VIP: an integrated pipeline for metagenomics of virus identification and discovery
暂无分享,去创建一个
Yi Zhang | Yang Li | Xuejun Ma | Hao Wang | P. Niu | Xuejun Ma | Ji Wang | Peihua Niu | Kai Nie | Chen Zhang | Ji Wang | Yi Zhang | Yang Li | K. Nie | Hao Wang | Chen Zhang
[1] Reinhard Simon,et al. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. , 2009, Virology.
[2] Yun Zhang,et al. ViPR: an open bioinformatics database and analysis resource for virology research , 2011, Nucleic Acids Res..
[3] C. Glaser,et al. Diagnostic approaches for patients with suspected encephalitis , 2007, Current infectious disease reports.
[4] J. Derisi,et al. Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing , 2012, PLoS neglected tropical diseases.
[5] I. Tzanetakis,et al. Development of a virus detection and discovery pipeline using next generation sequencing. , 2014, Virology.
[6] Siu-Ming Yiu,et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..
[7] C. Joshi,et al. Complete Genome Sequence of Bluetongue Virus Serotype 16 of Goat Origin from India , 2012, Journal of Virology.
[8] Chengsheng Jiang,et al. Dengue fever: a new challenge for China? , 2014, Global Health Action.
[9] Robert A. Edwards,et al. Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..
[10] I. Dworkin,et al. A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach , 2014, BMC Genomics.
[11] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[12] Richard H Scheuermann,et al. Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance , 2012, Influenza and other respiratory viruses.
[13] M. Zaharia,et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples , 2014, Genome research.
[14] H. Swerdlow,et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.
[15] Terry Ng,et al. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data , 2015, Nucleic acids research.
[16] Weiqi Wang,et al. Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) from the First Imported MERS-CoV Case in China , 2015, Genome Announcements.
[17] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[18] Zhongming Zhao,et al. VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data , 2013, PloS one.
[19] Yongan Zhao,et al. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data , 2011, Bioinform..
[20] Kun Qu,et al. Rapid identification of non-human sequences in high-throughput sequencing datasets , 2012, Bioinform..
[21] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[22] Garrett E. Schramm,et al. Predictors of 30-day mortality and hospital costs in patients with ventilator-associated pneumonia attributed to potentially antibiotic-resistant gram-negative bacteria. , 2008, Chest.
[23] Christian Drosten,et al. Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome , 2003, Science.
[24] S. Altschul,et al. Improved Sensitivity of Nucleic Acid Database Searches Using Application-Specific Scoring Matrices , 1991 .
[25] L. Finelli,et al. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. , 2009, The New England journal of medicine.
[26] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[27] Jie Dong,et al. Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus. , 2018 .
[28] M. Cáccamo,et al. A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing , 2011, PloS one.
[29] G. Getz,et al. PathSeq: software to identify or discover microbes by deep sequencing of human tissue , 2011, Nature Biotechnology.
[30] Joaquín Dopazo,et al. ETE: a python Environment for Tree Exploration , 2010, BMC Bioinformatics.
[31] Hideaki Tanaka,et al. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads , 2011, BCB '11.
[32] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[33] A. Akobeng,et al. Understanding diagnostic tests 3: receiver operating characteristic curves , 2007, Acta paediatrica.
[34] W. M. Dunne,et al. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory , 2012, European Journal of Clinical Microbiology & Infectious Diseases.
[35] Mikiko Senga,et al. Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections. , 2014, The New England journal of medicine.
[36] K. Stedman,et al. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses , 2012, Biology Direct.
[37] Martin Vingron,et al. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..
[38] A. Kumar,et al. Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans , 2010 .
[39] C. Chiu. Viral pathogen discovery , 2013, Current Opinion in Microbiology.
[40] Po-E Li,et al. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures , 2015, Nucleic acids research.