenberg ML Meropol N J Poplin EA | 2001 | J Clin Oncol2001，19，18： | 1 |
| 9 | Environmental arsenic exposure and sputum metalloproteinase concentrations显示文摘 | Josyula AB Poplin GS Kurzius-Spencer M | | 0，，： | 1 |
| 10 | Envirortmental arsenic exposure and sputum metalloproteinase concentrations显示文摘 | Arun B Josyula Gerald S Poplin Margaret Kurzius-Spencer | 2006 | Environmental Research2006，102，： | 1 |
| 11 | A framework for variation dis- covery and genotyping using next-generation DNA sequencing data 显示文摘 | DePristo M A Banks E Poplin R | 2011 | Nature genetics2011，43，5： | 1 |
| 12 | A framework for variation discovery and genotyping using next-generation DNA sequencing data 显示文摘 | DePristo MA Banks E Poplin R | 2011 | Nat Genet2011，43，5： | 1 |
| 13 | Determinantal identities over commutative semirings 显示文摘 | Poplin P Hartwig R | 2004 | Linear Algebra Appl2004，387，： | 1 |
| 14 | An enigmatic ac- tinopterygian( Pisces : Osteichthyes) from the Upper Per- mian of China显示文摘 | Poplin C Wang N C Richter M | 1991 | Zoological Journal of the Linnean So- ciety1991，103，1： | 1 |
| 15 | 'Spontaneous'delayed colon and rectal anastomotic complications associated with bevacizumab therapy显示文摘 | August DA Serrano D Poplin E | | 0，，： | 1 |
| 16 | Determinantal identities over commutative semirings显示文摘 | Poplin P L Hartwig R E | | 0，，： | 1 |
| 17 | Mortality associated with irinotecan plus bolus fluorouracil/leucovorin:summary findings of an independent panel显示文摘 | Rothenberg ML Meropol NJ Poplin EA | 2001 | J Clin Oncol2001，19，18： | 1 |
| 18 | Mortality associated with irinotecan plus bolus Fluorouracil/Leucovorin:summary findings of an independent panel显示文摘 | Rothenberg ML Meropol NJ Poplin EA | 2001 | J Clin Oncol2001，19，18： | 1 |
| 19 | Mortality associated with irinotecan plus bolus Fluorouracil/Leucovorin:summary findings of an independent panel显示文摘 | Rothenberg ML Meropol NJ Poplin EA | 2001 | J Clin Oncol2001，19，18： | 1 |
| 20 | Safety and efficacy of EPO906 in patients with advanced colorectal cancer: a re- view of 2 phase II trials 显示文摘 | Poplin E Moore M O'Dwyer P | 2003 | Pro Am Soc Clin Oncol2003，，： | 1 |
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