Topic 37 -- Abstracts with Biological Entities (English) - 75 Topics

cite ad title authors publish year publish time dataset abstract mentions covid pmcid pubmed id doi cord uid topic weight Similarity scispacy Similarity specter
1 Smits_2014 Assembly of viral genomes from metagenomes Smits, Saskia L.; Bodewes, Rogier; Ruiz-Gonzalez, Aritz; Baumgärtner, Wolfgang; Koopmans, Marion P.; Osterhaus, Albert D. M. E.; Schürch, Anita C. 2014 2014-12-18 COMM-USE N PMC4270193 25566226.0 10.3389/fmicb.2014.00714 jw4n2j6y 0.768618 Rice_1992, Auewarakul_2005, Wang_2018, Cheng_2013 Cook_2013, Satyanarayana_2003
2 Shifman_2019 Identification and genetic characterization of a novel Orthobunyavirus species by a straightforward high-throughput sequencing-based approach Shifman, Ohad; Cohen-Gihon, Inbar; Beth-Din, Adi; Zvi, Anat; Laskar, Orly; Paran, Nir; Epstein, Eyal; Stein, Dana; Dorozko, Marina; Wolf, Dana; Yitzhaki, Shmuel; Shapira, Shmuel C.; Melamed, Sharon; Israeli, Ofir 2019 2019-03-04 COMM-USE N PMC6399452 30833612.0 10.1038/s41598-019-40036-4 15cxc32n 0.748629 Rice_1992, Chang_2011, Cheng_2013, Smits_2014, Deng_2015 Ren_X_2008, Shabman_2016, Di_Martino_2009, Pignatelli_2009
3 Warren_2007 Assembling millions of short DNA sequences using SSAKE Warren, René L.; Sutton, Granger G.; Jones, Steven J. M.; Holt, Robert A. 2007 2007-02-15 NONCOMM N PMC7109930 17158514.0 10.1093/bioinformatics/btl629 ojy6s49w 0.745285 Deng_2015, Whiteford_2005, Cheng_2013, Chang_2011 Viehweger_2019, Viehweger_2018, Harel_2019
4 Deng_2015 An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data Deng, Xutao; Naccache, Samia N.; Ng, Terry; Federman, Scot; Li, Linlin; Chiu, Charles Y.; Delwart, Eric L. 2015 2015-04-20 COMM-USE N PMC4402509 25586223.0 10.1093/nar/gkv002 gr108zuo 0.730402 Cheng_2013, Chang_2011, Whiteford_2005, Lee_C_2017 Wang_2010, Lin_Y_2017, Wang_2013, Viehweger_2019
5 Whiteford_2005 An analysis of the feasibility of short read sequencing Whiteford, Nava; Haslam, Niall; Weber, Gerald; Prügel-Bennett, Adam; Essex, Jonathan W.; Roach, Peter L.; Bradley, Mark; Neylon, Cameron 2005 2005-11-07 PMC N PMC1278949 16275781.0 10.1093/nar/gni170 g2f151oc 0.720595 Deng_2015, Phillippy_2009, Warren_2007, Chang_2011 Harel_2019, Viehweger_2019, Viehweger_2018
6 Hewson_2011 Description of viral assemblages associated with the Gorgonia ventalina holobiont Hewson, I.; Brown, J. M.; Burge, C. A.; Couch, C. S.; LaBarre, B. A.; Mouchka, M. E.; Naito, M.; Harvell, C. D. 2011 2011-12-29 PMC N PMC7087884 10.1007/s00338-011-0864-x cy049zbi 0.683875 Wang_2018, Rice_1992, Payne_2017, Xu_L_2018 Becker_2019, Walker_2011, Harper_2013
7 Cheng_2013 CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes Cheng, Jinkui; Zeng, Xu; Ren, Guomin; Liu, Zhihua 2013 2013-03-14 COMM-USE N PMC3636126 23496817.0 10.1186/1471-2105-14-95 tg06vxza 0.679351 Montgomery_2004, O'Leary_2016, UNKNOWN_2018, Xu_Z_2009 Wang_2010, Francis_2016, Yu_Z_2010
8 Cotten_2014 Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm Cotten, Matthew; Oude Munnink, Bas; Canuti, Marta; Deijs, Martin; Watson, Simon J.; Kellam, Paul; van der Hoek, Lia 2014 2014-04-02 COMM-USE N PMC3973683 24695106.0 10.1371/journal.pone.0093269 j9nllb4f 0.677992 Rice_1992, Armesto_2007, Bickerton_2017, Langelier_2017 Yang_2018, Ren_X_2008
9 Lin_H_2017 drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes Lin, Hsin-Hung; Liao, Yu-Chieh 2017 2017-01-20 COMM-USE N PMC5466706 28369462.0 10.1093/gigascience/gix003 47kmwl6s 0.671423 Cheng_2013, Deng_2015, Montgomery_2004, Brister_2015 Wang_2010, Smits_2014
10 O'Flaherty_2018 Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing O'Flaherty, Brigid M.; Li, Yan; Tao, Ying; Paden, Clinton R.; Queen, Krista; Zhang, Jing; Dinwiddie, Darrell L.; Gross, Stephen M.; Schroth, Gary P.; Tong, Suxiang 2018 2018-04-27 None N PMC5991510 29703817.0 10.1101/gr.226316.117 bg1s2i6d 0.665032 Deng_2015, Rice_1992, Naito_2007, Smits_2014, Harel_2019 Yang_2018, Alquezar-Planas_2013
11 Kumar_2017 Evolution of selective-sequencing approaches for virus discovery and virome analysis Kumar, Arvind; Murthy, Satyapramod; Kapoor, Amit 2017 2017-07-15 PMC N PMC5819613 28583442.0 10.1016/j.virusres.2017.06.005 lrrkuist 0.664702 Djikeng_2009, Siridechadilok_2013, Yadav_2013, Deng_2015 Jensen_2015, Satyanarayana_2003, Shabman_2016
12 Castro_2019 The effect of variant interference on de novo assembly for viral deep sequencing Christina J. Castro; Rachel L. Marine; Edward Ramos; Terry Fei Fan Ng 2019 2019-10-22 BioRxiv N 10.1101/815480 d5ghy39g 0.661191 Deng_2015, Whiteford_2005, Harel_2019, Price_2019 Masante_2015, Satyanarayana_2003
13 Rego_2012 Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis Rego, Natalia; Bianchi, Sergio; Moreno, Pilar; Persson, Helena; Kvist, Anders; Pena, Alvaro; Oppezzo, Pablo; Naya, Hugo; Rovira, Carlos; Dighiero, Guillermo; Pritsch, Otto 2012 2012-04-10 None N PMC7161782 22489537.0 10.1111/j.1365-2141.2012.09116.x 71fp78kx 0.655419 Cheng_2013, Langelier_2017, Whiteford_2005, O'Leary_2016
14 Gardner_2004 Sequencing Needs for Viral Diagnostics Gardner, Shea N.; Lam, Marisa W.; Mulakken, Nisha J.; Torres, Clinton L.; Smith, Jason R.; Slezak, Tom R. 2004 2004-12-01 None N PMC535215 15583268.0 10.1128/jcm.42.12.5472-5476.2004 sd81bz0m 0.643749 Rice_1992, Auewarakul_2005, Chang_2011, Li_D_2019 Wang_2010
15 Langelier_2017 Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community-Acquired Pneumonia in Colorado, USA Langelier, Charles; White, Corin V.; Sontag, Marci K.; Mourani, Peter M.; DeRisi, Joseph L. 2017 2017-11-30 COMM-USE N PMC5722057 29192071.0 10.1128/genomea.01245-17 sdy70r7d 0.642784 Taboada_2016, Chieochansin_2010, Armesto_2007, Rice_1992 Brandão_2016, Pan_C_2018, Ren_X_2008
16 Urayama_2016 FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance Urayama, Syun-ichi; Takaki, Yoshihiro; Nunoura, Takuro 2016 2016-02-13 COMM-USE N PMC4791113 26877136.0 10.1264/jsme2.me15171 iwfidoer 0.640684 Rice_1992, Wang_2018, den_Boon_2010, Stork_2011 Wulan_2015
17 Metsky_2019 Capturing sequence diversity in metagenomes with comprehensive and scalable probe design Metsky, Hayden C.; Siddle, Katherine J.; Gladden-Young, Adrianne; Qu, James; Yang, David K.; Brehio, Patrick; Goldfarb, Andrew; Piantadosi, Anne; Wohl, Shirlee; Carter, Amber; Lin, Aaron E.; Barnes, Kayla G.; Tully, Damien C.; Corleis, Bjӧrn; Hennigan, Scott; Barbosa-Lima, Giselle; Vieira, Yasmine R.; Paul, Lauren M.; Tan, Amanda L.; Garcia, Kimberly F.; Parham, Leda A.; Odia, Ikponmwosa; Eromon, Philomena; Folarin, Onikepe A.; Goba, Augustine; Simon-Lorière, Etienne; Hensley, Lisa; Balmaseda, Angel; Harris, Eva; Kwon, Douglas S.; Allen, Todd M.; Runstadler, Jonathan A.; Smole, Sandra; Bozza, Fernando A.; Souza, Thiago M. L.; Isern, Sharon; Michael, Scott F.; Lorenzana, Ivette; Gehrke, Lee; Bosch, Irene; Ebel, Gregory; Grant, Donald S.; Happi, Christian T.; Park, Daniel J.; Gnirke, Andreas; Sabeti, Pardis C.; Matranga, Christian B. 2019 2019-02-04 None N PMC6587591 30718881.0 10.1038/s41587-018-0006-x hyg14q69 0.640256 Chang_2011, Deng_2015, Cheng_2013, Smits_2014 Metsky_2018, Selvin_2019, Li_C_2020
18 Oba_M_2018 A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system Oba, Mami; Tsuchiaka, Shinobu; Omatsu, Tsutomu; Katayama, Yukie; Otomaru, Konosuke; Hirata, Teppei; Aoki, Hiroshi; Murata, Yoshiteru; Makino, Shinji; Nagai, Makoto; Mizutani, Tetsuya 2018 2018-01-08 None N PMC7124307 29223400.0 10.1016/j.bbrc.2017.12.017 sv6uh7hh 0.636151 Rice_1992, Armesto_2007, Naito_2007, Majerciak_2018 Anis_2018, Ren_X_2008
19 Dutilh_2014 Metagenomic ventures into outer sequence space Dutilh, Bas E 2014 2014-12-15 NONCOMM N PMC4588555 26458273.0 10.4161/21597081.2014.979664 ybd8hi8y 0.631760 Francis_2016, Lee_C_2017, Chang_2011, Brister_2015 Walker_2011, Selvin_2019, McGuire_2012, Maaty_2012
20 Fertil_2005 GENSTYLE: exploration and analysis of DNA sequences with genomic signature Fertil, Bernard; Massin, Matthieu; Lespinats, Sylvain; Devic, Caroline; Dumee, Philippe; Giron, Alain 2005 2005-07-01 PMC N PMC1160249 15980524.0 10.1093/nar/gki489 x8zdlml2 0.625936 Cheng_2013, Chang_2011, Zheng_2008, Gardner_2008, Phillippy_2009 Dufraigne_2005, Shabman_2016, Jonassen_2007
21 Warwick-Dugdale_2019 Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen; Chittick, Lauren; Gregory, Ann C.; Allen, Michael J.; Sullivan, Matthew B.; Temperton, Ben 2019 2019-04-25 COMM-USE N PMC6487183 31086738.0 10.7717/peerj.6800 8pr5ispb 0.617038 Deng_2015, Cheng_2013, Brister_2015, Chang_2011, Djikeng_2009 Becker_2019, Selvin_2019, Bergner_2019
22 Valdivia-Granda_2009 ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies Valdivia-Granda, Willy; Larson, Francis 2009 2009-10-12 NONCOMM N PMC2790308 20157487.0 10.1093/database/bap014 7bkf7wrs 0.611176 Murray_2017, UNKNOWN_2018, O'Leary_2016, Cheng_2013, Brister_2015 Ren_X_2008, Tzeng_2006, Gorbalenya_2006
23 Neill_2014 Simultaneous rapid sequencing of multiple RNA virus genomes Neill, John D.; Bayles, Darrell O.; Ridpath, Julia F. 2014 2014-06-01 PMC N PMC7119728 24589514.0 10.1016/j.jviromet.2014.02.016 crtpzad7 0.610161 Rice_1992, Armesto_2007, Chen_2018, Keep_2015, Bickerton_2017 Satyanarayana_2003, Yang_2018
24 Metsky_2018 Capturing diverse microbial sequence with comprehensive and scalable probe design Hayden C. Metsky; Katherine J. Siddle; Adrianne Gladden-Young; James Qu; David K. Yang; Patrick Brehio; Andrew Goldfarb; Anne Piantadosi; Shirlee Wohl; Amber Carter; Aaron E. Lin; Kayla G. Barnes; Damien C. Tully; Björn Corleis; Scott Hennigan; Giselle Barbosa-Lima; Yasmine R. Vieira; Lauren M. Paul; Amanda L. Tan; Kimberly F. Garcia; Leda A. Parham; Ikponmwonsa Odia; Philomena Eromon; Onikepe A. Folarin; Augustine Goba; Etienne Simon-Lorière; Lisa Hensley; Angel Balmaseda; Eva Harris; Douglas Kwon; Todd M. Allen; Jonathan A. Runstadler; Sandra Smole; Fernando A. Bozza; Thiago M. L. Souza; Sharon Isern; Scott F. Michael; Ivette Lorenzana; Lee Gehrke; Irene Bosch; Gregory Ebel; Donald Grant; Christian Happi; Daniel J. Park; Andreas Gnirke; Pardis C. Sabeti; Christian B. Matranga 2018 2018-03-12 BioRxiv N 10.1101/279570 a9lkhayg 0.609694 Chang_2011, Deng_2015, Cheng_2013, Gardner_2004, Brister_2015 Metsky_2019, Li_C_2020, Lewandowski_2019
25 Woo_P_2014 Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses Woo, Patrick C.Y.; Lau, Susanna K.P.; Teng, Jade L.L.; Tsang, Alan K.L.; Joseph, Marina; Wong, Emily Y.M.; Tang, Ying; Sivakumar, Saritha; Bai, Ru; Wernery, Renate; Wernery, Ulrich; Yuen, Kwok-Yung 2014 2014-12-31 PMC N PMC7112128 25461537.0 10.1016/j.virol.2014.09.020 81t59up3 0.608931 Ryu_W_2017, Chieochansin_2010, Xu_L_2018, Kamau_2019, Crowe_2014 Conceição-Neto_2015, Ghazisaeedi_2017, Lee_D_2019
26 Chen_2018 Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng 2018 2018-05-09 PMC N PMC7088580 29744712.0 10.1007/s11262-018-1568-x utvf8yh6 0.608433 Deng_2015, Rice_1992, Harel_2019, Xu_L_2019 Yang_2018, Qiu_Y_2017, Mikel_2015
27 Shi_M_2018 Meta-transcriptomics and the evolutionary biology of RNA viruses Shi, Mang; Zhang, Yong-Zhen; Holmes, Edward C. 2018 2018-01-02 PMC N PMC7127328 29111455.0 10.1016/j.virusres.2017.10.016 5qri915n 0.607403 Wang_2018, Holmes_2007, Siridechadilok_2013, Chang_2011, Grewelle_2020 Harper_2013, Wulan_2015
28 Daly_2015 Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data Daly, Gordon M.; Leggett, Richard M.; Rowe, William; Stubbs, Samuel; Wilkinson, Maxim; Ramirez-Gonzalez, Ricardo H.; Caccamo, Mario; Bernal, William; Heeney, Jonathan L. 2015 2015-06-22 COMM-USE N PMC4476701 26098299.0 10.1371/journal.pone.0129059 yxd32zwk 0.604854 Deng_2015, Whiteford_2005, Cheng_2013, Pandya_2007 Shabman_2016, Shepard_2016, Anderson_2020, Knutson_2017
29 Ayginin_2018 The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels Ayginin, Andrey A.; Pimkina, Ekaterina V.; Matsvay, Alina D.; Speranskaya, Anna S.; Safonova, Marina V.; Blinova, Ekaterina A.; Artyushin, Ilya V.; Dedkov, Vladimir G.; Shipulin, German A.; Khafizov, Kamil 2018 2018-08-12 COMM-USE N PMC6109506 30158979.0 10.1155/2018/3248285 6w8qcv1c 0.601796 Chang_2011, Naito_2007, Rice_1992, Wang_2018 Dacheux_2014, Lee_J_2017
30 Jensen_2015 Target-Dependent Enrichment of Virions Determines the Reduction of High-Throughput Sequencing in Virus Discovery Jensen, Randi Holm; Mollerup, Sarah; Mourier, Tobias; Hansen, Thomas Arn; Fridholm, Helena; Nielsen, Lars Peter; Willerslev, Eske; Hansen, Anders Johannes; Vinner, Lasse 2015 2015-04-08 COMM-USE N PMC4390369 25853649.0 10.1371/journal.pone.0122636 5g2i36zz 0.601796 Rice_1992, Auewarakul_2005, Naito_2007, Urayama_2016, Oba_M_2018 van_der_Linden_2014, Anderson_2020, Satyanarayana_2003
31 Gao_L_2007 Whole genome molecular phylogeny of large dsDNA viruses using composition vector method Gao, Lei; Qi, Ji 2007 2007-03-15 COMM-USE N PMC1839080 17359548.0 10.1186/1471-2148-7-41 p529ylc1 0.600730 Chang_2011, Zheng_2008, Wang_2018, Wang_2013, Francis_2016 Yu_Z_2010, Pride_2006, Yun_S_2015
32 Gardner_2005 Draft versus finished sequence data for DNA and protein diagnostic signature development Gardner, Shea N.; Lam, Marisa W.; Smith, Jason R.; Torres, Clinton L.; Slezak, Tom R. 2005 2005-10-20 PMC N PMC1266063 16243783.0 10.1093/nar/gki896 t40ybhgb 0.599019 Chang_2011, Deng_2015, Cheng_2013, Lee_C_2017 Gardner_2004, Wang_2010, Viehweger_2019
33 Wang_2003 Viral Discovery and Sequence Recovery Using DNA Microarrays Wang, David; Urisman, Anatoly; Liu, Yu-Tsueng; Springer, Michael; Ksiazek, Thomas G; Erdman, Dean D; Mardis, Elaine R; Hickenbotham, Matthew; Magrini, Vincent; Eldred, James; Latreille, J. Phillipe; Wilson, Richard K; Ganem, Don; DeRisi, Joseph L 2003 2003-11-17 COMM-USE N PMC261870 14624234.0 10.1371/journal.pbio.0000002 yy96yeu9 0.597302 Rice_1992, Armesto_2007, Wang_2018, Naito_2007, Bickerton_2017 Usme-Ciro_2014, Baric_2005, Satyanarayana_2003
34 Djikeng_2008 Viral genome sequencing by random priming methods Djikeng, Appolinaire; Halpin, Rebecca; Kuzmickas, Ryan; DePasse, Jay; Feldblyum, Jeremy; Sengamalay, Naomi; Afonso, Claudio; Zhang, Xinsheng; Anderson, Norman G; Ghedin, Elodie; Spiro, David J 2008 2008-01-07 COMM-USE N PMC2254600 18179705.0 10.1186/1471-2164-9-5 4i9fc0r7 0.591063 Rice_1992, Ryu_W_2017, Wang_2018, Lu_P_2016, Karlsson_2012 Ren_X_2008, Lachheb_2019, Anderson_2020
35 ZHANG_2018 VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens ZHANG, Yi; ZHANG, Chen; LI, Bo; LI, Yang; Zhou, HE Xiao; LI, Acher; WU, Wei; DUAN, Su Xia; QIU, Fang Zhou; WANG, Ji; SHEN, Xin Xin; YANG, Meng Jie; LI, De Xin; MA, Xue Jun 2018 2018-04-30 PMC N PMC7135048 29773090.0 10.3967/bes2018.035 7dcl9txk 0.589162 Endoh_2005, Brown_1984, Auewarakul_2005, Whiteford_2005, Rice_1992 Lachheb_2019, Zaher_2020, Ren_X_2008
36 Yu_Z_2010 Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model Yu, Zu-Guo; Chu, Ka Hou; Li, Chi Pang; Anh, Vo; Zhou, Li-Qian; Wang, Roger Wei 2010 2010-06-22 COMM-USE N PMC2898692 20565983.0 10.1186/1471-2148-10-192 gf718lbl 0.589113 Zheng_2008, Chang_2011, Lee_C_2017, Cheng_2013, Wang_2013 Zhou_2017, Suzuki_2020
37 Chou_2006 Design of microarray probes for virus identification and detection of emerging viruses at the genus level Chou, Cheng-Chung; Lee, Te-Tsui; Chen, Chun-Houh; Hsiao, Hsiang-Yun; Lin, Yi-Ling; Ho, Mei-Shang; Yang, Pan-Chyr; Peck, Konan 2006 2006-04-28 COMM-USE N PMC1523220 16643672.0 10.1186/1471-2105-7-232 xz7rzjqv 0.589113 Rice_1992, Naito_2007, Chang_2011, Wang_2018 Wang_2003, Hu_T_2012, Yadav_2013
38 Delwart_2007 Viral metagenomics Delwart, Eric L. 2007 2007-02-12 PMC N PMC7169062 17295196.0 10.1002/rmv.532 7eild8ni 0.587905 Rice_1992, Wang_2018, Djikeng_2009, den_Boon_2010, Smits_2014
39 Zhang_2017 Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer Zhang, Qian; Jun, Se-Ran; Leuze, Michael; Ussery, David; Nookaew, Intawat 2017 2017-01-19 COMM-USE N PMC5244389 28102365.0 10.1038/srep40712 641pmd1d 0.584413 Chang_2011, Cheng_2013, Zheng_2008, Lee_C_2017 Shabman_2016, Ren_X_2008, Godeny_1990, Goldberg_1991
40 Mbareche_2020 Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols Mbareche, Hamza; Veillette, Marc; Bilodeau, Guillaume; Duchaine, Caroline 2020 2020-02-17 COMM-USE N PMC7032056 32110484.0 10.7717/peerj.8523 nsttoyr2 0.581770 Chang_2011, Zheng_2008, Cheng_2013, Harel_2019 Sazmand_2019, Selvin_2019, Sun_J_2010
41 Palmeira_2010 PhEVER: a database for the global exploration of virus–host evolutionary relationships Palmeira, Leonor; Penel, Simon; Lotteau, Vincent; Rabourdin-Combe, Chantal; Gautier, Christian 2010 2010-11-16 NONCOMM N PMC3013642 21081560.0 10.1093/nar/gkq1013 b66bb2ri 0.578626 Rice_1992, Wang_2018, den_Boon_2010, Cheng_2013, Cullen_2009 Rodríguez_2020
42 Paez-Espino_2017 IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses Paez-Espino, David; Chen, I.-Min A.; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor M.; Nielsen, Torben; Huntemann, Marcel; K. Reddy, T. B.; Pavlopoulos, Georgios A.; Sullivan, Matthew B.; Campbell, Barbara J.; Chen, Feng; McMahon, Katherine; Hallam, Steve J.; Denef, Vincent; Cavicchioli, Ricardo; Caffrey, Sean M.; Streit, Wolfgang R.; Webster, John; Handley, Kim M.; Salekdeh, Ghasem H.; Tsesmetzis, Nicolas; Setubal, Joao C.; Pope, Phillip B.; Liu, Wen-Tso; Rivers, Adam R.; Ivanova, Natalia N.; Kyrpides, Nikos C. 2017 2017-01-04 NONCOMM N PMC5210529 27799466.0 10.1093/nar/gkw1030 hmgmsviu 0.578626 Cheng_2013, Brister_2015, Smits_2014, Deng_2015, Rice_1992 Shabman_2016, Ren_X_2008
43 Yozwiak_2012 Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing Yozwiak, Nathan L.; Skewes-Cox, Peter; Stenglein, Mark D.; Balmaseda, Angel; Harris, Eva; DeRisi, Joseph L. 2012 2012-02-07 COMM-USE N PMC3274504 22347512.0 10.1371/journal.pntd.0001485 6gow0x1v 0.574606 Ryu_W_2017, Rice_1992, Smits_2014, Wang_2015, Chieochansin_2010 Agoti_2019, Uhlenhaut_2009
44 Briese_2015 Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis Briese, Thomas; Kapoor, Amit; Mishra, Nischay; Jain, Komal; Kumar, Arvind; Jabado, Omar J.; Lipkin, W. Ian 2015 2015-09-22 NONCOMM N PMC4611031 26396248.0 10.1128/mbio.01491-15 gbguv4r2 0.570998 Rice_1992, Oba_M_2018, Chen_2018, Wang_2018, Auewarakul_2005 Yang_2018, Li_L_2015
45 Pride_2006 Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses Pride, David T; Wassenaar, Trudy M; Ghose, Chandrabali; Blaser, Martin J 2006 2006-01-18 COMM-USE N PMC1360066 16417644.0 10.1186/1471-2164-7-8 er3mnkyf 0.568508 Chang_2011, Zheng_2008, Wang_2013, Francis_2016, Auewarakul_2005 Bahir_2009, Chen_2020, Ren_X_2008
46 Roux_2019 Metagenomics in Virology Roux, Simon; Matthijnssens, Jelle; Dutilh, Bas E. 2019 2019-12-31 PMC N PMC7157462 10.1016/b978-0-12-809633-8.20957-6 1qj9ri18 0.564270 Wang_2018, Djikeng_2009, Conzelmann_1996, Vernikos_2008 Haagmans_2009, Li_C_2020, Selvin_2019, Dacheux_2014
47 Chen_2019 TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data Chen, Jiao; Huang, Jiating; Sun, Yanni 2019 2019-06-04 None N PMC6549370 31164077.0 10.1186/s12859-019-2878-2 6frnbfh4 0.563825 Cheng_2013, Lee_C_2017, Deng_2015, Montgomery_2004, Chang_2011 Anderson_2020
48 Chen_2019 A binning tool to reconstruct viral haplotypes from assembled contigs Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun 2019 2019-07-16 BioRxiv N 10.1101/704288 2basllfv 0.563332 Chang_2011, Deng_2015, Lee_C_2017, Harel_2019 Chen_2019, Dacheux_2014
49 Viehweger_2019 Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis Viehweger, Adrian; Krautwurst, Sebastian; Lamkiewicz, Kevin; Madhugiri, Ramakanth; Ziebuhr, John; Hölzer, Martin; Marz, Manja 2019 2019-08-22 None N PMC6724671 31439691.0 10.1101/gr.247064.118 fcvddgvy 0.562858 Rice_1992, Auewarakul_2005, Payne_2017, Stork_2011, den_Boon_2010 Viehweger_2018, Bhullar_2014
50 Myrmel_2017 Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) Myrmel, Mette; Oma, Veslemøy; Khatri, Mamata; Hansen, Hanne H.; Stokstad, Maria; Berg, Mikael; Blomström, Anne-Lie 2017 2017-11-07 COMM-USE Y PMC5675387 29112950.0 10.1371/journal.pone.0187780 urnbggzs 0.561058 Armesto_2007, Whiteford_2005, Auewarakul_2005, Keep_2015, Keep_2014 Crucière_1988
51 Aguiar_2015 Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host Aguiar, Eric Roberto Guimarães Rocha; Olmo, Roenick Proveti; Paro, Simona; Ferreira, Flavia Viana; de Faria, Isaque João da Silva; Todjro, Yaovi Mathias Honore; Lobo, Francisco Pereira; Kroon, Erna Geessien; Meignin, Carine; Gatherer, Derek; Imler, Jean-Luc; Marques, João Trindade 2015 2015-07-27 None N PMC4513865 26040701.0 10.1093/nar/gkv587 gsl4m1mc 0.560888 Rice_1992, Trobaugh_2017, Naito_2007, Berkhout_2006, Auewarakul_2005 Baric_1987
52 Guo_F_2006 ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes Guo, Feng-Biao; Zhang, Chun-Ting 2006 2006-01-10 COMM-USE N PMC1352377 16401352.0 10.1186/1471-2105-7-9 h640qddv 0.558668 Lee_C_2017, Cheng_2013, Chang_2011, Gardner_2004, Francis_2016 Wang_2010, Chen_2003, Tzeng_2006, Yun_S_2015
53 Maurier_2019 A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43 Maurier, Florence; Beury, Delphine; Fléchon, Léa; Varré, Jean-Stéphane; Touzet, Hélène; Goffard, Anne; Hot, David; Caboche, Ségolène 2019 2019-05-31 None N PMC7112119 30878524.0 10.1016/j.virol.2019.03.006 3r244w9a 0.558556 Rice_1992, Armesto_2007, Mizutani_2007, Chang_2011 Ren_X_2008, Lewandowska_2017
54 Fauquet_2008 Taxonomy, Classification and Nomenclature of Viruses Fauquet, C.M. 2008 2008-12-31 PMC N PMC7150148 10.1016/b978-012374410-4.00509-4 o6m5wz1z 0.556091 Murray_2017, UNKNOWN_2010, Mack_2007, Mooney_2013, Rodier_2007 Fermin_2018, FENNER_1987, Petric_2003
55 Sampath_2012 Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry Sampath, Rangarajan; Mulholland, Niveen; Blyn, Lawrence B.; Massire, Christian; Whitehouse, Chris A.; Waybright, Nicole; Harter, Courtney; Bogan, Joseph; Miranda, Mary Sue; Smith, David; Baldwin, Carson; Wolcott, Mark; Norwood, David; Kreft, Rachael; Frinder, Mark; Lovari, Robert; Yasuda, Irene; Matthews, Heather; Toleno, Donna; Housley, Roberta; Duncan, David; Li, Feng; Warren, Robin; Eshoo, Mark W.; Hall, Thomas A.; Hofstadler, Steven A.; Ecker, David J. 2012 2012-06-29 COMM-USE N PMC3387173 22768032.0 10.1371/journal.pone.0036528 w75flrwv 0.554643 Gardner_2004, Chang_2011, Priest_2012, Gamermann_2014 Wolk_2012, Jia_B_2020, Jordana-Lluch_2014
56 Liu_P_2019 Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica) Liu, Ping; Chen, Wu; Chen, Jin-Ping 2019 2019-10-24 COMM-USE N PMC6893680 31652964.0 10.3390/v11110979 wrmfxkoa 0.551262 Wang_2018, Rice_1992, Grewelle_2020, Ryu_W_2017, Wang_2015 Niemeyer_2018, Ren_X_2008, Kim_D_2016
57 Tithi_2018 FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data Tithi, Saima Sultana; Aylward, Frank O.; Jensen, Roderick V.; Zhang, Liqing 2018 2018-01-12 COMM-USE N PMC5768174 29340239.0 10.7717/peerj.4227 sjl8x1jt 0.549390 Deng_2015, Cheng_2013, Montgomery_2004, Chang_2011 Tithi_2017, Li_C_2020, Dacheux_2014, Selvin_2019
58 Knutson_2017 A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease Knutson, Todd P.; Velayudhan, Binu T.; Marthaler, Douglas G. 2017 2017-06-08 COMM-USE N PMC5656790 28590234.0 10.1099/jgv.0.000799 og2vsgjn 0.547031 Rice_1992, Langelier_2017, Smits_2014, Deng_2015, Cheng_2013 Ren_X_2008, Kim_D_2016, Lachheb_2019, Mohamed_2018
59 Debat_2018 Expanding the size limit of RNA viruses: Evidence of a novel divergent nidovirus in California sea hare, with a ~35.9 kb virus genome Humberto J Debat 2018 2018-04-24 BioRxiv N 10.1101/307678 n78fga3r 0.547031 Rice_1992, Ryu_W_2017, Wang_2018, Wolf_2018, den_Boon_2010 Nowak_1984, Firth_2009
60 Urisman_2005 E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns Urisman, Anatoly; Fischer, Kael F; Chiu, Charles Y; Kistler, Amy L; Beck, Shoshannah; Wang, David; DeRisi, Joseph L 2005 2005-08-30 COMM-USE N PMC1242213 16168085.0 10.1186/gb-2005-6-9-r78 kqithgfo 0.546581 Chang_2011, Gamermann_2014, Sen_D_2018, Deng_2015 Giles_2015, Wong_2007, Mukai_2006
61 Soffer_2013 Potential role of viruses in white plague coral disease Soffer, Nitzan; Brandt, Marilyn E; Correa, Adrienne MS; Smith, Tyler B; Thurber, Rebecca Vega 2013 2013-08-15 PMC N PMC3906806 23949663.0 10.1038/ismej.2013.137 pgqsezq2 0.545857 Wang_2018, Tong_2009, Schountz_2013, Longdon_2018, Longdon_2017 de_Groof_2015, Pickering_2015
62 Fancello_2012 Computational tools for viral metagenomics and their application in clinical research Fancello, L.; Raoult, D.; Desnues, C. 2012 2012-12-20 PMC N PMC7111993 23062738.0 10.1016/j.virol.2012.09.025 h9ryhpcv 0.545132 Wang_2018, Rice_1992, Li_L_2014, Brister_2015, Djikeng_2009 Dacheux_2014, Sun_D_2016, Anderson_2020, Ren_X_2008
63 Friis-Nielsen_2016 Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Mollerup, Sarah; Asplund, Maria; Mourier, Tobias; Jensen, Randi Holm; Hansen, Thomas Arn; Rey-Iglesia, Alba; Richter, Stine Raith; Nielsen, Ida Broman; Alquezar-Planas, David E.; Olsen, Pernille V. S.; Vinner, Lasse; Fridholm, Helena; Nielsen, Lars Peter; Willerslev, Eske; Sicheritz-Pontén, Thomas; Lund, Ole; Hansen, Anders Johannes; Izarzugaza, Jose M. G.; Brunak, Søren 2016 2016-02-19 COMM-USE N PMC4776208 26907326.0 10.3390/v8020053 wjf3c7a7 0.543445 Chang_2011, Deng_2015, Lee_C_2017, Harel_2019, Gardner_2004 Alquezar-Planas_2013, Zou_X_2016, Wang_2003, Yang_2018
64 Li_P_2020 A tripartite ssDNA mycovirus from a plant pathogenic fungus is infectious as cloned DNA and purified virions Li, Pengfei; Wang, Shuangchao; Zhang, Lihang; Qiu, Dewen; Zhou, Xueping; Guo, Lihua 2020 2020-04-03 NONCOMM N PMC7138691 10.1126/sciadv.aay9634 ckgmv7rt 0.543210 Rice_1992, den_Boon_2010, Payne_2017, Wolf_2018, Stork_2011 Nowak_1984, Tzeng_2006
65 Timoshenko_2009 Identification of mutations in a temperature‐sensitive mutant (tsm5) of murine cytomegalovirus using complementary genome sequencing Timoshenko, Olga; Al‐Ali, Abdulaziz; Martin, Brian A.B.; Sweet, Clive 2009 2009-01-16 PMC N PMC7166533 19152394.0 10.1002/jmv.21419 awi7bnsc 0.540938 Whiteford_2005, Xu_J_2016, Harel_2019, Armesto_2007, Keep_2015
66 Fahsbender_2019 Lyon-IARC Polyomavirus DNA in Feces of Diarrheic Cats Fahsbender, Elizabeth; Altan, Eda; Estrada, Marko; Seguin, M. Alexis; Young, Pauline; Leutenegger, Christian M.; Delwart, Eric 2019 2019-07-18 COMM-USE N PMC6639616 31320414.0 10.1128/mra.00550-19 aj7texe6 0.537906 Kamau_2019, Kin_N_2017, Li_W_2012, Zhang_2020 Lee_S_2018, Park_2007, Catry_2004
67 Harel_2019 Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations Harel, Noam; Meir, Moran; Gophna, Uri; Stern, Adi 2019 2019-12-16 PMC N PMC7107797 31665473.0 10.1093/nar/gkz907 rloey02j 0.532750 Deng_2015, Chang_2011, Whiteford_2005, Phillippy_2009 Viehweger_2019, Viehweger_2018, Yang_2018
68 Oude_Munnink_2013 Autologous Antibody Capture to Enrich Immunogenic Viruses for Viral Discovery Oude Munnink, Bas B.; Jazaeri Farsani, Seyed Mohammad; Deijs, Martin; Jonkers, Jiri; Verhoeven, Joost T. P.; Ieven, Margareta; Goossens, Herman; de Jong, Menno D.; Berkhout, Ben; Loens, Katherine; Kellam, Paul; Bakker, Margreet; Canuti, Marta; Cotten, Matthew; van der Hoek, Lia 2013 2013-11-04 COMM-USE N PMC3817278 24223808.0 10.1371/journal.pone.0078454 0mu4tkui 0.531895 Rice_1992, Naito_2007, Auewarakul_2005, Armesto_2007, Smits_2014 Fournier_2007, Xue_G_2013, Xie_X_2015
69 Zhang_2019 Identification of viruses with the potential to infect human Zheng Zhang; Zena Cai; Zhiying Tan; Congyu Lu; Gaihua Zhang; Yousong Peng 2019 2019-04-05 BioRxiv N 10.1101/597963 lnch3qsq 0.529434 Lee_C_2017, Chang_2011, Wang_2018, Smits_2014, Rice_1992 Van_Hoeven_2009, Paulson_2013
70 Malik_2017 Do Viruses Exchange Genes across Superkingdoms of Life? Malik, Shahana S.; Azem-e-Zahra, Syeda; Kim, Kyung Mo; Caetano-Anollés, Gustavo; Nasir, Arshan 2017 2017-10-31 COMM-USE N PMC5671483 29163404.0 10.3389/fmicb.2017.02110 12dee0lv 0.527813 Rice_1992, Wang_2018, den_Boon_2010, Cullen_2009, Koonin_2015 Wulan_2015, Chen_2020, Durmuş_2017
71 Paez-Espino_2019 IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes Paez-Espino, David; Roux, Simon; Chen, I-Min A; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Huntemann, Marcel; Reddy, T B K; Pons, Joan Carles; Llabrés, Mercè; Eloe-Fadrosh, Emiley A; Ivanova, Natalia N; Kyrpides, Nikos C 2019 2019-01-08 COMM-USE N PMC6323928 30407573.0 10.1093/nar/gky1127 mgmbdfhe 0.527602 Cheng_2013, O'Leary_2016, UNKNOWN_2018, UNKNOWN_2016, Brister_2015 Paez-Espino_2017, Wang_2010, Murtaugh_1995
72 Malboeuf_2012 Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification Malboeuf, Christine M.; Yang, Xiao; Charlebois, Patrick; Qu, James; Berlin, Aaron M.; Casali, Monica; Pesko, Kendra N.; Boutwell, Christian L.; DeVincenzo, John P.; Ebel, Gregory D.; Allen, Todd M.; Zody, Michael C.; Henn, Matthew R.; Levin, Joshua Z. 2012 2012-09-08 NONCOMM N PMC3592391 22962364.0 10.1093/nar/gks794 s76c5ebd 0.527602 Rice_1992, Ryu_W_2017, den_Boon_2010, Tallmadge_2008, Armesto_2007 Majerciak_2018, Masante_2015, Viehweger_2019
73 Ye_F_2020 First Identification of Human Adenovirus Subtype 21a in China With MinION and Illumina Sequencers Ye, Fuqiang; Han, Yifang; Zhu, Juanjuan; Li, Peng; Zhang, Qi; Lin, Yanfeng; Wang, Taiwu; Lv, Heng; Wang, Changjun; Wang, Chunhui; Zhang, Jinhai 2020 2020-04-07 COMM-USE N PMC7155751 10.3389/fgene.2020.00285 18b2foud 0.527504 Langelier_2017, Chieochansin_2010, Whiteford_2005, Brown_1984, Cheng_2013
74 Sachsenröder_2012 Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing Sachsenröder, Jana; Twardziok, Sven; Hammerl, Jens A.; Janczyk, Pawel; Wrede, Paul; Hertwig, Stefan; Johne, Reimar 2012 2012-04-13 COMM-USE N PMC3326065 22514648.0 10.1371/journal.pone.0034631 jwbuwa9k 0.526918 Rice_1992, Armesto_2007, Keep_2015, Bickerton_2017, Keep_2014 Ren_X_2008, Sazmand_2019
75 Koonin_2015 Origins and evolution of viruses of eukaryotes: The ultimate modularity Koonin, Eugene V.; Dolja, Valerian V.; Krupovic, Mart 2015 2015-05-31 PMC N 25771806.0 10.1016/j.virol.2015.02.039 rjthvtul 0.524921 Rice_1992, den_Boon_2010, Wang_2018, Payne_2017
76 Brister_2015 NCBI Viral Genomes Resource Brister, J. Rodney; Ako-adjei, Danso; Bao, Yiming; Blinkova, Olga 2015 2015-01-28 PMC N PMC4383986 25428358.0 10.1093/nar/gku1207 wjf8t8vp 0.523541 Cheng_2013, Smith_2013, Chang_2011, Montgomery_2004 Wang_2010, Satyanarayana_2003, Viehweger_2019
77 Chong_2019 Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics Chong, Rowena; Shi, Mang; Grueber, Catherine E.; Holmes, Edward C.; Hogg, Carolyn J.; Belov, Katherine; Barrs, Vanessa R. 2019 2019-05-15 COMM-USE N PMC6532096 30867308.0 10.1128/jvi.00205-19 t1anr8gd 0.522001 Wang_2018, Wang_2015, Rice_1992, Grewelle_2020, Roux_2019 Chong_2018, Conceição-Neto_2015, Wray_2016, Ghazisaeedi_2017
78 Viehweger_2018 Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis Adrian Viehweger; Sebastian Krautwurst; Kevin Lamkiewicz; Ramakanth Madhugiri; John Ziebuhr; Martin Hölzer; Manja Marz 2018 2018-11-30 BioRxiv N 10.1101/483693 xr2bs4bk 0.519669 Rice_1992, Payne_2017, Auewarakul_2005, Stork_2011, den_Boon_2010 Viehweger_2019, Bhullar_2014
79 Lian_2014 Novel Circovirus from Mink, China Lian, Hai; Liu, Ye; Li, Nan; Wang, Yuying; Zhang, Shoufeng; Hu, Rongliang 2014 2014-09-23 PMC N PMC4178405 25148585.0 10.3201/eid2009.140015 w9vnk3i6 0.519314 Lu_P_2016, Ryu_W_2017, Wang_2015, Crowe_2014 Dang_2019, Liais_2014, Brandão_2016, Decaro_2007
80 Marthaler_2014 Complete Genome Sequence of Strain SDCV/USA/Illinois121/2014, a Porcine Deltacoronavirus from the United States Marthaler, Douglas; Jiang, Yin; Collins, Jim; Rossow, Kurt 2014 2014-04-10 COMM-USE N PMC3983293 24723704.0 10.1128/genomea.00218-14 shizpehg 0.519314 Langelier_2017, Kin_N_2017, Taboada_2016, Whiteford_2005 Li_K_2018, Liang_2019, Suzuki_2017, Lee_S_2014
81 Kuhring_2019 An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples Mathias Kuhring; Joerg Doellinger; Andreas Nitsche; Thilo Muth; Bernhard Y. Renard 2019 2019-10-24 BioRxiv N 10.1101/812313 k7hm3aow 0.519249 Lee_C_2017, Chang_2011, Cheng_2013, Montgomery_2004, Saw_A_2019 Naidoo_2014, Shifman_2019, McGarvey_2009
82 Phillippy_2009 Efficient oligonucleotide probe selection for pan-genomic tiling arrays Phillippy, Adam M; Deng, Xiangyu; Zhang, Wei; Salzberg, Steven L 2009 2009-09-16 COMM-USE N PMC2753849 19758451.0 10.1186/1471-2105-10-293 g4sjyytr 0.519244 Cheng_2013, Chang_2011, Deng_2015, Whiteford_2005 Tan_J_2009, Wang_2010, Karaman_2005, Giles_2015
83 Wang_2018 The fecal virome of red-crowned cranes Wang, Yan; Yang, Shixing; Liu, Dawei; Zhou, Chenglin; Li, Wang; Lin, Yuan; Wang, Xiaochun; Shen, Quan; Wang, Hua; Li, Chuang; Zong, Minghui; Ding, Yuzhu; Song, Qianben; Deng, Xutao; Qi, Dunwu; Zhang, Wen; Delwart, Eric 2018 2018-09-17 PMC N PMC7086969 30225519.0 10.1007/s00705-018-4037-x db45qdjl 0.518070 Xu_L_2018, Ryu_W_2017, Wang_2015, Tong_2009, Whittaker_2017 Teoh_2015, Wray_2016, Crawford_2019
84 Moreno_2017 Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics Moreno, Paloma S.; Wagner, Josef; Mansfield, Caroline S.; Stevens, Matthew; Gilkerson, James R.; Kirkwood, Carl D. 2017 2017-06-01 COMM-USE N PMC5453527 28570584.0 10.1371/journal.pone.0178433 pue5q5wp 0.518070 Ryu_W_2017, Wang_2015, Tong_2009, Xu_L_2018, Macy_2020 Yinda_2019, Duijvestijn_2016
85 Smits_2015 Recovering full-length viral genomes from metagenomes Smits, Saskia L.; Bodewes, Rogier; Ruiz-González, Aritz; Baumgärtner, Wolfgang; Koopmans, Marion P.; Osterhaus, Albert D. M. E.; Schürch, Anita C. 2015 2015-10-01 COMM-USE N PMC4589665 26483782.0 10.3389/fmicb.2015.01069 tybes52g 0.517096 Lee_C_2017, Chang_2011, Deng_2015, Smits_2014, Brister_2015 Case_2017, Sun_D_2016, Li_C_2020
86 Dufraigne_2005 Detection and characterization of horizontal transfers in prokaryotes using genomic signature Dufraigne, Christine; Fertil, Bernard; Lespinats, Sylvain; Giron, Alain; Deschavanne, Patrick 2005 2005-01-13 PMC N PMC546175 15653627.0 10.1093/nar/gni004 yba7mdtb 0.515605 Chang_2011, Francis_2016, Gardner_2004, Zheng_2008, Auewarakul_2005 Ren_X_2008, Shabman_2016, Suzuki_2020, Lima_2015
87 KREUTZ_2005 Viral respiratory tract infections increase platelet reactivity and activation: an explanation for the higher rates of myocardial infarction and stroke during viral illness KREUTZ, R. P.; BLIDEN, K. P.; TANTRY, U. S.; GURBEL, P. A. 2005 2005-08-11 PMC N PMC7166489 16102122.0 10.1111/j.1538-7836.2005.01474.x 9f5ebiuj 0.514950
88 SCHAT_2008 16 AVIAN IMMUNOSUPPRESSIVE DISEASES AND IMMUNE EVASION SCHAT, KAREL A.; SKINNER, MICHAEL A. 2008 2008-12-31 PMC N PMC7150292 10.1016/b978-012370634-8.50019-6 9qsce2jg 0.514950 Vande_Vusse_2018, Zhou_2004, Vakil_2017, Yu_W_2004, Bersanelli_2020
89 Bao_Y_2008 Virus Classification by Pairwise Sequence Comparison (PASC) Bao, Y.; Kapustin, Y.; Tatusova, T. 2008 2008-12-31 PMC N 10.1016/b978-012374410-4.00710-x aa88gtzr 0.514577 Chang_2011, Lee_C_2017, Brister_2015, Wang_2013
90 Kuchibhatla_2014 Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently “Orphan” Viral Proteins Kuchibhatla, Durga B.; Sherman, Westley A.; Chung, Betty Y. W.; Cook, Shelley; Schneider, Georg; Eisenhaber, Birgit; Karlin, David G. 2014 2014-01-23 COMM-USE N PMC3911697 24155369.0 10.1128/jvi.02595-13 fvj3cpie 0.512873 Rice_1992, Gardner_2004, Lee_C_2017, Smits_2014, Odom_2009 Pavesi_2018, Zhang_2017, Han_L_2005
91 Siridechadilok_2013 A Simplified Positive-Sense-RNA Virus Construction Approach That Enhances Analysis Throughput Siridechadilok, Bunpote; Gomutsukhavadee, Methee; Sawaengpol, Thunyarat; Sangiambut, Sutha; Puttikhunt, Chunya; Chin-inmanu, Kwanrutai; Suriyaphol, Prapat; Malasit, Prida; Screaton, Gavin; Mongkolsapaya, Juthathip 2013 2013-12-23 COMM-USE N PMC3838137 24049164.0 10.1128/jvi.02261-13 84gvwb35 0.512436 Rice_1992, Wang_2018, Armesto_2007, Conzelmann_1996 Usme-Ciro_2014, Satyanarayana_2003, Yun_S_2015
92 Zeigler_Allen_2017 The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses Zeigler Allen, Lisa; McCrow, John P.; Ininbergs, Karolina; Dupont, Christopher L.; Badger, Jonathan H.; Hoffman, Jeffery M.; Ekman, Martin; Allen, Andrew E.; Bergman, Birgitta; Venter, J. Craig 2017 2017-02-14 COMM-USE N PMC5309335 28217745.0 10.1128/msystems.00125-16 r6y06zwj 0.512247 Wang_2018, Bergner_2019, Roux_2019, Zheng_2008, Gay_N_2014 Selvin_2019, Shabman_2016, Walker_2011
93 Chen_2019 A binning tool to reconstruct viral haplotypes from assembled contigs Chen, Jiao; Shang, Jiayu; Wang, Jianrong; Sun, Yanni 2019 2019-11-04 COMM-USE N PMC6829986 31684876.0 10.1186/s12859-019-3138-1 6tss9ydx 0.511702 Chang_2011, Deng_2015, Lee_C_2017, Chen_2019, Cheng_2013 Chen_2019, Wang_2010
94 Geldenhuys_2018 A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa Geldenhuys, Marike; Mortlock, Marinda; Weyer, Jacqueline; Bezuidt, Oliver; Seamark, Ernest C. J.; Kearney, Teresa; Gleasner, Cheryl; Erkkila, Tracy H.; Cui, Helen; Markotter, Wanda 2018 2018-03-26 COMM-USE N PMC5868816 29579103.0 10.1371/journal.pone.0194527 uf7usvuu 0.511478 Chieochansin_2010, Xu_L_2018, Tong_2009, Wang_2015, Ryu_W_2017 Lee_D_2019, Dacheux_2014
95 Pokhriyal_2019 Bioinformatics and Microarray-Based Technologies to Viral Genome Sequence Analysis Pokhriyal, Mayank; Ratta, Barkha; Yadav, Brijesh S. 2019 2019-11-06 PMC N PMC7121691 10.1007/978-981-13-8739-5_6 ag3n4ecn 0.511037 Djikeng_2009, Yadav_2013, UNKNOWN_2004, Leiva-Torres_2017 Wang_2003, Wang_2010, Baldwin_2014
96 Cacciabue_2019 A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing Cacciabue, Marco; Currá, Anabella; Carrillo, Elisa; König, Guido; Gismondi, María Inés 2019 2019-11-04 PMC N PMC7110011 31697321.0 10.1093/bib/bbz086 hphn7cs6 0.507457 Siridechadilok_2013, Djikeng_2009, Smith_2013, Brister_2015 Lachheb_2019, Shabman_2016, Dacheux_2014, Alquezar-Planas_2013
97 Li_L_2015 Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent Li, Linlin; Deng, Xutao; Mee, Edward T.; Collot-Teixeira, Sophie; Anderson, Rob; Schepelmann, Silke; Minor, Philip D.; Delwart, Eric 2015 2015-03-01 None N PMC4344864 25497414.0 10.1016/j.jviromet.2014.12.002 iq6j2z9d 0.506459 Rice_1992, Chen_2018, Oba_M_2018, Auewarakul_2005 Mikel_2015, Yang_2018
98 Lima_2015 Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil Lima, Francisco Esmaile de Sales; Cibulski, Samuel Paulo; dos Santos, Helton Fernandes; Teixeira, Thais Fumaco; Varela, Ana Paula Muterle; Roehe, Paulo Michel; Delwart, Eric; Franco, Ana Cláudia 2015 2015-02-17 COMM-USE N PMC4331541 25688970.0 10.1371/journal.pone.0118070 i34vmfpp 0.506145 Chieochansin_2010, Li_D_2019, Rice_1992, Auewarakul_2005, Zheng_2008 Ren_X_2008, Lee_D_2019, Mohamed_2018
99 Conceição-Neto_2015 Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis Conceição-Neto, Nádia; Zeller, Mark; Lefrère, Hanne; De Bruyn, Pieter; Beller, Leen; Deboutte, Ward; Yinda, Claude Kwe; Lavigne, Rob; Maes, Piet; Ranst, Marc Van; Heylen, Elisabeth; Matthijnssens, Jelle 2015 2015-11-12 COMM-USE N PMC4642273 26559140.0 10.1038/srep16532 l99g2wgz 0.504334 Chang_2011, Harel_2019, Rice_1992, Auewarakul_2005, Smits_2014 Li_L_2015, van_der_Linden_2014, Shabman_2016, Mikel_2015
100 Bibby_2011 Viral Metagenome Analysis to Guide Human Pathogen Monitoring in Environmental Samples Bibby, Kyle; Viau, Emily; Peccia, Jordan 2011 2011-02-21 PMC N PMC3055918 21272046.0 10.1111/j.1472-765x.2011.03014.x rv8397f9 0.503909 Rice_1992, Cheng_2013, Naito_2007, Smits_2014, Ryu_W_2017 Dacheux_2014, Anderson_2020, Wu_Z_2018, Ren_X_2008
101 Rose_2015 Challenges of the Unknown: Clinical Application of Microbial Metagenomics Rose, Graham; Wooldridge, David J.; Anscombe, Catherine; Mee, Edward T.; Misra, Raju V.; Gharbia, Saheer 2015 2015-09-14 COMM-USE N PMC4584244 26451363.0 10.1155/2015/292950 n92j9y0j 0.500498 Gamermann_2014, Djikeng_2009, Brister_2015, Deng_2015, Roux_2019 Li_C_2020, Miller_2013, Baldwin_2014, Takhampunya_2019
102 Chen-Harris_2013 Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs Chen-Harris, Haiyin; Borucki, Monica K; Torres, Clinton; Slezak, Tom R; Allen, Jonathan E 2013 2013-02-12 COMM-USE N PMC3599684 23402258.0 10.1186/1471-2164-14-96 604gho1u 0.500482 Harel_2019, Chang_2011, Deng_2015, Whiteford_2005, Schlub_2018 Harel_2019, Lewandowska_2017, Lu_I_2020, Isakov_2015
103 Tcherepanov_2006 Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris 2006 2006-06-13 COMM-USE N PMC1534038 16772042.0 10.1186/1471-2164-7-150 1e2kkhht 0.500316 Cheng_2013, UNKNOWN_2018, Brister_2015, O'Leary_2016 Wang_2010, Godeny_1990
104 Shean_2019 VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank Shean, Ryan C.; Makhsous, Negar; Stoddard, Graham D.; Lin, Michelle J.; Greninger, Alexander L. 2019 2019-01-23 COMM-USE N PMC6343335 30674273.0 10.1186/s12859-019-2606-y u3q36o3e 0.500313 Garcia–Moliner_2013, Davaro_2013, Ryu_W_2017, UNKNOWN_2018 Wang_2012, Wang_2010, Ren_X_2008
105 Slezak_2020 Chapter 20 Design of genomic signatures for pathogen identification and characterization Slezak, Tom; Hart, Bradley; Jaing, Crystal 2020 2020-12-31 PMC N PMC7153316 10.1016/b978-0-12-815379-6.00020-9 cydvmm4r 0.493599 Chang_2011, Francis_2016, Brister_2015, Priest_2012, Denison_2008 Slezak_2011, Wu_Z_2011, Giles_2015
106 Yadav_2013 Sequencing and Computational Approaches to Identification and Characterization of Microbial Organisms Yadav, Brijesh Singh; Ronda, Venkateswarlu; Vashista, Dinesh P; Sharma, Bhaskar 2013 2013-05-20 PMC N PMC4147756 25288901.0 10.4137/becb.s10886 xrxttrh2 0.491968 Vernikos_2008, Djikeng_2009, Smith_2013, Johnson_2018 Pokhriyal_2019, Shifman_2019, Selvin_2019, McGuire_2012
107 Wei_C_2011 Identification and Typing of Human Enterovirus: A Genomic Barcode Approach Wei, Chengguo; Wang, Guoqing; Chen, Xin; Huang, Honglan; Liu, Bin; Xu, Ying; Li, Fan 2011 2011-10-14 COMM-USE N PMC3194813 22022592.0 10.1371/journal.pone.0026296 qkymwvwb 0.491438 Chang_2011, Zheng_2008, Lee_C_2017, Saw_A_2019 Ren_X_2008, de_Souza_Luna_2008
108 Jiang_2015 Optimized DNA extraction and metagenomic sequencing of airborne microbial communities Jiang, Wenjun; Liang, Peng; Wang, Buying; Fang, Jianhuo; Lang, Jidong; Tian, Geng; Jiang, Jingkun; Zhu, Ting F 2015 2015-04-23 PMC N PMC7086576 25906115.0 10.1038/nprot.2015.046 zqedc4ie 0.489980 Tithi_2018, Deng_2015, Roux_2019, Smith_2013 Selvin_2019, Twin_2013, Nostrand_2012
109 Shah_2014 Comparison of tissue sample processing methods for harvesting the viral metagenome and a snapshot of the RNA viral community in a turkey gut Shah, Jigna D.; Baller, Joshua; Zhang, Ying; Silverstein, Kevin; Xing, Zheng; Cardona, Carol J. 2014 2014-12-01 PMC N 25181646.0 10.1016/j.jviromet.2014.08.011 rh1ad6bv 0.487238 Rice_1992, Wang_2018, Auewarakul_2005, den_Boon_2010, Smits_2014
110 Zou_X_2016 Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique Zou, Xiaohui; Tang, Guangpeng; Zhao, Xiang; Huang, Yan; Chen, Tao; Lei, Mingyu; Chen, Wenbing; Yang, Lei; Zhu, Wenfei; Zhuang, Li; Yang, Jing; Feng, Zhaomin; Wang, Dayan; Wang, Dingming; Shu, Yuelong 2016 2016-12-02 COMM-USE N PMC7088591 27921234.0 10.1007/s11427-016-0244-8 z8thv6ar 0.487238 Zhang_2020, Langelier_2017, Chieochansin_2010, Rice_1992, Kamau_2019 Galmès_2012, Ren_X_2008
111 Gardner_2010 A microbial detection array (MDA) for viral and bacterial detection Gardner, Shea N; Jaing, Crystal J; McLoughlin, Kevin S; Slezak, Tom R 2010 2010-11-25 COMM-USE N PMC3017867 21108826.0 10.1186/1471-2164-11-668 qi2knswx 0.486513 Rice_1992, Gardner_2004, Chang_2011, Smits_2014, Phillippy_2009 Giles_2015, Wang_2003
112 Watanabe_2010 Novel Betaherpesvirus in Bats Watanabe, Shumpei; Maeda, Ken; Suzuki, Kazuo; Ueda, Naoya; Iha, Koichiro; Taniguchi, Satoshi; Shimoda, Hiroshi; Kato, Kentaro; Yoshikawa, Yasuhiro; Morikawa, Shigeru; Kurane, Ichiro; Akashi, Hiroomi; Mizutani, Tetsuya 2010 2010-06-23 None N PMC3086227 20507753.0 10.3201/eid1606.091567 yhoyu4fw 0.485735 Lu_P_2016, Ryu_W_2017, Rice_1992, Wang_2015 Lee_D_2019, Lian_2014, Ng_T_2013, Carrington_2008
113 Marthaler_2015 Next-Generation Sequencing for Porcine Coronaviruses Marthaler, Douglas; Bohac, Ann; Becker, Aaron; Peterson, Nichole 2015 2015-09-10 PMC N PMC7120291 10.1007/978-1-4939-3414-0_19 jlono0x7 0.485277 Ryu_W_2017, Lu_P_2016, Rice_1992, Wang_2015, Crowe_2014 Ren_X_2008, Thimmasandra_Narayanappa_2015
114 Cook_2013 Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts Cook, Shelley; Chung, Betty Y.-W.; Bass, David; Moureau, Gregory; Tang, Shuoya; McAlister, Erica; Culverwell, C. Lorna; Glücksman, Edvard; Wang, Hui; Brown, T. David K.; Gould, Ernest A.; Harbach, Ralph E.; de Lamballerie, Xavier; Firth, Andrew E. 2013 2013-11-18 COMM-USE N PMC3832450 24260463.0 10.1371/journal.pone.0080720 tvhybr82 0.484818 Xu_L_2018, Rice_1992, Liu_S_2013, Wang_2018 Zhou_2017
115 Mizutani_2007 Rapid Genome Sequencing of RNA Viruses Mizutani, Tetsuya; Endoh, Daiji; Okamoto, Michiko; Shirato, Kazuya; Shimizu, Hiroyuki; Arita, Minetaro; Fukushi, Shuetsu; Saijo, Masayuki; Lim, Chang Kweng; Ito, Mikako; Nerome, Reiko; Takasaki, Tomohiko; Ishii, Koji; Suzuki, Tetsuro; Kurane, Ichiro; Morikawa, Shigeru; Nishimura, Hidekazu 2007 2007-02-23 PMC N PMC2725858 17479903.0 10.3201/eid1302.061032 gzxeud8h 0.484749 Rice_1992, Armesto_2007, Bickerton_2017, Keep_2015 Rice_1992, Nowak_1984, Tzeng_2006
116 Hall_2014 Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery Hall, Richard J.; Wang, Jing; Todd, Angela K.; Bissielo, Ange B.; Yen, Seiha; Strydom, Hugo; Moore, Nicole E.; Ren, Xiaoyun; Huang, Q. Sue; Carter, Philip E.; Peacey, Matthew 2014 2014-01-31 PMC N PMC7113663 24036074.0 10.1016/j.jviromet.2013.08.035 n6xp5mlz 0.484181 Chang_2011, Rice_1992, Siridechadilok_2013, Lee_C_2017, Naito_2007 Lewandowska_2017, Dacheux_2014, Giles_2015, Shifman_2019
117 O'Leary_2016 Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney; Ciufo, Stacy; Haddad, Diana; McVeigh, Rich; Rajput, Bhanu; Robbertse, Barbara; Smith-White, Brian; Ako-Adjei, Danso; Astashyn, Alexander; Badretdin, Azat; Bao, Yiming; Blinkova, Olga; Brover, Vyacheslav; Chetvernin, Vyacheslav; Choi, Jinna; Cox, Eric; Ermolaeva, Olga; Farrell, Catherine M.; Goldfarb, Tamara; Gupta, Tripti; Haft, Daniel; Hatcher, Eneida; Hlavina, Wratko; Joardar, Vinita S.; Kodali, Vamsi K.; Li, Wenjun; Maglott, Donna; Masterson, Patrick; McGarvey, Kelly M.; Murphy, Michael R.; O'Neill, Kathleen; Pujar, Shashikant; Rangwala, Sanjida H.; Rausch, Daniel; Riddick, Lillian D.; Schoch, Conrad; Shkeda, Andrei; Storz, Susan S.; Sun, Hanzhen; Thibaud-Nissen, Francoise; Tolstoy, Igor; Tully, Raymond E.; Vatsan, Anjana R.; Wallin, Craig; Webb, David; Wu, Wendy; Landrum, Melissa J.; Kimchi, Avi; Tatusova, Tatiana; DiCuccio, Michael; Kitts, Paul; Murphy, Terence D.; Pruitt, Kim D. 2016 2016-01-04 PMC N PMC4702849 26553804.0 10.1093/nar/gkv1189 jsg0yc2t 0.482920 UNKNOWN_2016, UNKNOWN_2018, Cheng_2013, Gardner_2008 UNKNOWN_2016, Schäffer_2019
118 Morfopoulou_2015 Bayesian mixture analysis for metagenomic community profiling Morfopoulou, Sofia; Plagnol, Vincent 2015 2015-09-15 COMM-USE N PMC4565032 26002885.0 10.1093/bioinformatics/btv317 z29xsj1o 0.481635 Chang_2011, Montgomery_2004, Cheng_2013, Deng_2015, Lee_C_2017 Morfopoulou_2014, Baldwin_2014, Selvin_2019, Giles_2015
119 Hoffmann_2020 PriSeT: Efficient De Novo Primer Discovery Marie Hoffmann; Michael T. Monaghan; Knut Reinert 2020 2020-04-07 BioRxiv Y 10.1101/2020.04.06.027961 3b3hv53b 0.480933 Chang_2011, Lee_C_2017, Deng_2015, Phillippy_2009 Zhang_2017, Severgnini_2009, Ayginin_2018, Mukai_2006
120 Gardner_2008 Rfam: updates to the RNA families database Gardner, Paul P.; Daub, Jennifer; Tate, John G.; Nawrocki, Eric P.; Kolbe, Diana L.; Lindgreen, Stinus; Wilkinson, Adam C.; Finn, Robert D.; Griffiths-Jones, Sam; Eddy, Sean R.; Bateman, Alex 2008 2008-10-25 NONCOMM N PMC2686503 18953034.0 10.1093/nar/gkn766 wj7yonjw 0.479681 Cheng_2013, O'Leary_2016, Lee_C_2017, Wang_2006 Xia_H_2015, Yamasaki_2019, Muppirala_2011
121 Schlüter_2008 Mass spectrometry for monitoring protease reactions Schlüter, H.; Hildebrand, D.; Gallin, C.; Schulz, A.; Thiemann, J.; Trusch, M. 2008 2008-06-27 PMC N PMC7080141 18584157.0 10.1007/s00216-008-2213-7 ozljm6kl 0.479508 Sharon_2010, Lee_C_2017, Hu_S_2010, Liu_Z_2008 Zheng_2011, Turner_2010, van_der_Linden_2014
122 Yang_2018 Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis Yang, Yu; Walls, Shannon D.; Gross, Stephen M.; Schroth, Gary P.; Jarman, Richard G.; Hang, Jun 2018 2018-05-12 PMC N PMC7121196 30128994.0 10.1007/978-1-4939-8682-8_10 pbhggsh2 0.477789 Chen_2018, Cheng_2013, Deng_2015, Pandya_2007 Lewandowska_2017, Ren_X_2008
123 Noell_2019 Further Defining the Human Virome using NGS: Identification of Redondoviridae Noell, Kristin; Kolls, Jay K. 2019 2019-05-08 PMC N PMC6849504 31071291.0 10.1016/j.chom.2019.04.010 ru8nyydl 0.473805 Wang_2018, Li_L_2014, Taschuk_2020, den_Boon_2010, Berkhout_2006 Conant_2013, Ansuini_2013, Murray_2008
124 Fontenele_2019 Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil Fontenele, Rafaela S.; Lacorte, Cristiano; Lamas, Natalia S.; Schmidlin, Kara; Varsani, Arvind; Ribeiro, Simone G. 2019 2019-08-02 COMM-USE N PMC6723397 31382446.0 10.3390/v11080710 4e3wgv4e 0.472235 Xu_L_2018, Tong_2009, Wang_2015, Ryu_W_2017, Wang_2014 Crawford_2019, Wray_2016, Lee_D_2019, Maganga_2014
125 Wittekindt_2010 Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics Wittekindt, Nicola E.; Padhi, Abinash; Schuster, Stephan C.; Qi, Ji; Zhao, Fangqing; Tomsho, Lynn P.; Kasson, Lindsay R.; Packard, Michael; Cross, Paul; Poss, Mary 2010 2010-10-18 COMM-USE N PMC2956653 20976145.0 10.1371/journal.pone.0013432 v4jochbe 0.472056 Wang_2018, Rice_1992, Zheng_2008, Li_D_2019 Selvin_2019, Ren_X_2008, Takhampunya_2019, Wei_J_2016
126 Alquezar-Planas_2013 Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing Alquezar-Planas, David E.; Mourier, Tobias; Bruhn, Christian A. W.; Hansen, Anders J.; Vitcetz, Sarah Nathalie; Mørk, Søren; Gorodkin, Jan; Nielsen, Hanne Abel; Guo, Yan; Sethuraman, Anand; Paxinos, Ellen E.; Shan, Tongling; Delwart, Eric L.; Nielsen, Lars P. 2013 2013-09-03 None N PMC3760282 24002378.0 10.1038/srep02468 t4215imq 0.470058 Rice_1992, Zhang_2020, Chieochansin_2010, Langelier_2017, Kamau_2019 Ren_X_2008, Galmès_2012
127 Minot_2014 SIANN: Strain Identification by Alignment to Near Neighbors Samuel Minot; Stephen D Turner; Krista L Ternus; Dana R Kadavy 2014 2014-01-10 BioRxiv N 10.1101/001727 vho70jcx 0.468979 Chang_2011, Lee_C_2017, Deng_2015, Montgomery_2004, Dai_Q_2012 Shifman_2019, Tausch_2018, ZHANG_2018, Morfopoulou_2014
128 McGowan_2014 Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray McGowan, Sarah; Nunez-Garcia, Javier; Steinbach, Falko; La Rocca, Anna; Blake, Damer; Dastjerdi, Akbar 2014 2014-10-31 PMC N PMC7119560 25034125.0 10.1016/j.jviromet.2014.07.012 ddge24x7 0.468409 Chang_2011, Chen_2018, Auewarakul_2005, Rice_1992 Majerciak_2018, Schoenike_1999, Zhong_2007
129 Pickett_2011 ViPR: an open bioinformatics database and analysis resource for virology research Pickett, Brett E.; Sadat, Eva L.; Zhang, Yun; Noronha, Jyothi M.; Squires, R. Burke; Hunt, Victoria; Liu, Mengya; Kumar, Sanjeev; Zaremba, Sam; Gu, Zhiping; Zhou, Liwei; Larson, Christopher N.; Dietrich, Jonathan; Klem, Edward B.; Scheuermann, Richard H. 2011 2011-10-17 NONCOMM N PMC3245011 22006842.0 10.1093/nar/gkr859 48ym7eti 0.467085 Garcia–Moliner_2013, Ryu_W_2017, Crowe_2014, Davaro_2013 McGuire_2012, Pickett_2012, Wang_2020
130 Li_Y_2017 Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates Li, Yan; Khalafalla, Abdelmalik Ibrahim; Paden, Clinton R.; Yusof, Mohammed F.; Eltahir, Yassir M.; Al Hammadi, Zulaikha M.; Tao, Ying; Queen, Krista; Hosani, Farida Al; Gerber, Susan I.; Hall, Aron J.; Al Muhairi, Salama; Tong, Suxiang 2017 2017-09-13 COMM-USE N PMC5597213 28902913.0 10.1371/journal.pone.0184718 udlf9t1t 0.467043 Ryu_W_2017, Crowe_2014, Kamau_2019, Chieochansin_2010, Wang_2015 Kandeil_2019, Lau_S_2020, Kandeil_2019, Woo_P_2016
131 Naccache_2014 A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples Naccache, Samia N.; Federman, Scot; Veeraraghavan, Narayanan; Zaharia, Matei; Lee, Deanna; Samayoa, Erik; Bouquet, Jerome; Greninger, Alexander L.; Luk, Ka-Cheung; Enge, Barryett; Wadford, Debra A.; Messenger, Sharon L.; Genrich, Gillian L.; Pellegrino, Kristen; Grard, Gilda; Leroy, Eric; Schneider, Bradley S.; Fair, Joseph N.; Martínez, Miguel A.; Isa, Pavel; Crump, John A.; DeRisi, Joseph L.; Sittler, Taylor; Hackett, John; Miller, Steve; Chiu, Charles Y. 2014 2014-06-04 None N PMC4079973 24899342.0 10.1101/gr.171934.113 tg52towp 0.466598 Deng_2015, Djikeng_2009, Cheng_2013, Manning_2020, Brister_2015 Anis_2018, Tausch_2018, Li_C_2020, Lewandowski_2019
132 Paskey_2019 Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples Paskey, Adrian C.; Frey, Kenneth G.; Schroth, Gary; Gross, Stephen; Hamilton, Theron; Bishop-Lilly, Kimberly A. 2019 2019-02-26 COMM-USE N PMC6390631 30808306.0 10.1186/s12864-019-5543-2 cnvxlv6h 0.465282 Brister_2015, Rice_1992, Djikeng_2009, Deng_2015, Smits_2014 Lewandowska_2017, Yang_2018, Jensen_2015
133 Shepard_2016 Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler Shepard, Samuel S.; Meno, Sarah; Bahl, Justin; Wilson, Malania M.; Barnes, John; Neuhaus, Elizabeth 2016 2016-09-05 COMM-USE N PMC5011931 27595578.0 10.1186/s12864-016-3030-6 xyru2q9o 0.463689 Cheng_2013, Deng_2015, Lee_C_2017, Montgomery_2004, Chang_2011 Anderson_2020, Masante_2015
134 Djikeng_2009 Advancing full length genome sequencing for human RNA viral pathogens Djikeng, Appolinaire; Spiro, David 2009 2009-01-01 PMC N PMC2638583 19884976.0 10.2217/17460794.4.1.47 uvm72cpi 0.463526 Gupta_2009, Smith_2013, Conzelmann_1996, Dugan_2012 Viehweger_2019, Dugan_2012, Masante_2015
135 Schäffer_2019 VADR: validation and annotation of virus sequence submissions to GenBank Alejandro A Schäffer; Eneida Hatcher; Linda Yankie; Lara Shonkwiler; J Rodney Brister; Ilene Karsch-Mizrachi; Eric P Nawrocki 2019 2019-11-22 BioRxiv N 10.1101/852657 besvz92f 0.462594 UNKNOWN_2018, Cheng_2013, O'Leary_2016, UNKNOWN_2016 Shean_2019, Godeny_1990, Meulenberg_1995
136 Chong_2018 Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics Rowena Chong; Mang Shi; Catherine E Grueber; Edward C Holmes; Carolyn Hogg; Katherine Belov; Vanessa R Barrs 2018 2018-10-15 BioRxiv N 10.1101/443457 4uahwkp8 0.462317 Wang_2015, Wang_2018, Xu_L_2018, Ryu_W_2017, Lu_P_2016 Chong_2019, Conceição-Neto_2015, Zhou_2017, Ghazisaeedi_2017
137 Pyrc_2007 Detection of New Viruses by VIDISCA: Virus Discovery Based on cDNA-Amplified Fragment Length Polymorphism Pyrc, Krzysztof; Jebbink, Maarten F.; Berkhout, Ben; van der Hoek, Lia 2007 2007-11-28 PMC N PMC7121709 19057862.0 10.1007/978-1-59745-181-9_7 nxutmxp6 0.462259 Majerciak_2018, Armesto_2007, Rice_1992, Keep_2015, Keep_2014 Hu_T_2012
138 Cholleti_2018 Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique Cholleti, Harindranath; Hayer, Juliette; Mulandane, Fernando Chanisso; Falk, Kerstin; Fafetine, Jose; Berg, Mikael; Blomström, Anne-Lie 2018 2018-05-28 NONCOMM N PMC5974704 29868166.0 10.1080/20008686.2018.1478585 moxleyjg 0.461391 Ryu_W_2017, Chieochansin_2010, Wang_2015, Xu_L_2018, Lu_P_2016 Ghazisaeedi_2017, Ren_X_2008, Lachheb_2019, Hammerschmitt_2020
139 Georgiev_2009 Genomic and Postgenomic Research Georgiev, Vassil St. 2009 2009-01-01 PMC N PMC7122628 10.1007/978-1-60327-297-1_25 vmtjc8ct 0.460670 Murray_2017, Cheng_2013, Vernikos_2008, O'Leary_2016 Shabman_2016, Goldberg_1991
140 Kew_O_1984 2 Applications of Oligonucleotide Fingerprinting to the Identification of Viruses Kew, Olen M.; Nottay, Baldev K.; Obijeski, John F. 1984 1984-12-31 PMC N 10.1016/b978-0-12-470208-0.50008-6 06pj7zkp 0.460561 Chang_2011, Lee_C_2017, Schlub_2018, Harel_2019, Deng_2015
141 Morfopoulou_2014 Bayesian mixture analysis for metagenomic community profiling. Sofia Morfopoulou; Vincent Plagnol 2014 2014-07-25 BioRxiv N 10.1101/007476 058r9486 0.460263 Chang_2011, Liou_2013, Lee_C_2017, Saw_A_2019, Bocharov_2018 Morfopoulou_2015, Giles_2015, Miller_2013, Baldwin_2014
142 Gamermann_2014 New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks Gamermann, Daniel; Montagud, Arnaud; Conejero, J. Alberto; Urchueguía, Javier F.; de Córdoba, Pedro Fernández 2014 2014-07-01 PMC N PMC4082356 24611553.0 10.1089/cmb.2013.0150 qlwc8g2s 0.459500 Chang_2011, Zheng_2008, Bocharov_2018, Sen_D_2018 Zhang_2017, Francis_2016, McGuire_2012
143 Manning_2020 Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia Jessica E. Manning; Jennifer A. Bohl; Sreyngim Lay; Sophana Chea; Ly Sovann; Yi Sengdoeurn; Seng Heng; Chan Vuthy; Katrina Kalantar; Vida Ahyong; Michelle Tan; Jonathan Sheu; Cristina M. Tato; Joseph L. DeRisi; Laurence Baril; Veasna Duong; Philippe Dussart; Erik A. Karlsson 2020 2020-03-05 BioRxiv N 10.1101/2020.03.02.968818 fu3cl7lq 0.459500 Vernikos_2008, Djikeng_2009, Cui_H_2015, Gupta_2009 Crawford_2019, Lachheb_2019, Dang_2019, Knutson_2017
144 Baldwin_2014 Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues Baldwin, Don A.; Feldman, Michael; Alwine, James C.; Robertson, Erle S. 2014 2014-09-16 NONCOMM N PMC4172075 25227467.0 10.1128/mbio.01714-14 xlqdn0c7 0.458799 Rice_1992, Djikeng_2009, Leiva-Torres_2017, Chen_2018, Harel_2019 Giles_2015, Li_C_2020, Anis_2018, Anderson_2020
145 Jonassen_2007 Detection and Sequence Characterization of the 3′-End of Coronavirus Genomes Harboring the Highly Conserved RNA Motif s2m Jonassen, Christine Monceyron 2007 2007-11-28 PMC N PMC7122199 19057866.0 10.1007/978-1-59745-181-9_3 xl4u7n6r 0.458575 Rice_1992, Firth_2009, Lamb_1991, Armesto_2007 Goldberg_1991, Lin_T_2004, Monceyron_2014
146 Höper_2017 Chapter Two Loeffler 4.0: Diagnostic Metagenomics Höper, Dirk; Wylezich, Claudia; Beer, Martin 2017 2017-12-31 PMC N PMC7112322 29029726.0 10.1016/bs.aivir.2017.08.001 oni76pna 0.456703 Vernikos_2008, Djikeng_2009, Dove_2004, Johnson_2018 Kaszab_2020, Haagmans_2009, Anderson_2020, Alquezar-Planas_2013
147 Chan_2014 Deep Sequencing to Identify the Causes of Viral Encephalitis Chan, Benjamin K.; Wilson, Theodore; Fischer, Kael F.; Kriesel, John D. 2014 2014-04-03 COMM-USE N PMC3974838 24699691.0 10.1371/journal.pone.0093993 65drhnk8 0.455997 Rice_1992, Falcone_1997, Armesto_2007, Majerciak_2018 Ren_X_2008
148 Wang_2016 Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China Wang, Y.; Zhu, N.; Li, Y.; Lu, R.; Wang, H.; Liu, G.; Zou, X.; Xie, Z.; Tan, W. 2016 2016-05-31 PMC N 26802214.0 10.1016/j.cmi.2016.01.006 p0cxsrzb 0.455738 Crowe_2014, Chieochansin_2010, Ryu_W_2017, Lu_P_2016, Zhang_2020
149 Kulkarni-Kale_2006 Curation of viral genomes: challenges, applications and the way forward Kulkarni-Kale, Urmila; Bhosle, Shriram G; Manjari, G Sunitha; Joshi, Manali; Bansode, Sandeep; Kolaskar, Ashok S 2006 2006-12-18 COMM-USE N PMC1764468 17254296.0 10.1186/1471-2105-7-s5-s12 3xq5jwof 0.454384 Cheng_2013, Brister_2015, Montgomery_2004, Chang_2011, O'Leary_2016 Wang_2010, Zhang_2017
150 Lewandowska_2017 Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples Lewandowska, Dagmara W.; Zagordi, Osvaldo; Geissberger, Fabienne-Desirée; Kufner, Verena; Schmutz, Stefan; Böni, Jürg; Metzner, Karin J.; Trkola, Alexandra; Huber, Michael 2017 2017-08-08 COMM-USE N PMC5549297 28789678.0 10.1186/s40168-017-0317-z 3jxyipbn 0.453930 Chen_2018, Rice_1992, Mizutani_2007, Oba_M_2018, Dinh_2011 Yang_2018
151 Moser_2016 A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses Moser, Lindsey A.; Ramirez-Carvajal, Lisbeth; Puri, Vinita; Pauszek, Steven J.; Matthews, Krystal; Dilley, Kari A.; Mullan, Clancy; McGraw, Jennifer; Khayat, Michael; Beeri, Karen; Yee, Anthony; Dugan, Vivien; Heise, Mark T.; Frieman, Matthew B.; Rodriguez, Luis L.; Bernard, Kristen A.; Wentworth, David E.; Stockwell, Timothy B.; Shabman, Reed S. 2016 2016-06-07 COMM-USE N PMC5069770 27822536.0 10.1128/msystems.00039-15 6c6er06a 0.453342 Rice_1992, Chen_2018, Mizutani_2007, Payne_2017, Armesto_2007 Satyanarayana_2003, Chen_2017
152 Faber_2019 Saturation mutagenesis genome engineering of infective ΦX174 bacteriophage via unamplified oligo pools and golden gate assembly Matthew S. Faber; James T. Van Leuven; Martina M. Ederer; Yesol Sapozhnikov; Zoë L. Wilson; Holly A. Wichman; Timothy A. Whitehead; Craig R. Miller 2019 2019-10-09 BioRxiv N 10.1101/798546 02zzb7v1 0.452210 Armesto_2007, Rice_1992, Bickerton_2017, Keep_2014, Keep_2015 Satyanarayana_2003, Tzeng_2006
153 Moshiri_2020 ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes Niema Moshiri 2020 2020-04-21 BioRxiv N 10.1101/2020.04.20.052068 l9a7upui 0.450923 Cheng_2013, Montgomery_2004, Chang_2011, Lee_C_2017
154 Chang_2011 Genome analysis with the conditional multinomial distribution profile Chang, Guisong; Wang, Tianming 2011 2011-02-21 PMC N PMC7094119 21129383.0 10.1016/j.jtbi.2010.11.034 1ef1cxc8 0.449229 Zheng_2008, Qi_Z_2018, Liu_L_2012, Saw_A_2019 Zhang_2017, Sheikh_2020, Pavlović-Lažetić_2004
155 Lin_Y_2017 De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi 2017 2017-04-26 COMM-USE N PMC5406902 28446139.0 10.1186/s12859-017-1630-z rbwgi0ql 0.448362 Cheng_2013, Deng_2015, Chang_2011, Lee_C_2017, Whiteford_2005 Wang_2013, Deng_2015, Shepard_2016, Bassano_2017
156 WANG_2017 An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens WANG, Chun Hua; NIE, Kai; ZHANG, Yi; WANG, Ji; ZHOU, Shuai Feng; LI, Xin Na; ZHOU, Hang Yu; QI, Shun Xiang; MA, Xue Jun 2017 2017-01-31 PMC N PMC7136949 28245896.0 10.3967/bes2017.003 p17tju4c 0.447731 Chen_2018, Pandya_2007, Djikeng_2009, Deng_2015, Harel_2019 Lewandowska_2017, Anis_2018, Yang_2018
157 Chrzastek_2017 Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses Chrzastek, Klaudia; Lee, Dong-hun; Smith, Diane; Sharma, Poonam; Suarez, David L.; Pantin-Jackwood, Mary; Kapczynski, Darrell R. 2017 2017-09-30 PMC N PMC7111618 28646651.0 10.1016/j.virol.2017.06.019 c5s0qkh6 0.447603 Tallmadge_2008, Rice_1992, Armesto_2007, Ryu_W_2017, Bickerton_2017 Ren_X_2008, Nowak_1984, Zhao_2019
158 Wille_2019 Virome heterogeneity and connectivity in waterfowl and shorebird communities Wille, Michelle; Shi, Mang; Klaassen, Marcel; Hurt, Aeron C.; Holmes, Edward C. 2019 2019-06-25 None N PMC6775988 31239538.0 10.1038/s41396-019-0458-0 9flgtv0z 0.446921 Ryu_W_2017, Wang_2015, Lu_P_2016, Crowe_2014, Xu_L_2018 Wille_2019, Becker_2019
159 Fawaz_2016 Duck gut viral metagenome analysis captures snapshot of viral diversity Fawaz, Mohammed; Vijayakumar, Periyasamy; Mishra, Anamika; Gandhale, Pradeep N.; Dutta, Rupam; Kamble, Nitin M.; Sudhakar, Shashi B.; Roychoudhary, Parimal; Kumar, Himanshu; Kulkarni, Diwakar D.; Raut, Ashwin Ashok 2016 2016-06-09 COMM-USE N PMC4899906 27284287.0 10.1186/s13099-016-0113-5 54s1fae3 0.446533 Ryu_W_2017, Wang_2015, Crowe_2014, Lu_P_2016, Xu_L_2018 Dacheux_2014, Wray_2016, Park_2007, Becker_2019
160 Gibbs_2005 Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences Gibbs, Mark J; Armstrong, John S; Gibbs, Adrian J 2005 2005-04-08 COMM-USE N PMC1090557 15817134.0 10.1186/1471-2105-6-90 oad4l4fa 0.446318 Chang_2011, Zheng_2008, Gardner_2004, Phillippy_2009, Lee_C_2017 Mukai_2006, Severgnini_2009, Nowak_1984, Schlub_2018
161 Cleemput_2020 Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes Sara Cleemput; Wim Dumon; Vagner Fonseca; Wasim Abdool Karim; Marta Giovanetti; Luiz Carlos Alcantara; Koen Deforche; Tulio de Oliveira 2020 2020-02-02 BioRxiv Y 10.1101/2020.01.31.928796 gxstlzuk 0.445955 Cheng_2013, Brister_2015, Lee_C_2017, Xu_Z_2009, Montgomery_2004 Cleemput_2020, Phan_2018, Ren_X_2008, Tanaka_2015
162 Zhou_2006 An Oligonucleotide Microarray for High-Throughput Sequencing of the Mitochondrial Genome Zhou, Shaoyu; Kassauei, Keyaunoosh; Cutler, David J.; Kennedy, Giulia C.; Sidransky, David; Maitra, Anirban; Califano, Joseph 2006 2006-09-01 PMC N PMC1867623 16931588.0 10.2353/jmoldx.2006.060008 hr1ehth1 0.445743 Whiteford_2005, Karaman_2005, Phillippy_2009, Harel_2019, Langelier_2017 Nowak_1984, Shabman_2016, Zamzami_2011
163 Huang_2007 CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes Huang, Yi; Lau, Susanna K. P.; Woo, Patrick C. Y.; Yuen, Kwok-yung 2007 2007-10-02 NONCOMM N PMC2238867 17913743.0 10.1093/nar/gkm754 ujhgb3b0 0.444022 Cheng_2013, Lee_C_2017, O'Leary_2016, Gardner_2008 Tao_Y_2012, Wang_2009
164 Kim_H_2017 MRPrimerV: a database of PCR primers for RNA virus detection Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Kim, Doyun; Koo, JaeHyung; Kim, Min-Soo 2017 2017-01-04 NONCOMM N PMC5210568 27899620.0 10.1093/nar/gkw1095 bo215gm9 0.444022 Rice_1992, Majerciak_2018, Armesto_2007, Naito_2007, Gardner_2004 Majerciak_2018, Mikel_2015
165 Xu_L_2017 Characterization of the nasopharyngeal viral microbiome from children with community‐acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection Xu, Lili; Zhu, Yun; Ren, Lili; Xu, Baoping; Liu, Chunyan; Xie, Zhengde; Shen, Kunling 2017 2017-07-25 PMC N PMC7166964 28671295.0 10.1002/jmv.24895 qw7gcrqa 0.443956 Chieochansin_2010, Ryu_W_2017, Crowe_2014, Kamau_2019, Rice_1992
166 Routh_2013 Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data Routh, Andrew; Johnson, John E. 2013 2013-10-09 COMM-USE N PMC3902915 24137010.0 10.1093/nar/gkt916 55ge7kmr 0.443914 Whiteford_2005, Chang_2011, Deng_2015, Warren_2007 Routh_2012
167 Lu_I_2020 Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies Lu, I-Na; Muller, Claude P.; He, Feng Q. 2020 2020-07-02 PMC N 10.1016/j.virusres.2020.197963 1zw09fo5 0.443806 Djikeng_2009, Leiva-Torres_2017, Johnson_2018, Smith_2013 Lachheb_2019, Kautz_2018, Masante_2015, Anderson_2020
168 Madi_2017 Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait Madi, Nada; Al‐Nakib, Widad; Mustafa, Abu Salim; Habibi, Nazima 2017 2017-11-11 PMC N PMC7167075 29083040.0 10.1002/jmv.24984 7w7fffqk 0.443442 Chieochansin_2010, Zhang_2020, Langelier_2017, Taboada_2016, Kamau_2019
169 Cottam_2009 Full Sequencing of Viral Genomes: Practical Strategies Used for the Amplification and Characterization of Foot-and-Mouth Disease Virus Cottam, Eleanor M.; Wadsworth, Jemma; Knowles, Nick J.; King, Donald P. 2009 2009-03-16 PMC N PMC7122775 19521878.0 10.1007/978-1-60327-999-4_17 a5myh752 0.440547 Djikeng_2009, Chang_2011, Brister_2015, Conzelmann_1996 Ren_X_2008, Lazouskaya_2014, Satyanarayana_2003
170 Gresham_2008 Comparing whole genomes using DNA microarrays Gresham, David; Dunham, Maitreya J.; Botstein, David 2008 2008-01-01 PMC N PMC7097741 18347592.0 10.1038/nrg2335 4zkbjpru 0.440222 Chang_2011, Deng_2015, Harel_2019, Cheng_2013 Phillippy_2009, Routh_2012, Wang_2010, Francis_2016
171 Greninger_2010 A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America Greninger, Alexander L.; Chen, Eunice C.; Sittler, Taylor; Scheinerman, Alex; Roubinian, Nareg; Yu, Guixia; Kim, Edward; Pillai, Dylan R.; Guyard, Cyril; Mazzulli, Tony; Isa, Pavel; Arias, Carlos F.; Hackett, John; Schochetman, Gerald; Miller, Steve; Tang, Patrick; Chiu, Charles Y. 2010 2010-10-18 COMM-USE N PMC2956640 20976137.0 10.1371/journal.pone.0013381 bbv6f5gf 0.439861 Walker_2010, Lu_P_2016, Yasui_2016, Yang_2010, Karlsson_2012 Lachheb_2019, Yan_N_2019, Monamele_2017
172 Lee_J_2017 Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species Lee, Justin S.; Mackie, Ryan S.; Harrison, Thomas; Shariat, Basir; Kind, Trey; Kehl, Timo; Löchelt, Martin; Boucher, Christina; VandeWoude, Sue 2017 2017-05-23 COMM-USE N PMC5442522 28330894.0 10.1128/jcm.01463-16 qohrnpgq 0.439062 Djikeng_2009, Priest_2012, Urisman_2005, Gardner_2004, Rice_1992 Anis_2018, Sazmand_2019
173 Postel_2016 The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools Postel, Alexander; Schmeiser, Stefanie; Zimmermann, Bernd; Becher, Paul 2016 2016-11-07 COMM-USE N PMC5127016 27827988.0 10.3390/v8110302 w2sj3dns 0.438730 Brister_2015, Rodier_2007, Murray_2017, Cheng_2013, Djikeng_2009 Ren_X_2008, Lachheb_2019
174 Deng_2020 Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance Deng, Xianding; Achari, Asmeeta; Federman, Scot; Yu, Guixia; Somasekar, Sneha; Bártolo, Inês; Yagi, Shigeo; Mbala-Kingebeni, Placide; Kapetshi, Jimmy; Ahuka-Mundeke, Steve; Muyembe-Tamfum, Jean-Jacques; Ahmed, Asim A.; Ganesh, Vijay; Tamhankar, Manasi; Patterson, Jean L.; Ndembi, Nicaise; Mbanya, Dora; Kaptue, Lazare; McArthur, Carole; Muñoz-Medina, José E.; Gonzalez-Bonilla, Cesar R.; López, Susana; Arias, Carlos F.; Arevalo, Shaun; Miller, Steve; Stone, Mars; Busch, Michael; Hsieh, Kristina; Messenger, Sharon; Wadford, Debra A.; Rodgers, Mary; Cloherty, Gavin; Faria, Nuno R.; Thézé, Julien; Pybus, Oliver G.; Neto, Zoraima; Morais, Joana; Taveira, Nuno; R. Hackett, John; Chiu, Charles Y. 2020 2020-01-13 None N PMC7047537 31932713.0 10.1038/s41564-019-0637-9 z4j8p55m 0.438265 Rice_1992, Djikeng_2009, Dinh_2011, Chen_2018, Armesto_2007 Lewandowska_2017, Yang_2018
175 Dumarest_2015 Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing Dumarest, Marine; Muth, Erika; Cheval, Justine; Gratigny, Marlène; Hébert, Charles; Gagnieur, Léa; Eloit, Marc 2015 2015-01-31 PMC N 25466699.0 10.1016/j.biologicals.2014.10.004 dkqi22z0 0.435934 Ryu_W_2017, Wang_2015, Rice_1992, Crowe_2014, Modrow_2013
176 Sun_Y_2019 A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes Sun, Yan; Kim, Eun Ji; Felt, Sébastien A.; Taylor, Louis J.; Agarwal, Divyansh; Grant, Gregory R.; López, Carolina B. 2019 2019-04-17 COMM-USE N PMC6504078 30995283.0 10.1371/journal.ppat.1007707 nivrrsqg 0.435529 Trobaugh_2017, Rice_1992, Volmer_2010, Berkhout_2006, Haasnoot_2010 Sun_Y_2018, Sun_D_2016, Ren_X_2008
177 Holmes_2011 The Evolution of Endogenous Viral Elements Holmes, Edward C. 2011 2011-10-20 PMC N 22018237.0 10.1016/j.chom.2011.09.002 nyb20mhi 0.435373 Wang_2018, Rice_1992, den_Boon_2010, Auewarakul_2005
178 Caprari_2015 Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses Caprari, Silvia; Metzler, Saskia; Lengauer, Thomas; Kalinina, Olga V. 2015 2015-10-19 COMM-USE N PMC4632390 26492264.0 10.3390/v7102882 jempqbk6 0.435255 Dolja_2006, Volmer_2010, Mushegian_2018, Odom_2009 Walker_2011
179 Ecker_2008 Ibis T5000: a universal biosensor approach for microbiology Ecker, David J.; Sampath, Rangarajan; Massire, Christian; Blyn, Lawrence B.; Hall, Thomas A.; Eshoo, Mark W.; Hofstadler, Steven A. 2008 2008-06-03 PMC N PMC7097577 18521073.0 10.1038/nrmicro1918 fduv4yk2 0.434987 Li_L_2014, Leiva-Torres_2017, Djikeng_2009, Wang_2018 Wolk_2012, Hoppe_2014
180 Xiao_2020 Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples Minfeng Xiao; Xiaoqing Liu; Jingkai Ji; Min Li; Jiandong Li; Lin Yang; Wanying Sun; Peidi Ren; Guifang Yang; Jincun Zhao; Tianzhu Liang; Huahui Ren; Tian Chen; Huanzi Zhong; Wenchen Song; Yanqun Wang; Ziqing Deng; Yanping Zhao; Zhihua Ou; Daxi Wang; Jielun Cai; Xinyi Cheng; Taiqing Feng; Honglong Wu; Yanping Gong; Huanming Yang; Jian Wang; Xun Xu; Shida Zhu; Fang Chen; Yanyan Zhang; Weijun Chen; Yimin Li; Junhua Li 2020 2020-03-17 BioRxiv N 10.1101/2020.03.16.993584 wbyqmvhs 0.434389 Chang_2011, Lee_C_2017, Leiva-Torres_2017, Harel_2019, Djikeng_2009 Alquezar-Planas_2013, Park_2016
181 Firth_2010 Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning Firth, Andrew E; Atkins, John F 2010 2010-01-25 COMM-USE N PMC2832772 20100346.0 10.1186/1743-422x-7-17 ojfp7yey 0.434238 Rice_1992, Lamb_1991, Ryu_W_2017, Naito_2007 Walker_2011, Wang_2019, Firth_2009, Zhang_2007
182 Scarpellini_2015 The human gut microbiota and virome: Potential therapeutic implications Scarpellini, Emidio; Ianiro, Gianluca; Attili, Fabia; Bassanelli, Chiara; De Santis, Adriano; Gasbarrini, Antonio 2015 2015-12-31 PMC N 26257129.0 10.1016/j.dld.2015.07.008 51s1u7gd 0.433548 Wang_2018, Orvedahl_2008, Fauci_2006, Berkhout_2006, Lester_2014 Ilinskaya_2017, Li_H_2019, Villena_2018, Hedblom_2018
183 Wolf_2018 Origins and Evolution of the Global RNA Virome Yuri I. Wolf; Darius Kazlauskas; Jaime Iranzo; Adriana LucÍa-Sanz; Jens H. Kuhn; Mart Krupovic; Valerian V. Dolja; Eugene V. Koonin 2018 2018-10-24 BioRxiv N 10.1101/451740 8z78shbf 0.433418 Rice_1992, Wolf_2018, Wang_2018, den_Boon_2010, Ryu_W_2017 Wolf_2018, Tzeng_2006
184 Lyon_2018 Evaluating an Upper Respiratory Disease Panel on the Portable MinION Sequencer Wanda J. Lyon; Zachary K. Smith; Brian Grier; James Baldwin; Clarise R. Starr 2018 2018-10-05 BioRxiv N 10.1101/436600 3begdfx2 0.431185 Harel_2019, Djikeng_2009, Chang_2011, Pandya_2007, Deng_2015 Xue_G_2013, Alquezar-Planas_2013, Galmès_2012
185 Law_J_2013 Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool Law, John; Jovel, Juan; Patterson, Jordan; Ford, Glenn; O’keefe, Sandra; Wang, Weiwei; Meng, Bo; Song, Deyong; Zhang, Yong; Tian, Zhijian; Wasilenko, Shawn T.; Rahbari, Mandana; Mitchell, Troy; Jordan, Tracy; Carpenter, Eric; Mason, Andrew L.; Wong, Gane Ka-Shu 2013 2013-04-17 COMM-USE N PMC3629200 23613733.0 10.1371/journal.pone.0060595 8vk89i4h 0.431139 Rice_1992, Auewarakul_2005, Chieochansin_2010, Ryu_W_2017, Armesto_2007 Xue_G_2013
186 Dacheux_2014 A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses Dacheux, Laurent; Cervantes-Gonzalez, Minerva; Guigon, Ghislaine; Thiberge, Jean-Michel; Vandenbogaert, Mathias; Maufrais, Corinne; Caro, Valérie; Bourhy, Hervé 2014 2014-01-29 None N PMC3906132 24489870.0 10.1371/journal.pone.0087194 g3rfwhwr 0.430821 Ryu_W_2017, Wang_2015, Xu_L_2018, Lu_P_2016, Wang_2018 Wu_Z_2018, Lachheb_2019, Becker_2019
187 Ackermann_1998 Tailed Bacteriophages: The Order Caudovirales Ackermann, Hans-W. 1998 1998-12-31 PMC N 9891587.0 10.1016/s0065-3527(08)60785-x v5avfe7l 0.429957 Mushegian_2018, Rice_1992, Staple_2005, Gorbalenya_1988, Li_D_2019
188 Burrell_2017 Chapter 2 Classification of Viruses and Phylogenetic Relationships Burrell, Christopher J.; Howard, Colin R.; Murphy, Frederick A. 2017 2017-12-31 PMC N PMC7149777 10.1016/b978-0-12-375156-0.00002-3 y8c60w4a 0.429672 Wang_2018, Chang_2011, Rice_1992, Zheng_2008 Ward_1993, Rodríguez_2020, Kuhn_2020, Fermin_2018
189 Medvedev_2018 Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold Medvedev, Kirill E.; Kinch, Lisa N.; Grishin, Nick V. 2018 2018-06-13 PMC N PMC6153405 29722076.0 10.1002/pro.3438 4fota9rl 0.429121 Odom_2009, Dolja_2006, Mushegian_2018, Rice_1992, Auewarakul_2005 Ao_D_2015, Zhang_2015, Sun_D_2016, Xia_H_2015
190 Lin_B_2006 Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays Lin, Baochuan; Wang, Zheng; Vora, Gary J.; Thornton, Jennifer A.; Schnur, Joel M.; Thach, Dzung C.; Blaney, Kate M.; Ligler, Adam G.; Malanoski, Anthony P.; Santiago, Jose; Walter, Elizabeth A.; Agan, Brian K.; Metzgar, David; Seto, Donald; Daum, Luke T.; Kruzelock, Russell; Rowley, Robb K.; Hanson, Eric H.; Tibbetts, Clark; Stenger, David A. 2006 2006-03-13 None N PMC1457032 16481660.0 10.1101/gr.4337206 l4b5pezm 0.428999 Djikeng_2009, Brister_2015, Chang_2011, Leiva-Torres_2017, Deng_2015 Shirato_2007
191 Xie_X_2018 Prevalence of fecal viruses and bacteriophage in Canadian farmed mink (Neovison vison) Xie, Xiao‐Ting; Kropinski, Andrew M.; Tapscott, Brian; Weese, J. Scott; Turner, Patricia V. 2018 2018-04-10 COMM-USE N PMC6341152 29635866.0 10.1002/mbo3.622 qcpcr7uv 0.428892 Chieochansin_2010, Kamau_2019, Wang_2015, Xu_L_2018, Taboada_2016 Ren_X_2008, Lachheb_2019, Woo_P_2016, Mohamed_2018
192 Vibin_2018 Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds Vibin, Jessy; Chamings, Anthony; Collier, Fiona; Klaassen, Marcel; Nelson, Tiffanie M.; Alexandersen, Soren 2018 2018-06-06 None N PMC5989203 29875375.0 10.1038/s41598-018-26851-1 l2n0xvmd 0.427853 Ryu_W_2017, Rice_1992, Wang_2015, Lu_P_2016, Auewarakul_2005 Woo_P_2016, Klem_2014, Dacheux_2014
193 Zhao_2018 Metagenomic Analysis of the Jinding Duck Fecal Virome Zhao, Lili; Niu, Yinjie; Lu, Taofeng; Yin, Haichang; Zhang, Yuanyuan; Xu, Lijing; Wang, Yiping; Chen, Hongyan 2018 2018-01-24 PMC N PMC7080049 29368024.0 10.1007/s00284-018-1430-3 r03hisns 0.427810 Ryu_W_2017, Crowe_2014, Wang_2015, Chieochansin_2010, Xu_L_2018 Kim_D_2016, Valle-Casuso_2020
194 Ho_Y_2010 Identification of Pathogens by Mass Spectrometry Ho, Yen-Peng; Reddy, P Muralidhar 2010 2010-04-01 PMC N PMC7108202 20167691.0 10.1373/clinchem.2009.138867 6j05yjjj 0.426554 May_E_2016, Weinrich_2009, Sharon_2010, Yadav_2013 Wolk_2012, Jordana-Lluch_2014, Kaleta_2011
195 Shcherbina_2016 Evaluating performance of metagenomic characterization algorithms using in silico datasets generated with FASTQSim Anna Shcherbina; Darrell O. Ricke; Nelson Chiu 2016 2016-03-31 BioRxiv N 10.1101/046532 csokkcqq 0.425596 Cheng_2013, Montgomery_2004, Lee_C_2017, Yu_H_2007, O'Leary_2016 Baldwin_2014, Twin_2013, Takhampunya_2019, Zinter_2018
196 Mendes_2019 DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics C I Mendes; E Lizarazo; M P Machado; D N Silva; A Tami; M Ramirez; N Couto; J W A Rossen; J A Carriço 2019 2019-05-06 BioRxiv N 10.1101/628073 46w17i8r 0.424567 Cheng_2013, Montgomery_2004, Deng_2015, Brister_2015, Chang_2011 Lachheb_2019, Takhampunya_2019, Ren_X_2008
197 Sahli_2012 Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes Sahli, Mohammed; Shibuya, Tetsuo 2012 2012-05-16 COMM-USE N PMC3441218 22591859.0 10.1186/1756-0500-5-243 nz4qpumr 0.424390 Lee_C_2017, Chang_2011, Cheng_2013, Deng_2015, Saw_A_2019 Wang_2010, Lauber_2013
198 Soueidan_2015 Finding and identifying the viral needle in the metagenomic haystack: trends and challenges Soueidan, Hayssam; Schmitt, Louise-Amélie; Candresse, Thierry; Nikolski, Macha 2015 2015-01-07 COMM-USE N PMC4285800 25610431.0 10.3389/fmicb.2014.00739 bkreu1s2 0.424160 Wang_2018, UNKNOWN_2004, Conzelmann_1996, Li_L_2014 Dacheux_2014, Selvin_2019, Becker_2019
199 Zinter_2018 Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children MS Zinter; CC Dvorak; MY Mayday; K Iwanaga; NP Ly; ME McGarry; GD Church; LE Faricy; CM Rowan; JR Hume; ME Steiner; ED Crawford; C Langelier; K Kalantar; ED Chow; S Miller; K Shimano; A Melton; GA Yanik; A Sapru; JL DeRisi 2018 2018-03-29 BioRxiv N 10.1101/291864 28nlawnb 0.423564 Brucker_2020, Gardner_2004, Wang_2018, Smits_2014, Li_L_2014 Zinter_2018, Galmès_2012, Malmo_2016, Hörster_2019
200 Mihalov-Kovács_2015 Candidate New Rotavirus Species in Sheltered Dogs, Hungary Mihalov-Kovács, Eszter; Gellért, Ákos; Marton, Szilvia; Farkas, Szilvia L.; Fehér, Enikő; Oldal, Miklós; Jakab, Ferenc; Martella, Vito; Bányai, Krisztián 2015 2015-04-23 None N PMC4378476 25811414.0 10.3201/eid2104.141370 5w7cubqo 0.422459 Lu_P_2016, Kamau_2019, Ryu_W_2017, Puranaveja_2009 Bányai_2017
201 Dinwiddie_2018 Complete Genome Sequences of Four Novel Human Coronavirus OC43 Isolates Associated with Severe Acute Respiratory Infection Dinwiddie, Darrell L.; Hardin, Olga; Denson, Jesse L.; Kincaid, John C.; Schwalm, Kurt C.; Stoner, Ashley N.; Abramo, Thomas J.; Thompson, Tonya M.; Putt, Claire M.; Young, Stephen A.; Dehority, Walter N.; Kennedy, Joshua L. 2018 2018-05-24 COMM-USE N PMC5968726 29798929.0 10.1128/genomea.00452-18 srk7xeb8 0.422459 Kamau_2019, Lim_T_2012, Kin_N_2017, Zhang_2020 Sipulwa_2016, Ren_X_2008, Huang_2020, Ehmann_2018
202 Wohl_2016 GENOMIC ANALYSIS OF VIRAL OUTBREAKS Wohl, Shirlee; Schaffner, Stephen F.; Sabeti, Pardis C. 2016 2016-09-29 None N PMC5210220 27501264.0 10.1146/annurev-virology-110615-035747 m2iiswan 0.421063 Johnson_2018, UNKNOWN_2004, Djikeng_2009, Castrignano_2015 Haagmans_2009, Robinson_2013, Mehrbod_2014
203 Xu_X_2020 Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data Xiaofeng Xu; Jinlong Bei; Yibo Xuan; Jianyuan Chen; Defu Chen; Stephen C. Barker; Samuel Kelava; Bingjun He; Shan Gao; Ze Chen 2020 2020-03-25 BioRxiv N 10.1101/2020.03.24.004796 tyun4zlh 0.420616 Ryu_W_2017, Chieochansin_2010, Armesto_2007, Wang_2015, Bickerton_2017 Ren_X_2008, Niu_J_2018
204 Sun_J_2010 Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach Sun, JianDong; Xu, Zhao; Hao, BaiLin 2010 2010-08-11 PMC N PMC7089326 10.1007/s11434-010-3008-8 xjmicuki 0.419638 Zheng_2008, Cheng_2013, Kinene_2016, Chang_2011 Selvin_2019, Yu_Z_2010, Li_S_2014, Zhou_2017
205 Lefkowitz_2018 Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV) Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B 2018 2018-01-04 COMM-USE N PMC5753373 29040670.0 10.1093/nar/gkx932 5q7deeby 0.419017 Murray_2017, Lipsitch_2014, MacIntyre_2020, UNKNOWN_2010 Fauquet_2008, Adams_2016, Kuhn_2012
206 Manara_2019 Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species Manara, Serena; Asnicar, Francesco; Beghini, Francesco; Bazzani, Davide; Cumbo, Fabio; Zolfo, Moreno; Nigro, Eleonora; Karcher, Nicolai; Manghi, Paolo; Metzger, Marisa Isabell; Pasolli, Edoardo; Segata, Nicola 2019 2019-12-28 COMM-USE N PMC6935492 31883524.0 10.1186/s13059-019-1923-9 ehcu68cg 0.418648 Wang_2018, Delwart_2012, Roux_2019, Han_B_2016, Gay_N_2014 Selvin_2019, Tun_H_2012, Li_H_2019
207 Li_C_2020 High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection Li, Ci-Xiu; Li, Wei; Zhou, Jun; Zhang, Bing; Feng, Yan; Xu, Chang-Ping; Lu, Yi-Yu; Holmes, Edward C.; Shi, Mang 2020 2020-03-03 COMM-USE N PMC7054269 32127629.0 10.1038/s41598-020-60992-6 aa4s7b21 0.418172 Gardner_2004, Chieochansin_2010, Rice_1992, Li_L_2014, Brucker_2020 Hörster_2019, Klein_2010, Galmès_2012
208 Schlub_2018 A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C 2018 2018-08-07 NONCOMM N PMC6188560 30099499.0 10.1093/molbev/msy155 yiqdsf9z 0.417853 Chang_2011, Francis_2016, Lee_C_2017, Lamb_1991 Wang_2010
209 Ladner_2014 Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing Ladner, Jason T.; Beitzel, Brett; Chain, Patrick S. G.; Davenport, Matthew G.; Donaldson, Eric; Frieman, Matthew; Kugelman, Jeffrey; Kuhn, Jens H.; O’Rear, Jules; Sabeti, Pardis C.; Wentworth, David E.; Wiley, Michael R.; Yu, Guo-Yun; Sozhamannan, Shanmuga; Bradburne, Christopher; Palacios, Gustavo 2014 2014-06-17 NONCOMM N PMC4068259 24939889.0 10.1128/mbio.01360-14 kqcx7lrq 0.417404 Brister_2015, Chang_2011, Deng_2015, Cheng_2013 Wang_2010, Harel_2019, Djikeng_2009, Yang_2018
210 Chiu_2013 Viral pathogen discovery Chiu, Charles Y 2013 2013-05-29 None N PMC5964995 23725672.0 10.1016/j.mib.2013.05.001 qv5r8a0l 0.415457 Djikeng_2009, Gupta_2009, Brucker_2020, Sharon_2010, Li_L_2014 Li_C_2020, Schäfer_2014, Haagmans_2009, Anderson_2020
211 Li_Y_2016 VIP: an integrated pipeline for metagenomics of virus identification and discovery Li, Yang; Wang, Hao; Nie, Kai; Zhang, Chen; Zhang, Yi; Wang, Ji; Niu, Peihua; Ma, Xuejun 2016 2016-03-30 None N PMC4824449 27026381.0 10.1038/srep23774 vn6x3fb0 0.413117 Deng_2015, Cheng_2013, Brister_2015, Smith_2013, Montgomery_2004 Dacheux_2014, Alquezar-Planas_2013, Shifman_2019, Shabman_2016
212 Berthet_2010 Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays Berthet, Nicolas; Deletoile, Alexis; Passet, Virginie; Kennedy, Giulia C.; Manuguerra, Jean-Claude; Cole, Stewart T.; Brisse, Sylvain 2010 2010-12-20 COMM-USE N PMC3004854 21187950.0 10.1371/journal.pone.0015243 u7gj6e10 0.412800 Chang_2011, Deng_2015, Lee_C_2017, Phillippy_2009, Dai_Q_2012 Ren_X_2008, Wu_Z_2011, Lima_2015
213 Dudas_2019 The ability of single genes vs full genomes to resolve time and space in outbreak analysis Dudas, Gytis; Bedford, Trevor 2019 2019-12-26 COMM-USE N PMC6933756 31878875.0 10.1186/s12862-019-1567-0 aupjlpfm 0.410841 Chang_2011, Brister_2015, Harel_2019, Deng_2015, Cheng_2013 Wang_2010, Schobel_2016
214 Linsuwanon_2015 The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses Linsuwanon, Piyada; Poovorawan, Yong; Li, Linlin; Deng, Xutao; Vongpunsawad, Sompong; Delwart, Eric 2015 2015-08-19 COMM-USE N PMC4545796 26288145.0 10.1371/journal.pone.0135573 84hxim2n 0.410272 Crowe_2014, Ryu_W_2017, Davaro_2013, Lu_P_2016, Macy_2020 Park_2007, Lau_S_2007, Gamiño‐Arroyo_2016, Duijvestijn_2016
215 Sun_Y_2018 A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes Yan Sun; Eun Ji Kim; Sébastien A. Felt; Louis J. Taylor; Divyansh Agarwal; Gregory R. Grant; Carolina B. López 2018 2018-06-15 BioRxiv N 10.1101/349001 zj8gf45p 0.409774 Trobaugh_2017, Rice_1992, Volmer_2010, Haasnoot_2010, Naito_2007 Sun_Y_2019, Sun_D_2016, Ren_X_2008
216 Xie_G_2013 New strategy for virus discovery: viruses identified in human feces in the last decade Xie, GuangCheng; Yu, JieMei; Duan, ZhaoJun 2013 2013-08-07 COMM-USE N PMC7089042 23917840.0 10.1007/s11427-013-4516-y 9i9dlx2y 0.408699 Walker_2010, Lu_P_2016, Wiwanitkit_2014, Brucker_2020, Conzelmann_1996 Barrette_2011, Shi_W_2017, Lachheb_2019, Davidson_2019
217 O’Carroll_2016 Viral Nucleic Acids O’Carroll, I.P.; Rein, A. 2016 2016-12-31 PMC N 10.1016/b978-0-12-394447-4.10061-6 fyxn0g3v 0.407668 Rice_1992, den_Boon_2010, Stork_2011, Payne_2017
218 Cann_2012 Chapter 3 Genomes Cann, Alan J. 2012 2012-12-31 PMC N PMC7149632 10.1016/b978-0-12-384939-7.10003-1 aioomgjk 0.407016 Rice_1992, Wang_2018, den_Boon_2010, Auewarakul_2005 Wulan_2015, Yun_S_2015
219 Li_K_2010 ANDES: Statistical tools for the ANalyses of DEep Sequencing Li, Kelvin; Venter, Eli; Yooseph, Shibu; Stockwell, Timothy B; Eckerle, Lance D; Denison, Mark R; Spiro, David J; Methé, Barbara A 2010 2010-07-15 COMM-USE N PMC2921379 20633290.0 10.1186/1756-0500-3-199 2n5vetzw 0.406881 Chang_2011, Cheng_2013, Saw_A_2019, Saw_A_2019, Dai_Q_2012 Harel_2019, Twin_2013, Lewandowska_2017, Baldwin_2014
220 Routh_2012 Nucleotide-Resolution Profiling of RNA Recombination in the Encapsidated Genome of a Eukaryotic RNA Virus by Next-Generation Sequencing Routh, Andrew; Ordoukhanian, Phillip; Johnson, John E. 2012 2012-12-14 None N PMC3502730 23069247.0 10.1016/j.jmb.2012.10.005 ks3nryfh 0.405877 Rice_1992, Wang_2018, Trobaugh_2017, Auewarakul_2005 YU_W_1995, Masante_2015
221 Irina_2020 Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa Irina, Kurina; Anna, Popenko; Natalia, Klimenko; Stanislav, Koshechkin; Liubov, Chuprikova; Maxim, Filipenko; Alexander, Tyakht; Dmitry, Alexeev 2020 2020-04-15 PMC N 10.1016/j.mcp.2020.101570 gbrx801u 0.405384 Urisman_2005, Djikeng_2009, Cheng_2013, Yadav_2013 Selvin_2019, Baldwin_2014, Twin_2013, Li_H_2019
222 Schürch_2014 Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units Schürch, Anita C.; Schipper, Debby; Bijl, Maarten A.; Dau, Jim; Beckmen, Kimberlee B.; Schapendonk, Claudia M. E.; Raj, V. Stalin; Osterhaus, Albert D. M. E.; Haagmans, Bart L.; Tryland, Morten; Smits, Saskia L. 2014 2014-08-20 COMM-USE N PMC4139337 25140520.0 10.1371/journal.pone.0105227 4if0m4if 0.404796 Brucker_2020, Lu_P_2016, Karlsson_2012, Webster_2006, Wang_2015 Wu_Z_2018, Dacheux_2014, Lee_D_2019, Takhampunya_2019
223 Calusinska_2016 Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity Calusinska, Magdalena; Marynowska, Martyna; Goux, Xavier; Lentzen, Esther; Delfosse, Philippe 2016 2016-01-18 NONCOMM N PMC7163765 26568175.0 10.1111/1462-2920.13127 au5aqr02 0.402154 Auewarakul_2005, Francis_2016, Rice_1992, Bahir_2009, Koonin_2015
224 Tithi_2017 Fast Virome Explorer: A Pipeline for Virus and Phage Identification and Abundance Profiling in Metagenomics Data Saima Sultana Tithi; Roderick V. Jensen; Liqing Zhang 2017 2017-10-02 BioRxiv N 10.1101/196998 uw76y16g 0.400742 Tithi_2018, Djikeng_2009, Brister_2015, Lee_C_2017 Tithi_2018, Li_C_2020, Anderson_2020, Dacheux_2014
225 Barzon_2011 Applications of Next-Generation Sequencing Technologies to Diagnostic Virology Barzon, Luisa; Lavezzo, Enrico; Militello, Valentina; Toppo, Stefano; Palù, Giorgio 2011 2011-11-14 COMM-USE N PMC3233444 22174638.0 10.3390/ijms12117861 01nuj0lk 0.400611 Djikeng_2009, Dugan_2012, Rice_1992, Conzelmann_1996 Yang_2018, Boland_2017, Baric_2005
226 Fischer_2008 Diagnostic Techniques: Microarrays Fischer, K.; Urisman, A.; DeRisi, J. 2008 2008-12-31 PMC N PMC7149722 10.1016/b978-012374410-4.00704-4 lgzjnivt 0.400399 Djikeng_2009, Leiva-Torres_2017, Conzelmann_1996, Castrignano_2015, Sharon_2010 Giles_2015, Wang_2003
227 Han_L_2015 Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses Han, Lu; He, Haochen; Li, Fei; Cui, Xiuliang; Xie, Dafei; Liu, Yang; Zheng, Xiaofei; Bai, Hui; Wang, Shengqi; Bo, Xiaochen 2015 2015-10-28 COMM-USE N PMC4623713 26508266.0 10.1038/srep15820 jgwvjkbj 0.400358 Chasman_2016, Gamermann_2014, Leiva-Torres_2017, Chang_2011, Gupta_2009 McDermott_2016, Chasman_2016, Wilson_2005, Chang_2011
228 Mokili_2012 Metagenomics and future perspectives in virus discovery Mokili, John L; Rohwer, Forest; Dutilh, Bas E 2012 2012-02-29 PMC N PMC7102772 22440968.0 10.1016/j.coviro.2011.12.004 x7jpsnxg 0.399168 Wang_2018, Li_L_2014, Castrignano_2015, Fauci_2006, Grewelle_2020 Mittelholzer_1997, Lachheb_2019, Dacheux_2014
229 Pontius_2007 Initial sequence and comparative analysis of the cat genome Pontius, Joan U.; Mullikin, James C.; Smith, Douglas R.; Lindblad-Toh, Kerstin; Gnerre, Sante; Clamp, Michele; Chang, Jean; Stephens, Robert; Neelam, Beena; Volfovsky, Natalia; Schäffer, Alejandro A.; Agarwala, Richa; Narfström, Kristina; Murphy, William J.; Giger, Urs; Roca, Alfred L.; Antunes, Agostinho; Menotti-Raymond, Marilyn; Yuhki, Naoya; Pecon-Slattery, Jill; Johnson, Warren E.; Bourque, Guillaume; Tesler, Glenn; O’Brien, Stephen J. 2007 2007-11-01 None N PMC2045150 17975172.0 10.1101/gr.6380007 x7e6e77d 0.398926 Li_D_2019, Cheng_2013, Whiteford_2005, Francis_2016 Goldberg_1991, Lapps_1987, Jouvenne_1992
230 Wahba_2020 Identification of a Pangolin Niche for a 2019-nCoV-like Coronavirus via an Extensive Meta-metagenomic Search Lamia Wahba; Nimit Jain; Andrew Z. Fire; Massa J. Shoura; Karen L. Artiles; Matthew J. McCoy; Dae-Eun Jeong 2020 2020-02-14 BioRxiv Y 10.1101/2020.02.08.939660 emr0eh0i 0.398842 Cheng_2013, Lee_C_2017, O'Leary_2016, Deng_2015, Brister_2015 Anderson_2020, Fahmi_2020, Niemeyer_2018
231 Kuhn_2020 Virus Taxonomy Kuhn, Jens H. 2020 2020-12-31 PMC N PMC7157452 10.1016/b978-0-12-809633-8.21231-4 0ckt6f92 0.398214 Wang_2018, Roux_2019, Munjal_2018, Conzelmann_1996 Ward_1993, Fermin_2018, Harper_2013, Rodríguez_2020
232 Camarasa_2018 Chapter Twelve Application of MALDI-TOF Mass Spectrometry in Clinical Virology Camarasa, Cristina Gómez; Cobo, Fernando 2018 2018-12-31 PMC N PMC7150354 10.1016/b978-0-12-814451-0.00012-5 izjcyd4d 0.397820 Hager_2003, Weinrich_2009, Ng_E_2013, Palacios_2010 Ng_E_2013, Wolk_2012, Jia_B_2020, Jordana-Lluch_2014
233 Herring_2007 An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes Herring, Christopher D; Palsson, Bernhard Ø 2007 2007-08-14 COMM-USE N PMC2072959 17697331.0 10.1186/1471-2164-8-274 sabz03c0 0.397341 Chang_2011, Phillippy_2009, Whiteford_2005, Francis_2016, Harel_2019 Satyanarayana_2003, Vashee_2017
234 Manso_2017 Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples Manso, Carmen F.; Bibby, David F.; Mbisa, Jean L. 2017 2017-06-23 COMM-USE N PMC5482852 28646219.0 10.1038/s41598-017-02239-5 xflhxb13 0.397236 Rice_1992, Trobaugh_2017, Wang_2018, Naito_2007, Auewarakul_2005 Valle-Casuso_2020, Li_C_2020, Case_2017
235 Lavezzo_2018 G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide Enrico Lavezzo; Michele Berselli; Ilaria Frasson; Rosalba Perrone; Giorgio Palù; Alessandra R. Brazzale; Sara N. Richter; Stefano Toppo 2018 2018-06-11 BioRxiv N 10.1101/344127 c3lmmll6 0.397236 Volmer_2010, Chang_2011, den_Boon_2010, Auewarakul_2005, Gardner_2004 Lavezzo_2018
236 Zinter_2018 Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children Zinter, Matt S; Dvorak, Christopher C; Mayday, Madeline Y; Iwanaga, Kensho; Ly, Ngoc P; McGarry, Meghan E; Church, Gwynne D; Faricy, Lauren E; Rowan, Courtney M; Hume, Janet R; Steiner, Marie E; Crawford, Emily D; Langelier, Charles; Kalantar, Katrina; Chow, Eric D; Miller, Steve; Shimano, Kristen; Melton, Alexis; Yanik, Gregory A; Sapru, Anil; DeRisi, Joseph L 2018 2018-09-15 PMC N PMC6784263 30239621.0 10.1093/cid/ciy802 x5yhy9w8 0.397099 Brucker_2020, Gardner_2004, Li_L_2014, Smits_2014, Francis_2016 Zinter_2018, Hörster_2019, Galmès_2012
237 Katsura_2019 Evolutionary Medicine of Retroviruses in the Human Genome Katsura, Yukako; Asai, Satoshi 2019 2019-12-31 PMC N PMC7093845 31813465.0 10.1016/j.amjms.2019.09.007 p1lpa4fu 0.396714 Rice_1992, den_Boon_2010, Wang_2018, Wang_2015
238 Takano_2018 Novel single-stranded, circular DNA virus identified in cats in Japan Takano, Tomomi; Yanai, Yoshitomo; Hiramatsu, Kanae; Doki, Tomoyoshi; Hohdatsu, Tsutomu 2018 2018-09-14 PMC N PMC7087140 30218220.0 10.1007/s00705-018-4020-6 h9smg0w9 0.395092 Chieochansin_2010, Armesto_2007, Kim_J_2018, Firth_2009, David_2013 Ren_X_2008, Lima_2015
239 Sabath_2012 Evolution of Viral Proteins Originated De Novo by Overprinting Sabath, Niv; Wagner, Andreas; Karlin, David 2012 2012-07-19 None N PMC3494269 22821011.0 10.1093/molbev/mss179 629fwmgk 0.394729 Lamb_1991, Wang_2007, Francis_2016, Auewarakul_2005 Tzeng_2006, Goldberg_1991, Shukla_2014
240 Wolf_2018 Origins and Evolution of the Global RNA Virome Wolf, Yuri I.; Kazlauskas, Darius; Iranzo, Jaime; Lucía-Sanz, Adriana; Kuhn, Jens H.; Krupovic, Mart; Dolja, Valerian V.; Koonin, Eugene V. 2018 2018-11-27 PMC N PMC6282212 30482837.0 10.1128/mbio.02329-18 p1b07b4t 0.393891 Rice_1992, den_Boon_2010, Payne_2017, Ryu_W_2017 Wolf_2018, Wulan_2015
241 Bellehumeur_2015 Propidium monoazide (PMA) and ethidium bromide monoazide (EMA) improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification Bellehumeur, Christian; Boyle, Brian; Charette, Steve J.; Harel, Josée; L’Homme, Yvan; Masson, Luke; Gagnon, Carl A. 2015 2015-09-15 None N PMC7119533 26129867.0 10.1016/j.jviromet.2015.06.014 7lrmc3qb 0.393880 Rice_1992, Auewarakul_2005, Oba_M_2018, Naito_2007, Trobaugh_2017 Ren_X_2008, Martinez_1993, Njiru_2008
242 Holtz_2014 Geographic variation in the eukaryotic virome of human diarrhea Holtz, Lori R.; Cao, Song; Zhao, Guoyan; Bauer, Irma K.; Denno, Donna M.; Klein, Eileen J.; Antonio, Martin; Stine, O. Colin; Snelling, Thomas L.; Kirkwood, Carl D.; Wang, David 2014 2014-11-30 None N PMC4254309 25262473.0 10.1016/j.virol.2014.09.012 e8ljkv2y 0.393837 Lu_P_2016, Tong_2009, Ryu_W_2017, Karlsson_2012, Wang_2014 Lachheb_2019, Park_2007, Ren_X_2008
243 Hager_2003 Recent trends in mass spectrometer development Hager, James W. 2003 2003-11-04 PMC N PMC7079868 14598011.0 10.1007/s00216-003-2287-1 o61jmpdf 0.393541 Ng_E_2013, Camarasa_2018, Majchrzykiewicz-Koehorst_2015, Thompson_2007 Ng_E_2013, Schlüter_2008, Ó’Fágáin_2016, Ó’Fágáin_2010
244 Zhang_2014 What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken Zhang, Wen; Li, Linlin; Deng, Xutao; Kapusinszky, Beatrix; Delwart, Eric 2014 2014-11-30 PMC N 25217712.0 10.1016/j.virol.2014.08.025 udo5x2nx 0.391862 Ryu_W_2017, Lu_P_2016, Wang_2015, Crowe_2014, Xu_L_2018
245 Berthet_2007 Massively parallel pathogen identification using high‐density microarrays Berthet, Nicolas; Dickinson, Philip; Filliol, Ingrid; Reinhardt, Anita K.; Batejat, Christophe; Vallaeys, Tatiana; Kong, Katherine A.; Davies, Christopher; Lee, Walter; Zhang, Shenglan; Turpaz, Yaron; Heym, Beate; Coralie, Gilberte; Dacheux, Laurent; Burguière, Ana Maria; Bourhy, Hervé; Old, Iain G.; Manuguerra, Jean‐Claude; Cole, Stewart T.; Kennedy, Giulia C. 2007 2007-11-22 None N PMC3864434 21261824.0 10.1111/j.1751-7915.2007.00012.x f9fhov0y 0.391751 Priest_2012, Leiva-Torres_2017, Chang_2011, Li_L_2014, Dorrell_2005 Giles_2015, Li_C_2020, Lee_J_2017
246 Shan_2011 Genomic Characterization and High Prevalence of Bocaviruses in Swine Shan, Tongling; Lan, Daoliang; Li, Linlin; Wang, Chunmei; Cui, Li; Zhang, Wen; Hua, Xiuguo; Zhu, Caixia; Zhao, Wei; Delwart, Eric 2011 2011-04-15 COMM-USE N PMC3078135 21525999.0 10.1371/journal.pone.0017292 u4649rtx 0.391676 Chieochansin_2010, Kamau_2019, Taboada_2016, Zhang_2020, Ryu_W_2017 Ren_X_2008, Choi_2015, Niu_J_2018, Zaher_2020
247 Cheung_2013 A divergent clade of circular single-stranded DNA viruses from pig feces Cheung, Andrew K.; Ng, Terry F.; Lager, Kelly M.; Bayles, Darrell O.; Alt, David P.; Delwart, Eric L.; Pogranichniy, Roman M.; Kehrli, Marcus E. 2013 2013-04-24 PMC N PMC4175981 23612924.0 10.1007/s00705-013-1701-z tu6g977q 0.391394 Rice_1992, den_Boon_2010, Payne_2017, Ryu_W_2017, Auewarakul_2005 Ren_X_2008, Lima_2015
248 Bhuvaneshwar_2018 viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors Bhuvaneshwar, Krithika; Song, Lei; Madhavan, Subha; Gusev, Yuriy 2018 2018-06-05 COMM-USE N PMC5996193 29922260.0 10.3389/fmicb.2018.01172 r707jl16 0.389832 Chang_2011, Lee_C_2017, Qi_Z_2018, Saw_A_2019, Cheng_2013 Anderson_2020, Dacheux_2014, Masante_2015
249 Pickett_2012 Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community Pickett, Brett E.; Greer, Douglas S.; Zhang, Yun; Stewart, Lucy; Zhou, Liwei; Sun, Guangyu; Gu, Zhiping; Kumar, Sanjeev; Zaremba, Sam; Larsen, Christopher N.; Jen, Wei; Klem, Edward B.; Scheuermann, Richard H. 2012 2012-11-19 COMM-USE N PMC3509690 23202522.0 10.3390/v4113209 facjsy92 0.388103 Cheng_2013, UNKNOWN_2018, O'Leary_2016, Brister_2015, Montgomery_2004 Pickett_2011, Fahmi_2020
250 Eshoo_2015 Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species Eshoo, Mark W.; Carolan, Heather E.; Massire, Christian; Chou, Danny M.; Crowder, Chris D.; Rounds, Megan A.; Phillipson, Curtis A.; Schutzer, Steven E.; Ecker, David J. 2015 2015-09-16 COMM-USE N PMC4574436 26375033.0 10.1371/journal.pone.0135828 a1t74jsm 0.388103 Kosoy_2010, Leemans_1999, Nicholson_2014, Liu_S_2013 Sazmand_2019, Pickering_2015, Ghazisaeedi_2017, Giner_2020
251 Kwok_2020 Virus Metagenomics in Farm Animals: A Systematic Review Kwok, Kirsty T. T.; Nieuwenhuijse, David F.; Phan, My V. T.; Koopmans, Marion P. G. 2020 2020-01-16 None N PMC7019290 31963174.0 10.3390/v12010107 47e37xl0 0.387993 Brucker_2020, Lu_P_2016, Tong_2009, Wang_2015, Webster_2006 Wu_Z_2018, Dacheux_2014, Takhampunya_2019, Kim_D_2016
252 Sällman_Almén_2012 The Dispanins: A Novel Gene Family of Ancient Origin That Contains 14 Human Members Sällman Almén, Markus; Bringeland, Nathalie; Fredriksson, Robert; Schiöth, Helgi B. 2012 2012-02-20 COMM-USE N PMC3282796 22363774.0 10.1371/journal.pone.0031961 dcid9emx 0.387847 Dolja_2006, Mushegian_2018, Odom_2009, Aouacheria_2013 Walker_2011, Kammerer_2010, Niemeyer_2018, Carmo_2014
253 Huang_2013 An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens Huang, Weiwei; Yang, Yinhui; Zhang, Xinlei; Zhao, Changan; Yin, Aihua; Zhang, Xiaozhuang; He, Zhengxin; Jiang, Yongqiang; Zhang, Liang 2013 2013-09-20 COMM-USE N PMC3848773 24053492.0 10.1186/1471-2334-13-437 cxqzac4a 0.387683 Li_L_2014, Djikeng_2009, Gupta_2009, Leiva-Torres_2017, Cheng_2013 Giles_2015, Wang_2017, Lee_J_2017, Anis_2018
254 Endoh_2005 Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription Endoh, Daiji; Mizutani, Tetsuya; Kirisawa, Rikio; Maki, Yoshiyuki; Saito, Hidetoshi; Kon, Yasuhiro; Morikawa, Shigeru; Hayashi, Masanobu 2005 2005-04-07 PMC N PMC1074749 15817564.0 10.1093/nar/gni064 402ls2aq 0.387007 Rice_1992, Banerjee_2001, An_S_1998, Stork_2011 Nowak_1984
255 Cleemput_2020 Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes Cleemput, Sara; Dumon, Wim; Fonseca, Vagner; Karim, Wasim Abdool; Giovanetti, Marta; Alcantara, Luiz Carlos; Deforche, Koen; de Oliveira, Tulio 2020 2020-02-28 None Y PMC7112083 32108862.0 10.1093/bioinformatics/btaa145 st5idleq 0.386983 Cheng_2013, Brister_2015, Lee_C_2017, Ryu_W_2017, UNKNOWN_2010 Cleemput_2020, Phan_2018, Ren_X_2008
256 Kang_2017 Prophage genomics reveals patterns in phage genome organization and replication Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards 2017 2017-03-07 BioRxiv N 10.1101/114819 0abutzb3 0.386750 Rice_1992, Auewarakul_2005, Lamb_1991, Payne_2017 Chen_2020, Satyanarayana_2003, Tzeng_2006
257 Lewandowska_2015 Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains Lewandowska, Dagmara W.; Zagordi, Osvaldo; Zbinden, Andrea; Schuurmans, Macé M.; Schreiber, Peter; Geissberger, Fabienne-Desirée; Huder, Jon B.; Böni, Jürg; Benden, Christian; Mueller, Nicolas J.; Trkola, Alexandra; Huber, Michael 2015 2015-10-31 PMC N 26231254.0 10.1016/j.diagmicrobio.2015.06.017 rrq4f5ki 0.386156 Dinh_2011, Rice_1992, Djikeng_2009, Armesto_2007
258 Wang_2015 Whole-Genome Sequencing of Porcine Epidemic Diarrhea Virus by Illumina MiSeq Platform Wang, Leyi; Stuber, Tod; Camp, Patrick; Robbe-Austerman, Suelee; Zhang, Yan 2015 2015-09-10 PMC N PMC7120957 10.1007/978-1-4939-3414-0_18 f8a6fjaj 0.386156 Lu_P_2016, Ryu_W_2017, Wang_2013, Rice_1992, Armesto_2007 Ren_X_2008, Lachheb_2019, Li_Z_2013
259 Bartoszewicz_2020 Interpretable detection of novel human viruses from genome sequencing data Jakub M Bartoszewicz; Anja Seidel; Bernhard Y Renard 2020 2020-01-30 BioRxiv Y 10.1101/2020.01.29.925354 ac00tai9 0.385174 Chang_2011, Lee_C_2017, Denison_2008, Deng_2015, Gamermann_2014 Lopez-Rincon_2020, Lachheb_2019, Shi_W_2017
260 van_Boheemen_2020 Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients van Boheemen, Sander; van Rijn, Anneloes L.; Pappas, Nikos; Carbo, Ellen C.; Vorderman, Ruben H.P.; Sidorov, Igor; van `t Hof, Peter J.; Mei, Hailiang; Claas, Eric C.J.; Kroes, Aloys C.M.; de Vries, Jutte J.C. 2020 2020-02-29 PMC N PMC7106021 31837435.0 10.1016/j.jmoldx.2019.10.007 dw1sfzqx 0.384456 Dinh_2011, Oba_M_2018, Chen_2018, Pandya_2007, Rice_1992
261 Leclercq_2010 Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm Leclercq, India; Berthet, Nicolas; Batéjat, Christophe; Rousseaux, Claudine; Dickinson, Philip; Old, Iain G; Kong, Katherine; Kennedy, Giulia C; Cole, Stewart T; Manuguerra, Jean-Claude 2010 2010-10-20 COMM-USE N PMC3091733 20961419.0 10.1186/1471-2164-11-586 t3etupgh 0.383910 Rice_1992, Naito_2007, Chang_2011, Gardner_2004, Armesto_2007 Ren_X_2008
262 Domingo-Calap_2018 An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides Domingo-Calap, Pilar; Schubert, Benjamin; Joly, Mélanie; Solis, Morgane; Untrau, Meiggie; Carapito, Raphael; Georgel, Philippe; Caillard, Sophie; Fafi-Kremer, Samira; Paul, Nicodème; Kohlbacher, Oliver; González-Candelas, Fernando; Bahram, Seiamak 2018 2018-10-18 COMM-USE N PMC6207329 30335851.0 10.1371/journal.ppat.1007368 81znlofa 0.382850 Rice_1992, den_Boon_2010, Trobaugh_2017, Auewarakul_2005, Tallmadge_2008 Ngandu_2009, Luo_C_2011
263 Zhu_X_2006 ProCAT: a data analysis approach for protein microarrays Zhu, Xiaowei; Gerstein, Mark; Snyder, Michael 2006 2006-11-16 COMM-USE N PMC1794587 17109749.0 10.1186/gb-2006-7-11-r110 ps3mnpzq 0.382740 Mendizabal-Ruiz_2018, Sen_D_2018, Liou_2013, Chang_2011 Stoevesandt_2014, Reymond_Sutandy_2013, Wingren_2008, Hu_S_2010
264 Cann_2016 Chapter 3 Genomes Cann, Alan J. 2016 2016-12-31 PMC N PMC7150238 10.1016/b978-0-12-801946-7.00003-1 47q0yaxr 0.381756 Wang_2018, Rice_1992, den_Boon_2010, Auewarakul_2005 Wulan_2015, Cann_2012
265 Priest_2012 From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence? Priest, Nicholas K.; Rudkin, Justine K.; Feil, Edward J.; van den Elsen, Jean M. H.; Cheung, Ambrose; Peacock, Sharon J.; Laabei, Maisem; Lucks, David A.; Recker, Mario; Massey, Ruth C. 2012 2012-10-16 PMC N PMC7097209 23070558.0 10.1038/nrmicro2880 l40dlb5d 0.381012 Chang_2011, Brister_2015, Francis_2016, Leiva-Torres_2017 Wu_Z_2011, McGuire_2012
266 Eden_2020 An emergent clade of SARS-CoV-2 linked to returned travellers from Iran Eden, John-Sebastian; Rockett, Rebecca; Carter, Ian; Rahman, Hossinur; de Ligt, Joep; Hadfield, James; Storey, Matthew; Ren, Xiaoyun; Tulloch, Rachel; Basile, Kerri; Wells, Jessica; Byun, Roy; Gilroy, Nicky; O’Sullivan, Matthew V; Sintchenko, Vitali; Chen, Sharon C; Maddocks, Susan; Sorrell, Tania C; Holmes, Edward C; Dwyer, Dominic E; Kok, Jen 2020 2020-04-10 NONCOMM Y PMC7147362 32296544.0 10.1093/ve/veaa027 yac7kzaf 0.380182 Lim_T_2012, Eden_2020, Wang_2014, Kim_D_2016
267 Rosario_2015 Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins Rosario, Karyna; Schenck, Ryan O.; Harbeitner, Rachel C.; Lawler, Stephanie N.; Breitbart, Mya 2015 2015-07-10 COMM-USE N PMC4498126 26217327.0 10.3389/fmicb.2015.00696 9o3ivbc2 0.379170 Rice_1992, Wang_2018, Mushegian_2018, Ryu_W_2017, Dolja_2006 Cook_2013, Lima_2015, Nowak_1984
268 Cortey_2019 High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea Cortey, Martí; Díaz, Ivan; Vidal, Anna; Martín-Valls, Gerard; Franzo, Giovanni; Gómez de Nova, Pedro José; Darwich, Laila; Puente, Héctor; Carvajal, Ana; Martín, Marga; Mateu, Enric 2019 2019-12-05 COMM-USE N PMC6896758 31805938.0 10.1186/s12917-019-2204-2 aaxvlktp 0.377675 Lu_P_2016, Kamau_2019, Ryu_W_2017, Crowe_2014, Puranaveja_2009 Lachheb_2019, Vidal_2019, Klem_2014, Ren_X_2008
269 Qiu_Y_2017 Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods Qiu, Yuan; Chen, Ji-Ming; Wang, Tong; Hou, Guang-Yu; Zhuang, Qing-Ye; Wu, Run; Wang, Kai-Cheng 2017 2017-06-02 PMC N PMC7111271 28501627.0 10.1016/j.virusres.2017.05.003 ecpicv5v 0.376498 Chen_2018, Endoh_2005, Thiel_2002, Falcone_1997, Chen_2016 Mikel_2015
270 Ye_Y_2010 Application of proteomics methods for pathogen discovery Ye, Yiming; Mar, Eng-Chun; Tong, Suxiang; Sammons, Scott; Fang, Sunan; Anderson, Larry J.; Wang, Dongxia 2010 2010-01-31 PMC N PMC7119679 19751767.0 10.1016/j.jviromet.2009.09.002 pfzb4is7 0.376402 Sharon_2010, Rice_1992, Djikeng_2009, Leiva-Torres_2017 Zheng_2011, Eshaghi_2005, Kong_2010, Ding_2012
271 Young_2016 Optimizing Viral Discovery in Bats Young, Cristin C. W.; Olival, Kevin J. 2016 2016-02-11 COMM-USE N PMC4750870 26867024.0 10.1371/journal.pone.0149237 xrfxfpuv 0.376318 Rice_1992, Naito_2007, Chang_2011, Trobaugh_2017 Wu_Z_2018, Dacheux_2014, Lee_D_2019, Banerjee_2018
272 Kilianski_2015 Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform Kilianski, Andy; Carcel, Patrick; Yao, Shijie; Roth, Pierce; Schulte, Josh; Donarum, Greg B.; Fochler, Ed T.; Hill, Jessica M.; Liem, Alvin T.; Wiley, Michael R.; Ladner, Jason T.; Pfeffer, Bradley P.; Elliot, Oliver; Petrosov, Alexandra; Jima, Dereje D.; Vallard, Tyghe G.; Melendrez, Melanie C.; Skowronski, Evan; Quan, Phenix-Lan; Lipkin, W. Ian; Gibbons, Henry S.; Hirschberg, David L.; Palacios, Gustavo F.; Rosenzweig, C. Nicole 2015 2015-12-29 COMM-USE N PMC4696252 26714571.0 10.1186/s12859-015-0840-5 9d6pqx19 0.375793 UNKNOWN_2018, Cheng_2013, Murray_2017, Cui_H_2015, Montgomery_2004 McGarvey_2009, Sazmand_2019, Zhang_2007, Tausch_2018
273 Moreira_2012 Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing Moreira, Rebeca; Balseiro, Pablo; Planas, Josep V.; Fuste, Berta; Beltran, Sergi; Novoa, Beatriz; Figueras, Antonio 2012 2012-04-19 COMM-USE N PMC3334963 22536348.0 10.1371/journal.pone.0035009 mkwpuav6 0.375299 Cheng_2013, Francis_2016, Deng_2015, Chang_2011, Strauss_1991 Xu_S_2020, Chathuranga_2019, Neves_2015
274 wen_s_2020 A High-Coverage SARS-CoV-2 Genome Sequence Acquired by Target Capture Sequencing shaoqing wen; Xiao Zhang 2020 2020-04-15 BioRxiv Y 10.1101/2020.04.11.20061507 yb6if23t 0.373508 Chang_2011, Cheng_2013, Brister_2015, Qi_Z_2018, Lee_C_2017 Kames_2020, Niemeyer_2018, OKBA_2020, Xie_X_2020
275 Zhang_2019 Rapid identification of human‐infecting viruses Zhang, Zheng; Cai, Zena; Tan, Zhiying; Lu, Congyu; Jiang, Taijiao; Zhang, Gaihua; Peng, Yousong 2019 2019-08-12 PMC N PMC7168554 31373773.0 10.1111/tbed.13314 mpp3ctem 0.373040 Chang_2011, Lee_C_2017, Brister_2015, Deng_2015, Smits_2014
276 Wang_2013 De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing Wang, Ren; Xu, Sheng; Jiang, Yumei; Jiang, Jingwei; Li, Xiaodan; Liang, Lijian; He, Jia; Peng, Feng; Xia, Bing 2013 2013-04-09 COMM-USE N PMC3621892 23593220.0 10.1371/journal.pone.0060449 cg463fbn 0.372794 Cheng_2013, Yu_H_2007, Deng_2015, O'Leary_2016, Whiteford_2005 Zhang_2016, Thibivilliers_2009, Zhu_L_2008
277 Yinda_2016 A single bat species in Cameroon harbors multiple highly divergent papillomaviruses in stool identified by metagenomics analysis Yinda, Claude Kwe; Rector, Annabel; Zeller, Mark; Conceição-Neto, Nádia; Heylen, Elisabeth; Maes, Piet; Ghogomu, Stephen Mbigha; Van Ranst, Marc; Matthijnssens, Jelle 2016 2016-12-31 PMC N PMC7103942 10.1016/j.virep.2016.08.001 g0n18gee 0.371348 Xu_L_2018, Zheng_2008, Chieochansin_2010, Kosoy_2010, Liu_S_2013 Maganga_2014, Lee_D_2019, Canuti_2011, Ghazisaeedi_2017
278 Rawlings_2019 Origins of peptidases Rawlings, Neil D.; Bateman, Alex 2019 2019-11-30 PMC N PMC7117030 31377195.0 10.1016/j.biochi.2019.07.026 xdzbwa6z 0.370986 Dolja_2006, Mushegian_2018, Li_D_2019, Koonin_2015 Michalska_2018, Walker_2011, Narra_2008
279 Zhang_2018 The diversity, evolution and origins of vertebrate RNA viruses Zhang, Yong-Zhen; Wu, Wei-Chen; Shi, Mang; Holmes, Edward C 2018 2018-08-31 PMC N PMC7102767 30114593.0 10.1016/j.coviro.2018.07.017 ndt8f812 0.370986 Wang_2018, Wang_2015, Schountz_2013, Rice_1992 Walker_2011, Koonin_2013
280 de_Vries_2011 A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples de Vries, Michel; Deijs, Martin; Canuti, Marta; van Schaik, Barbera D. C.; Faria, Nuno R.; van de Garde, Martijn D. B.; Jachimowski, Loes C. M.; Jebbink, Maarten F.; Jakobs, Marja; Luyf, Angela C. M.; Coenjaerts, Frank E. J.; Claas, Eric C. J.; Molenkamp, Richard; Koekkoek, Sylvie M.; Lammens, Christine; Leus, Frank; Goossens, Herman; Ieven, Margareta; Baas, Frank; van der Hoek, Lia 2011 2011-01-24 COMM-USE N PMC3025933 21283679.0 10.1371/journal.pone.0016118 mduxxe5y 0.370204 Rice_1992, Majerciak_2018, Auewarakul_2005, Stork_2011, Endoh_2005 Shirato_2007, Gueudin_2003
281 Medina-Chávez_2019 Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes Nahui Olin Medina-Chávez; Mariette Viladomat-Jasso; Gabriela Olmedo-Álvarez; Luis E Eguiarte; Valeria Souza; Susana De la Torre-Zavala 2019 2019-09-12 BioRxiv N 10.1101/766709 wewaf7ve 0.369744 McCoy_2003, Francis_2016, Bergner_2019, Zheng_2008, Trivellini_2016 Selvin_2019, Sivakumar_2020, Maaty_2012
282 Marcacci_2016 Genome characterization of feline morbillivirus from Italy Marcacci, Maurilia; De Luca, Eliana; Zaccaria, Guendalina; Di Tommaso, Morena; Mangone, Iolanda; Aste, Giovanni; Savini, Giovanni; Boari, Andrea; Lorusso, Alessio 2016 2016-08-31 PMC N 27155238.0 10.1016/j.jviromet.2016.05.002 dxf6qkpb 0.369295 Chieochansin_2010, Kin_N_2017, Armesto_2007, Kim_J_2018, Keep_2015
283 Firth_2014 Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses Firth, Andrew E. 2014 2014-11-10 None N PMC4227794 25326325.0 10.1093/nar/gku981 oicbf5l1 0.368795 Rice_1992, Chang_2011, Cullen_2009, Wang_2018 Nowak_1984
284 Xu_L_2019 Recent advances in the detection of base modifications using the Nanopore sequencer Xu, Liu; Seki, Masahide 2019 2019-10-11 COMM-USE N PMC7087776 31602005.0 10.1038/s10038-019-0679-0 5k3hq2e7 0.368388 Chen_2018, Wang_2017, Price_2019, Cheng_2013 Pradeepkumar_2012, Masante_2015, Jani_2012, Huang_2015
285 Victoria_2008 Rapid Identification of Known and New RNA Viruses from Animal Tissues Victoria, Joseph G.; Kapoor, Amit; Dupuis, Kent; Schnurr, David P.; Delwart, Eric L. 2008 2008-09-26 COMM-USE N PMC2533695 18818738.0 10.1371/journal.ppat.1000163 c7v0nstn 0.367403 Rice_1992, Ryu_W_2017, Chieochansin_2010, Wang_2015, Auewarakul_2005 Ren_X_2008, Mittelholzer_1997
286 Jackman_2011 The Microbe: The Basics of Structure, Morphology, and Physiology as They Relate to Microbial Characterization and Attribution Jackman, Joany 2011 2011-11-19 PMC N PMC7123343 10.1007/978-1-60327-219-3_2 1lb4g8tt 0.367218 Gamermann_2014, Sen_D_2018, UNKNOWN_2004, Munjal_2018, Chang_2011 Sivakumar_2020, Harper_2013, Tabares_2011, Alvin_2014
287 Adams_2016 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016) Adams, Michael J.; Lefkowitz, Elliot J.; King, Andrew M. Q.; Harrach, Balázs; Harrison, Robert L.; Knowles, Nick J.; Kropinski, Andrew M.; Krupovic, Mart; Kuhn, Jens H.; Mushegian, Arcady R.; Nibert, Max; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G.; Simmonds, Peter; Varsani, Arvind; Zerbini, Francisco Murilo; Gorbalenya, Alexander E.; Davison, Andrew J. 2016 2016-07-16 PMC N PMC7086986 27424026.0 10.1007/s00705-016-2977-6 dr5s2wyu 0.367080 Murray_2017, Rodier_2007, Tárnok_2020, Lipsitch_2014 Carstens_2009, Lefkowitz_2018, Kuhn_2012
288 Ratra_2008 Functional genomics as a tool in virus research Ratra, Ruchi; Lal, Sunil K. 2008 2008-06-01 PMC N PMC3450177 23100713.0 10.1007/s12088-008-0032-3 zaimorg0 0.366896 UNKNOWN_2004, Johnson_2018, Smith_2013, Brister_2015 Yun_S_2015, Satyanarayana_2003, Usme-Ciro_2014
289 WILUSZ_2005 CHAPTER 3 The Fundamentals of Human Virology WILUSZ, JEFFREY 2005 2005-12-31 PMC N 10.1016/b978-012088483-4/50006-8 3mfighm4 0.366156 Wang_2018, Li_L_2014, Johnson_2018, UNKNOWN_2004, Conzelmann_1996
290 Fan_X_2006 Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples Fan, Xiaofeng; Xu, Yanjuan; Di Bisceglie, Adrian M. 2006 2006-08-11 PMC N PMC7092855 16793008.0 10.1016/j.bbrc.2006.06.039 whv88ggl 0.366124 Rice_1992, Majerciak_2018, Armesto_2007, Stork_2011, Keep_2015 Lazouskaya_2014, Ren_X_2008
291 de_Vries_2012 Performance of VIDISCA-454 in Feces-Suspensions and Serum de Vries, Michel; Oude Munnink, Bas B.; Deijs, Martin; Canuti, Marta; Koekkoek, Sylvie M.; Molenkamp, Richard; Bakker, Margreet; Jurriaans, Suzanne; van Schaik, Barbera D. C.; Luyf, Angela C.; Olabarriaga, Silvia D.; van Kampen, Antoine H. C.; van der Hoek, Lia 2012 2012-08-22 COMM-USE N PMC3446766 23012629.0 10.3390/v4081328 q75rus8z 0.366124 Auewarakul_2005, Gardner_2004, Chang_2011, Francis_2016, Lee_C_2017 Xue_G_2013, Di_Martino_2009
292 Wei_L_2014 Transcriptome Analysis of Houttuynia cordata Thunb. by Illumina Paired-End RNA Sequencing and SSR Marker Discovery Wei, Lin; Li, Shenghua; Liu, Shenggui; He, Anna; Wang, Dan; Wang, Jie; Tang, Yulian; Wu, Xianjin 2014 2014-01-02 COMM-USE N PMC3879290 24392108.0 10.1371/journal.pone.0084105 9z4qcoqz 0.365523 Cheng_2013, Whiteford_2005, Yu_H_2007, Deng_2015 Chen_2013, Tang_2014, Sui_J_2019, Yang_2019
293 Gorbalenya_2018 Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank Gorbalenya, Alexander E. 2018 2018-06-26 COMM-USE N PMC6132925 29942981.0 10.1007/s00705-018-3915-6 upi9ie6d 0.364761 Chang_2011, Lipsitch_2014, Zheng_2008, Polverino_2017 Fahmi_2020, Ward_1993, Kuhn_2020
294 Isakov_2015 Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum Isakov, Ofer; Bordería, Antonio V.; Golan, David; Hamenahem, Amir; Celniker, Gershon; Yoffe, Liron; Blanc, Hervé; Vignuzzi, Marco; Shomron, Noam 2015 2015-07-01 NONCOMM N PMC4481840 25701575.0 10.1093/bioinformatics/btv101 h7zxyzca 0.364725 Chang_2011, Brister_2015, Lee_C_2017, Sen_D_2018, Cheng_2013 Lachheb_2019, Gutiérrez_2013
295 Dorrell_2005 Comparative phylogenomics of pathogenic bacteria by microarray analysis Dorrell, Nick; Hinchliffe, Stewart J; Wren, Brendan W 2005 2005-10-31 PMC N PMC7108221 16125441.0 10.1016/j.mib.2005.08.012 16e51s0a 0.364386 Wang_2018, Cullen_2009, Roux_2019, Rice_1992 Selvin_2019, Chen_2020, McGuire_2012
296 Kriesel_2012 Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain Kriesel, John D.; Hobbs, Maurine R.; Jones, Brandt B.; Milash, Brett; Nagra, Rashed M.; Fischer, Kael F. 2012 2012-03-08 COMM-USE N PMC3297595 22412845.0 10.1371/journal.pone.0031886 liqhbqxl 0.363901 Chieochansin_2010, Auewarakul_2005, Rice_1992, Langelier_2017, Payne_2017 Ren_X_2008, Kriesel_2017
297 Shaukat_2014 Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA Shaukat, Shahzad; Angez, Mehar; Alam, Muhammad Masroor; Jebbink, Maarten F; Deijs, Martin; Canuti, Marta; Sharif, Salmaan; de Vries, Michel; Khurshid, Adnan; Mahmood, Tariq; van der Hoek, Lia; Zaidi, Syed Sohail Zahoor 2014 2014-08-12 COMM-USE N PMC4254409 25112200.0 10.1186/1743-422x-11-146 b9shffb3 0.363430 Lee_C_2017, Cheng_2013, Chang_2011, Harel_2019, Rice_1992 Galmès_2012, Ren_X_2008, Di_Martino_2009
298 Slootstra_1996 Structural aspects of antibody-antigen interaction revealed through small random peptide libraries Slootstra, Jerry W.; Puijk, Wouter C.; Ligtvoet, Gerard J.; Langeveld, Jan P. M.; Meloen, Rob H. 1996 1996-01-01 PMC N PMC7088776 9237197.0 10.1007/bf01721323 oabo8wgp 0.363372 Naito_2007, Phillippy_2009, Chang_2011, Goradia_1988 Gordon_1991, Ádám_1987
299 Sintchenko_2007 Pathogen profiling for disease management and surveillance Sintchenko, Vitali; Iredell, Jonathan R.; Gilbert, Gwendolyn L. 2007 2007-05-08 PMC N PMC7097369 17487146.0 10.1038/nrmicro1656 71o58gcq 0.363034 Murray_2017, Vernikos_2008, Dove_2004, Gupta_2009 Haagmans_2009, Chan_2013, Hörster_2019, Miller_2013
300 Kilianski_2016 Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses Kilianski, Andy; Roth, Pierce A.; Liem, Alvin T.; Hill, Jessica M.; Willis, Kristen L.; Rossmaier, Rebecca D.; Marinich, Andrew V.; Maughan, Michele N.; Karavis, Mark A.; Kuhn, Jens H.; Honko, Anna N.; Rosenzweig, C. Nicole 2016 2016-08-23 None N PMC4982148 27191483.0 10.3201/eid2208.160270 icud629u 0.362752 Davaro_2013, Lu_P_2016, Tallmadge_2008, Garcia–Moliner_2013 Tan_C_2019
301 Kanduc_2008 Massive peptide sharing between viral and human proteomes Kanduc, Darja; Stufano, Angela; Lucchese, Guglielmo; Kusalik, Anthony 2008 2008-10-31 PMC N PMC7115663 18582510.0 10.1016/j.peptides.2008.05.022 knhkdlq7 0.361759 Rice_1992, Auewarakul_2005, Volmer_2010, den_Boon_2010 Zhang_2015, Jouvenne_1992
302 Lysholm_2012 Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing Lysholm, Fredrik; Wetterbom, Anna; Lindau, Cecilia; Darban, Hamid; Bjerkner, Annelie; Fahlander, Kristina; Lindberg, A. Michael; Persson, Bengt; Allander, Tobias; Andersson, Björn 2012 2012-02-15 COMM-USE N PMC3280267 22355331.0 10.1371/journal.pone.0030875 4zc8ivef 0.361759 Lu_P_2016, Crowe_2014, Ryu_W_2017, Brucker_2020, van_Riel_2007 Espinosa_2017, Memish_2014
303 Dolja_2018 Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer Dolja, Valerian V.; Koonin, Eugene V. 2018 2018-01-15 PMC N 29103997.0 10.1016/j.virusres.2017.10.020 3abf6al7 0.360554 Wang_2018, Rice_1992, den_Boon_2010, Wolf_2018, Wang_2015
304 Gu_X_2018 Geospatial distribution of viromes in tropical freshwater ecosystems Gu, Xiaoqiong; Tay, Qi Xiang Martin; Te, Shu Harn; Saeidi, Nazanin; Goh, Shin Giek; Kushmaro, Ariel; Thompson, Janelle R.; Gin, Karina Yew-Hoong 2018 2018-06-15 PMC N PMC7112100 29550725.0 10.1016/j.watres.2018.03.017 355q6k6k 0.360393 Xu_L_2018, Tong_2009, de_Sales_Lima_2015, Chieochansin_2010 Mendenhall_2019, Becker_2019
305 Sampath_2005 Rapid Identification of Emerging Pathogens: Coronavirus Sampath, Rangarajan; Hofstadler, Steven A.; Blyn, Lawrence B.; Eshoo, Mark W.; Hall, Thomas A.; Massire, Christian; Levene, Harold M.; Hannis, James C.; Harrell, Patina M.; Neuman, Benjamin; Buchmeier, Michael J.; Jiang, Yun; Ranken, Raymond; Drader, Jared J.; Samant, Vivek; Griffey, Richard H.; McNeil, John A.; Crooke, Stanley T.; Ecker, David J. 2005 2005-03-23 PMC N PMC3298233 15757550.0 10.3201/eid1103.040629 ll6lkhyd 0.359700 Rice_1992, Armesto_2007, Kamau_2019, Dinh_2011, Falcone_1997 OKBA_2020, Keyaerts_2006, Wolk_2012
306 Finkel_2018 Viral Short ORFs and Their Possible Functions Finkel, Yaara; Stern‐Ginossar, Noam; Schwartz, Michal 2018 2018-01-19 PMC N PMC7167739 29150926.0 10.1002/pmic.201700255 l9gb6znr 0.359153 Lamb_1991, Schlub_2018, Trobaugh_2017, Cullen_2009, Francis_2016
307 Bukhari_2018 Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus Bukhari, Khulud; Mulley, Geraldine; Gulyaeva, Anastasia A.; Zhao, Lanying; Shu, Guocheng; Jiang, Jianping; Neuman, Benjamin W. 2018 2018-11-30 PMC N PMC7112036 30199753.0 10.1016/j.virol.2018.08.010 i0hj01xv 0.358411 Wang_2018, Zheng_2008, Wolf_2018, Rice_1992, Li_D_2019 Firth_2009, Zhou_2017
308 Ducatez_2014 Identification of a Novel Coronavirus from Guinea Fowl Using Metagenomics Ducatez, Mariette F.; Guérin, Jean-Luc 2014 2014-12-18 PMC N PMC7120858 25720467.0 10.1007/978-1-4939-2438-7_2 9iailgv0 0.358310 Djikeng_2009, Li_L_2014, Siridechadilok_2013, Leiva-Torres_2017 Liais_2014, Ehmann_2018, Ren_X_2008, Di_Martino_2009
309 Erlandsson_2011 The Microbial Detection Array Combined with Random Phi29-Amplification Used as a Diagnostic Tool for Virus Detection in Clinical Samples Erlandsson, Lena; Rosenstierne, Maiken W.; McLoughlin, Kevin; Jaing, Crystal; Fomsgaard, Anders 2011 2011-08-10 COMM-USE N PMC3154197 21853040.0 10.1371/journal.pone.0022631 ngn9x3lc 0.356099 Rice_1992, Dinh_2011, Naito_2007, Urisman_2005 Giles_2015, Li_J_2012, Lewandowska_2017
310 Liu_J_2005 SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis Liu, Jianjun; Lim, Siew Lan; Ruan, Yijun; Ling, Ai Ee; Ng, Lisa F. P; Drosten, Christian; Liu, Edison T; Stanton, Lawrence W; Hibberd, Martin L 2005 2005-02-22 COMM-USE N PMC549591 15736999.0 10.1371/journal.pmed.0020043 4u2re1cu 0.355827 Castrignano_2015, Li_L_2014, Grewelle_2020, Lumby_2018, Chang_2011 Lachheb_2019, Park_2016
311 Zmasek_2019 Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO) Zmasek, Christian M.; Knipe, David M.; Pellett, Philip E.; Scheuermann, Richard H. 2019 2019-03-31 PMC N 30660046.0 10.1016/j.virol.2019.01.005 mqd4ioj4 0.355597 Cheng_2013, Chang_2011, Gorbalenya_1988, Zheng_2008, Dolja_2006
312 Thompson_2007 Electrospray ionisation-cleavable tandem nucleic acid mass tag–peptide nucleic acid conjugates: synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS Thompson, Andrew; Prescott, Mark; Chelebi, Noorhan; Smith, John; Brown, Tom; Schmidt, Günter 2007 2007-01-26 NONCOMM N PMC1994780 17259215.0 10.1093/nar/gkl1123 gyzbzx53 0.355597 Liu_H_2006, Jiang_2011, Hager_2003, Lin_C_2007 Kaleta_2011, Chen_2005, Ng_E_2013
313 Odom_2009 Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer events Odom, Mary R.; Curtis Hendrickson, R.; Lefkowitz, Elliot J. 2009 2009-09-30 None N PMC2779260 19464330.0 10.1016/j.virusres.2009.05.006 r397r5zv 0.355232 Rice_1992, Volmer_2010, Mushegian_2018, Haasnoot_2010 Walker_2011, Ren_X_2008, Zhang_2015
314 Okafor_2011 Taxonomy, Physiology, and Ecology of Aquatic Microorganisms Okafor, Nduka 2011 2011-03-04 PMC N PMC7120757 10.1007/978-94-007-1460-1_4 ho8k9qji 0.355184 Wang_2018, Saitou_2013, Sivakumar_2020, Zheng_2008 Sivakumar_2020, Walker_2011
315 Renault_2012 Chapter 16 RNA Viruses in Parasitoid Wasps Renault, Sylvaine 2012 2012-12-31 PMC N PMC7150315 10.1016/b978-0-12-384858-1.00016-3 399umczz 0.355048 Rice_1992, Wang_2018, Payne_2017, Berkhout_2006 Carmo_2012, Wulan_2015
316 Wong_2004 Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays Wong, Christopher W.; Albert, Thomas J.; Vega, Vinsensius B.; Norton, Jason E.; Cutler, David J.; Richmond, Todd A.; Stanton, Lawrence W.; Liu, Edison T.; Miller, Lance D. 2004 2004-03-01 None N PMC353227 14993206.0 10.1101/gr.2141004 2d7ekiyh 0.354675 Chang_2011, Harel_2019, Naito_2007, Deng_2015, Phillippy_2009 Niemeyer_2018, OKBA_2020, Wang_2009, Das_D_2006
317 Gong_2017 A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach Gong, Yu-Nong; Yang, Shu-Li; Chen, Guang-Wu; Chen, Yu-Wen; Huang, Yhu-Chering; Ning, Hsiao-Chen; Tsao, Kuo-Chien 2017 2017-04-19 PMC N PMC7087367 28424887.0 10.1007/s00705-017-3367-4 rv9t40fz 0.354421 Kamau_2019, Zhang_2020, Crowe_2014, Ryu_W_2017, Tallmadge_2008 Alquezar-Planas_2013
318 Thorburn_2015 The use of next generation sequencing in the diagnosis and typing of respiratory infections Thorburn, Fiona; Bennett, Susan; Modha, Sejal; Murdoch, David; Gunson, Rory; Murcia, Pablo R. 2015 2015-08-23 PMC N PMC4533236 26209388.0 10.1016/j.jcv.2015.06.082 q7jp224a 0.354206 Pandya_2007, Oba_M_2018, Dinh_2011, Chen_2018, Harel_2019 Anis_2018, Souza_2019
319 van_Hemert_2018 Euclidean Distance Analysis Enables Nucleotide Skew Analysis in Viral Genomes van Hemert, Formijn; Jebbink, Maarten; van der Ark, Andries; Scholer, Frits; Berkhout, Ben 2018 2018-10-30 COMM-USE N PMC6232797 30510593.0 10.1155/2018/6490647 fl5tybzb 0.353750 Chang_2011, Zheng_2008, Lee_C_2017, Liao_2006 van_Hemert_2016, Lauber_2013
320 Wong_2020 Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019 Matthew C. Wong; Sara J. Javornik Cregeen; Nadim J. Ajami; Joseph F. Petrosino 2020 2020-02-13 BioRxiv Y 10.1101/2020.02.07.939207 dnxhtbxn 0.353658 Chieochansin_2010, Kim_J_2018, Kamau_2019, Taboada_2016, Cho_Y_2014 Fahmi_2020, Lachheb_2019, Niemeyer_2018, Coutard_2020
321 Lee_C_2017 A Pairwise Alignment Algorithm for Long Sequences of High Similarity Lee, Chien-Tai; Peng, Sheng-Lung 2017 2017-10-13 PMC N PMC7123042 10.1007/978-981-10-5508-9_27 t1e0tr4w 0.352753 Saw_A_2019, Chang_2011, Dai_Q_2012, Liu_L_2012 Saw_A_2019, Song_2005
322 Majchrzykiewicz-Koehorst_2015 Rapid and generic identification of influenza A and other respiratory viruses with mass spectrometry Majchrzykiewicz-Koehorst, Joanna A.; Heikens, Esther; Trip, Hein; Hulst, Albert G.; de Jong, Ad L.; Viveen, Marco C.; Sedee, Norbert J.A.; van der Plas, Jan; Coenjaerts, Frank E.J.; Paauw, Armand 2015 2015-03-01 PMC N PMC7113647 25500183.0 10.1016/j.jviromet.2014.11.014 x7qtxaum 0.350627 Hager_2003, Ng_E_2013, Camarasa_2018, Li_J_2012 Chen_2011, Chen_2011, Jia_B_2020, Sails_2009
323 Haynes_2010 The Human Virome Haynes, Matthew; Rohwer, Forest 2010 2010-10-11 PMC N PMC7122492 10.1007/978-1-4419-7089-3_4 2y146igt 0.350485 Wang_2018, Castrignano_2015, Li_L_2014, Guery_2014, Fauci_2006 Valle-Casuso_2020, Hopkins_2015, Barrette_2011
324 He_B_2013 Virome Profiling of Bats from Myanmar by Metagenomic Analysis of Tissue Samples Reveals More Novel Mammalian Viruses He, Biao; Li, Zuosheng; Yang, Fanli; Zheng, Junfeng; Feng, Ye; Guo, Huancheng; Li, Yingying; Wang, Yiyin; Su, Nan; Zhang, Fuqiang; Fan, Quanshui; Tu, Changchun 2013 2013-04-22 COMM-USE N PMC3632529 23630620.0 10.1371/journal.pone.0061950 04d0koah 0.349989 Xu_L_2018, Chieochansin_2010, Liu_S_2013, Wang_2015, Tong_2009 Lee_D_2019, Doysabas_2019, Wu_Z_2018
325 Cifaldi_2019 Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies Cifaldi, Cristina; Brigida, Immacolata; Barzaghi, Federica; Zoccolillo, Matteo; Ferradini, Valentina; Petricone, Davide; Cicalese, Maria Pia; Lazarevic, Dejan; Cittaro, Davide; Omrani, Maryam; Attardi, Enrico; Conti, Francesca; Scarselli, Alessia; Chiriaco, Maria; Di Cesare, Silvia; Licciardi, Francesco; Davide, Montin; Ferrua, Francesca; Canessa, Clementina; Pignata, Claudio; Giliani, Silvia; Ferrari, Simona; Fousteri, Georgia; Barera, Graziano; Merli, Pietro; Palma, Paolo; Cesaro, Simone; Gattorno, Marco; Trizzino, Antonio; Moschese, Viviana; Chini, Loredana; Villa, Anna; Azzari, Chiara; Finocchi, Andrea; Locatelli, Franco; Rossi, Paolo; Sangiuolo, Federica; Aiuti, Alessandro; Cancrini, Caterina; Di Matteo, Gigliola 2019 2019-04-11 COMM-USE N PMC6470723 31031743.0 10.3389/fimmu.2019.00316 ds9se405 0.349750 Deng_2015, Yu_H_2007, Harel_2019, Phillippy_2009, Whiteford_2005 Trotta_2018, Linenberger_1995, Alsum_2020
326 Qin_S_2018 Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China Qin, Sinan; Ruan, Wenqiang; Yue, Hua; Tang, Cheng; Zhou, Kelei; Zhang, Bin 2018 2018-09-06 COMM-USE N PMC6127300 30190594.0 10.1038/s41598-018-31554-8 i7fkaohw 0.349647 Crowe_2014, Kamau_2019, Lu_P_2016, van_Riel_2007, Ryu_W_2017 Klem_2014, Park_2007, Thimmasandra_Narayanappa_2015, Xu_Z_2018
327 Zahin_2018 Identification of G-quadruplex forming sequences in three manatee papillomaviruses Zahin, Maryam; Dean, William L.; Ghim, Shin-je; Joh, Joongho; Gray, Robert D.; Khanal, Sujita; Bossart, Gregory D.; Mignucci-Giannoni, Antonio A.; Rouchka, Eric C.; Jenson, Alfred B.; Trent, John O.; Chaires, Jonathan B.; Chariker, Julia H. 2018 2018-04-09 COMM-USE N PMC5891072 29630682.0 10.1371/journal.pone.0195625 wbs5xvbp 0.349399 Li_D_2019, Krause_1987, Bertholet_1987, Liu_Y_2009, Staple_2005 Sun_D_2016, Crawford_2019, Walker_2011, Neves_2015
328 Villarreal_2008 Evolution of Viruses Villarreal, L.P. 2008 2008-12-31 PMC N PMC7149781 10.1016/b978-012374410-4.00706-8 01a8er2v 0.348851 Wang_2018, Rice_1992, den_Boon_2010, Grewelle_2020, Holmes_2007 Rodríguez_2020, Koonin_2013
329 Bexfield_2011 Metagenomics and the molecular identification of novel viruses Bexfield, Nicholas; Kellam, Paul 2011 2011-11-30 PMC N PMC7110547 21111643.0 10.1016/j.tvjl.2010.10.014 bxu3sklz 0.348527 Johnson_2018, Djikeng_2009, Tong_2011, Gupta_2009, Sharon_2010 Haagmans_2009, Davidson_2019, Dacheux_2014, Lachheb_2019
330 Fredricks_2005 The infectious aetiology of disease: the search for new agents Fredricks, David N; Relman, David A 2005 2005-03-01 PMC N PMC7128253 10.1383/medc.33.3.37.61122 cisrvghj 0.348352 Li_L_2014, Sharon_2010, Castrignano_2015, Ferris_2016, Grewelle_2020 Ansuini_2013, Marlier_2006, Davidson_2019, Walker_2014
331 Grewelle_2020 Larger viral genome size facilitates emergence of zoonotic diseases Richard E. Grewelle 2020 2020-03-11 BioRxiv N 10.1101/2020.03.10.986109 y12cq60a 0.347893 Lu_P_2016, Rice_1992, Wang_2018, Brucker_2020 Haagmans_2009, Pulliam_2009
332 Kaleta_2011 Comparative Analysis of PCR–Electrospray Ionization/Mass Spectrometry (MS) and MALDI-TOF/MS for the Identification of Bacteria and Yeast from Positive Blood Culture Bottles Kaleta, Erin J; Clark, Andrew E; Cherkaoui, Abdessalam; Wysocki, Vicki H; Ingram, Elizabeth L; Schrenzel, Jacques; Wolk, Donna M 2011 2011-07-01 PMC N PMC7108470 21576270.0 10.1373/clinchem.2011.161968 j0ntljqm 0.347856 Saw_A_2019, Chang_2011, Urisman_2005, Feng_2010, Dai_Q_2012 Jia_B_2020, Wolk_2012
333 te_Velthuis_2014 Common and unique features of viral RNA-dependent polymerases te Velthuis, Aartjan J. W. 2014 2014-08-01 PMC N PMC4207942 25080879.0 10.1007/s00018-014-1695-z snth4ah6 0.347082 Rice_1992, den_Boon_2010, Stork_2011, Payne_2017 Gopinath_2015, Diaz_2012
334 Duraisamy_2018 Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses Duraisamy, Raja; Akiana, Jean; Davoust, Bernard; Mediannikov, Oleg; Michelle, Caroline; Robert, Catherine; Parra, Henri-Joseph; Raoult, Didier; Biagini, Philippe; Desnues, Christelle 2018 2018-02-23 PMC N PMC7088520 29476397.0 10.1007/s11262-018-1543-6 4lsz69h6 0.346988 Wang_2018, Rice_1992, Ryu_W_2017, Wang_2015, Naito_2007 Lachheb_2019, Sazmand_2019
335 Cox_E_2015 Identification of SUMO E3 Ligase-Specific Substrates Using the HuProt Human Proteome Microarray Cox, Eric; Uzoma, Ijeoma; Guzzo, Catherine; Jeong, Jun Seop; Matunis, Michael; Blackshaw, Seth; Zhu, Heng 2015 2015-01-01 PMC N PMC5882486 25820740.0 10.1007/978-1-4939-2550-6_32 g15gtag8 0.346772 Choudhury_2017, Lindner_2007, Hodul_2017, Blank_2017 Wimmer_2015, Catic_2007
336 Osunmakinde_2018 Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes Osunmakinde, Cecilia Oluseyi; Selvarajan, Ramganesh; Sibanda, Timothy; Mamba, Bhekie B; Msagati, Titus A.M 2018 2018-08-14 COMM-USE N PMC6115975 30110939.0 10.3390/v10080429 ea9mzk6e 0.346525 Johnson_2018, Djikeng_2009, Roux_2019, UNKNOWN_2004, Leiva-Torres_2017 Selvin_2019, Dacheux_2014, Takhampunya_2019, Lachheb_2019
337 Mougari_2019 First evidence of host range expansion in virophages and its potential impact on giant viruses and host cells Said Mougari; Nisrine Chelkha; Dehia Sahmi-Bounsiar; Fabrizio Di Pinto; Philippe Colson; Jonatas Abrahao; Bernard La Scola 2019 2019-09-24 BioRxiv N 10.1101/780841 itxrhjns 0.346274 den_Boon_2010, Rice_1992, Wang_2018, Berkhout_2006 Giorda_2013, Usme-Ciro_2014
338 Lecuit_2013 The human virome: new tools and concepts Lecuit, Marc; Eloit, Marc 2013 2013-10-31 PMC N 23906500.0 10.1016/j.tim.2013.07.001 enqf0gm4 0.345658 Alves_2007, Guery_2014, UNKNOWN_2004, Francis_2016
339 Eden_2020 An emergent clade of SARS-CoV-2 linked to returned travellers from Iran John-Sebastian Eden; Rebecca Rockett; Ian Carter; Hossinur Rahman; Joep de Ligt; James Hadfield; Matthew Storey; Xiaoyun Ren; Rachel Tulloch; Kerri Basile; Jessica Wells; Roy Byun; Nicky Gilroy; Matthew V O’Sullivan; Vitali Sintchenko; Sharon C Chen; Susan Maddocks; Tania C Sorrell; Edward C Holmes; Dominic E Dwyer; Jen Kok 2020 2020-03-17 BioRxiv Y 10.1101/2020.03.15.992818 izkz1hz4 0.345658 Lim_T_2012, Eden_2020, Wang_2014, Kim_D_2016 Deng_2020, Niemeyer_2018, Liu_J_2017, Zhao_2007
340 Wang_2010 VIGOR, an annotation program for small viral genomes Wang, Shiliang; Sundaram, Jaideep P; Spiro, David 2010 2010-09-07 COMM-USE N PMC2942859 20822531.0 10.1186/1471-2105-11-451 0lbxvudt 0.345241 Cheng_2013, Rice_1992, Lee_C_2017, Brister_2015, Lamb_1991 Tzeng_2006
341 Wille_2019 Virome heterogeneity and connectivity in waterfowl and shorebird communities Michelle Wille; Mang Shi; Marcel Klaassen; Aeron C. Hurt; Edward C. Holmes 2019 2019-01-29 BioRxiv N 10.1101/528174 yzjh6ot3 0.344125 Lu_P_2016, Ryu_W_2017, Crowe_2014, Wang_2015, Xu_L_2018 Wille_2019, Becker_2019
342 Ma_M_2011 Discovery of DNA Viruses in Wild-Caught Mosquitoes Using Small RNA High throughput Sequencing Ma, Maijuan; Huang, Yong; Gong, Zhengda; Zhuang, Lu; Li, Cun; Yang, Hong; Tong, Yigang; Liu, Wei; Cao, Wuchun 2011 2011-09-20 COMM-USE N PMC3176773 21949749.0 10.1371/journal.pone.0024758 53lo5nip 0.343836 Rice_1992, Payne_2017, Auewarakul_2005, Stork_2011, Trobaugh_2017 Ren_X_2008, Hu_T_2012
343 Sachsenröder_2014 The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium Sachsenröder, Jana; Twardziok, Sven O.; Scheuch, Matthias; Johne, Reimar 2014 2014-02-19 COMM-USE N PMC3929612 24586429.0 10.1371/journal.pone.0088888 yjaiybwf 0.343677 Li_W_2012, Chieochansin_2010, Liu_S_2013, Auewarakul_2005, Zhao_2017 Kim_D_2016, Ren_X_2008, Debouck_1981
344 Conceição-Neto_2017 Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs Conceição-Neto, Nádia; Theuns, Sebastiaan; Cui, Tingting; Zeller, Mark; Yinda, Claude Kwe; Christiaens, Isaura; Heylen, Elisabeth; Van Ranst, Marc; Carpentier, Sebastien; Nauwynck, Hans J.; Matthijnssens, Jelle 2017 2017-09-08 NONCOMM N PMC5591953 28924489.0 10.1093/ve/vex024 kgoczioe 0.343314 Rice_1992, Volmer_2010, Auewarakul_2005, Lu_P_2016, Chieochansin_2010 Ren_X_2008, Knutson_2017, Lachheb_2019
345 Borucki_2013 The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host Environments Borucki, Monica K.; Allen, Jonathan E.; Chen-Harris, Haiyin; Zemla, Adam; Vanier, Gilda; Mabery, Shalini; Torres, Clinton; Hullinger, Pamela; Slezak, Tom 2013 2013-01-07 COMM-USE N PMC3538757 23308119.0 10.1371/journal.pone.0052752 95zjnp77 0.342652 Auewarakul_2005, Rice_1992, Armesto_2007, Bickerton_2017, Keep_2015 Ren_X_2008
346 BIBBY_2013 Identification of Viral Pathogen Diversity in Sewage Sludge by Metagenome Analysis BIBBY, KYLE; PECCIA, JORDAN 2013 2013-02-08 PMC N PMC3963146 23346855.0 10.1021/es305181x gmpjo9uz 0.342075 Rice_1992, Wang_2018, Roux_2019, Smits_2014, Brucker_2020 Ren_X_2008, Dacheux_2014, Fernandes_2013
347 Lienard_2014 Undressing of Waddlia chondrophila to enrich its outer membrane proteins to develop a new species-specific ELISA Lienard, J; Croxatto, A; Gervaix, A; Posfay-Barbe, K; Baud, D; Kebbi-Beghdadi, C; Greub, G 2014 2014-01-16 None N PMC4184618 25356333.0 10.1002/2052-2975.26 gm41zt85 0.341272 Volmer_2010, Shin_1993, Gardner_2004, Chieochansin_2010, Wang_2013 Xue_G_2013, Galmès_2012, Di_Lullo_2019, Crawford_2019
348 Kim_W_2016 Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing Kim, Won-Keun; Kim, Jeong-Ah; Song, Dong Hyun; Lee, Daesang; Kim, Yong Chul; Lee, Sook-Young; Lee, Seung-Ho; No, Jin Sun; Kim, Ji Hye; Kho, Jeong Hoon; Gu, Se Hun; Jeong, Seong Tae; Wiley, Michael; Kim, Heung-Chul; Klein, Terry A.; Palacios, Gustavo; Song, Jin-Won 2016 2016-05-25 COMM-USE N PMC4879520 27221218.0 10.1038/srep26017 zm38v6do 0.340610 Lu_P_2016, Ryu_W_2017, Rice_1992, Wang_2018, Wang_2015 Ren_X_2008, Linster_2018, Kossyvakis_2015, Takhampunya_2019
349 Mirvish_2016 Strategies for Human Tumor Virus Discoveries: From Microscopic Observation to Digital Transcriptome Subtraction Mirvish, Ezra D.; Shuda, Masahiro 2016 2016-05-13 COMM-USE N PMC4865503 27242703.0 10.3389/fmicb.2016.00676 e8cihwn1 0.340270 Rice_1992, Djikeng_2009, Houzet_2011, Trobaugh_2017, Cheng_2013 Anderson_2020, Shabman_2016
350 Miller_2013 Metagenomics for pathogen detection in public health Miller, Ruth R; Montoya, Vincent; Gardy, Jennifer L; Patrick, David M; Tang, Patrick 2013 2013-09-20 PMC N PMC3978900 24050114.0 10.1186/gm485 p2vuztsb 0.340073 Gupta_2009, Djikeng_2009, UNKNOWN_2004, Sharon_2010, Li_L_2014 Li_C_2020, Marlowe_2006, Hörster_2019
351 Ho_C_2013 Romance of the three domains: how cladistics transformed the classification of cellular organisms Ho, Chi-Chun; Lau, Susanna K. P.; Woo, Patrick C. Y. 2013 2013-07-19 PMC N PMC4875529 23873078.0 10.1007/s13238-013-3050-9 wbrzoyvr 0.339923 Murray_2017, Munjal_2018, Zheng_2008, Kinene_2016, UNKNOWN_2004 Banks_2006, Blazejewski_2015, Tibayrenc_2015
352 Rasmussen_2013 Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA Rasmussen, Thomas Bruun; Risager, Peter Christian; Fahnøe, Ulrik; Friis, Martin Barfred; Belsham, Graham J; Höper, Dirk; Reimann, Ilona; Beer, Martin 2013 2013-11-22 COMM-USE N PMC3840674 24262008.0 10.1186/1471-2164-14-819 rxmxog3e 0.338828 Rice_1992, Armesto_2007, Bickerton_2017, Keep_2015, Keep_2014 Satyanarayana_2003, Usme-Ciro_2014, Nowak_1984
353 Kriesel_2017 Enrichment of Retroviral Sequences in Brain Tissue from Patients with Severe Demyelinating Diseases Kriesel, JD; Bhetariya, PJ; Chan, BK; Wilson, T; Fischer, KF 2017 2017-07-16 COMM-USE N PMC5707126 29202119.0 jrlkp0pf 0.338770 Auewarakul_2005, Rice_1992, Xu_J_2016, Chieochansin_2010, Brown_1984 Ren_X_2008, Morfopoulou_2016
354 Devaney_2016 A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds Devaney, Ryan; Trudgett, James; Trudgett, Alan; Meharg, Caroline; Smyth, Victoria 2016 2016-10-04 PMC N PMC7113909 27215546.0 10.1080/03079457.2016.1193123 wbkfjz8r 0.337560 Lu_P_2016, Ryu_W_2017, Wang_2015, Rice_1992, Crowe_2014 Park_2007, Nemoto_2014, Lachheb_2019, Marlier_2006
355 Denner_2017 The porcine virome and xenotransplantation Denner, Joachim 2017 2017-09-06 COMM-USE N PMC5585927 28874166.0 10.1186/s12985-017-0836-z fxa2fagg 0.337343 Lu_P_2016, Rice_1992, Karlsson_2012, Wang_2015, Wang_2018 Kim_D_2016, Hartline_2018, Ren_X_2008
356 Shang_2020 CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning Jiayu Shang; Yanni Sun 2020 2020-03-27 BioRxiv N 10.1101/2020.03.26.009001 pd0cmefo 0.337343 Chang_2011, Lee_C_2017, Cheng_2013, Sen_D_2018, Montgomery_2004 Mock_2019, Yadav_2013, Lopez-Rincon_2020, Zhang_2017
357 Wylie_2012 Emerging view of the human virome Wylie, Kristine M.; Weinstock, George M.; Storch, Gregory A. 2012 2012-10-31 PMC N PMC3701101 22683423.0 10.1016/j.trsl.2012.03.006 c1ribu7f 0.336796 Brucker_2020, Fauci_2006, Wang_2018, Li_L_2014, UNKNOWN_2004 Li_Z_2019, Case_2017, Sun_D_2016
358 Li_W_2020 Virome diversity analysis reveals novel enteroviruses and a human picobirnavirus in stool samples from African green monkeys with diarrhea Li, Wenjuan; Qiang, Xin; Qin, Si; Huang, Yong; Hu, Yan; Bai, Bingke; Hou, Jun; Gao, Rong; Zhang, Xianglilan; Mi, Zhiqiang; Fan, Hang; Ye, Huahu; Tong, Yigang; Mao, Panyong 2020 2020-08-31 PMC N 32165243.0 10.1016/j.meegid.2020.104279 5q7wdamu 0.336704 Ryu_W_2017, Rice_1992, Wang_2015, Wang_2018, Chieochansin_2010 Ren_X_2008
359 Lavezzo_2018 G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide Lavezzo, Enrico; Berselli, Michele; Frasson, Ilaria; Perrone, Rosalba; Palù, Giorgio; Brazzale, Alessandra R.; Richter, Sara N.; Toppo, Stefano 2018 2018-12-13 COMM-USE N PMC6307822 30543627.0 10.1371/journal.pcbi.1006675 csl766xl 0.336534 Chang_2011, Gardner_2004, Auewarakul_2005, Francis_2016, Volmer_2010
360 Tsoleridis_2019 Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits Tsoleridis, Theocharis; Chappell, Joseph G.; Monchatre-Leroy, Elodie; Umhang, Gérald; Shi, Mang; Bennett, Malcolm; Tarlinton, Rachael E.; McClure, C. Patrick; Holmes, Edward C.; Ball, Jonathan K. 2019 2019-12-31 COMM-USE N PMC7019641 31906044.0 10.3390/v12010047 c1qqbhl8 0.336534 Ryu_W_2017, Lu_P_2016, Wang_2015, Chieochansin_2010, Rice_1992 Cook_2013, Wu_Z_2018
361 Hu_D_2017 Virome analysis for identification of novel mammalian viruses in bats from Southeast China Hu, Dan; Zhu, Changqiang; Wang, Yi; Ai, Lele; Yang, Lu; Ye, Fuqiang; Ding, Chenxi; Chen, Jiafeng; He, Biao; Zhu, Jin; Qian, Hui; Xu, Wenrong; Feng, Youjun; Tan, Weilong; Wang, Changjun 2017 2017-09-07 COMM-USE N PMC5589946 28883450.0 10.1038/s41598-017-11384-w lc9hvhn3 0.336380 Ryu_W_2017, Wang_2015, Tong_2009, Xu_L_2018, Lu_P_2016 Ren_X_2008, Doysabas_2019
362 Smith_2013 Sherlock Genomes — viral investigator Smith, Sarah E.; Wash, Rachael S. 2013 2013-02-15 PMC N PMC7097817 23411861.0 10.1038/nrmicro2979 dkfrk71a 0.335594 Vernikos_2008, Djikeng_2009, Brister_2015, UNKNOWN_2004 Vernikos_2008
363 Nicholson_2020 Complete Genome Sequence of Bordetella bronchiseptica Strain KM22 Nicholson, Tracy L.; Bayles, Darrell O.; Shore, Sarah M. 2020 2020-01-23 PMC N PMC6979298 31974149.0 10.1128/mra.01207-19 ceorbnfz 0.334770 Nicholson_2014, Squire_2013, Parthasarathy_2006, Lu_P_2016 Nicholson_2014, Nicholson_2016
364 Ambrose_2006 Virus discovery by sequence‐independent genome amplification Ambrose, Helen E.; Clewley, Jonathan P. 2006 2006-08-23 PMC N PMC7169205 16929467.0 10.1002/rmv.515 amm0hmji 0.334051 Lee_C_2017, Brister_2015, Harel_2019, Smits_2014, Rice_1992
365 Chiu_2019 Clinical metagenomics Chiu, Charles Y.; Miller, Steven A. 2019 2019-03-27 PMC N PMC6858796 30918369.0 10.1038/s41576-019-0113-7 3fsegyme 0.334020 Gupta_2009, Alves_2007, Knapp_2008, Griffiths_2010, Zhou_2020 Li_C_2020, Baldwin_2014, Hörster_2019, Takhampunya_2019
366 Hu_Y_2005 Rapid approach to identify an unrecognized viral agent Hu, Yuan; Hirshfield, Irvin 2005 2005-07-31 PMC N PMC7112820 15893569.0 10.1016/j.jviromet.2005.02.016 7bm6ffvv 0.333940 Armesto_2007, Chen_2018, Rice_1992, Keep_2015 Lachheb_2019, Ren_X_2008
367 Mordecai_2015 Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies Mordecai, Gideon J; Wilfert, Lena; Martin, Stephen J; Jones, Ian M; Schroeder, Declan C 2015 2015-11-17 NONCOMM N PMC5029213 26574686.0 10.1038/ismej.2015.178 k2n6ropo 0.333859 Wang_2018, Grewelle_2020, Longdon_2018, Longdon_2017 Harper_2013, Tibayrenc_2015
368 Smeele_2018 Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing Smeele, Zoe E.; Ainley, David G.; Varsani, Arvind 2018 2018-01-02 PMC N PMC7114543 29111456.0 10.1016/j.virusres.2017.10.017 jq3w0pnj 0.333842 Wang_2015, Ryu_W_2017, Xu_L_2018, Tong_2009, Lu_P_2016 Canuti_2011, Olarte-Castillo_2016
369 Zuo_G_2015 CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy Zuo, Guanghong; Hao, Bailin 2015 2015-11-10 None N PMC4678791 26563468.0 10.1016/j.gpb.2015.08.004 qutbqcwb 0.333772 Zheng_2008, Chang_2011, Cheng_2013, Lee_C_2017, Xu_Z_2009 Xu_Z_2009, Yu_Z_2010
370 Ludwig_2019 ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules Marcus Ludwig; Louis-Félix Nothias; Kai Dührkop; Irina Koester; Markus Fleischauer; Martin A. Hoffmann; Daniel Petras; Fernando Vargas; Mustafa Morsy; Lihini Aluwihare; Pieter C. Dorrestein; Sebastian Böcker 2019 2019-11-16 BioRxiv N 10.1101/842740 03uonbrv 0.333772 Saw_A_2019, Sen_D_2018, Deng_2015, Chang_2011, Liou_2013 Myler_2008, Plewczynski_2007, Li_J_2006, González-Díaz_2009
371 Hashimoto_2005 Comparative analysis of selected genes from Diachasmimorpha longicaudata entomopoxvirus and other poxviruses Hashimoto, Y.; Lawrence, P.O. 2005 2005-02-28 PMC N PMC7094658 15749105.0 10.1016/j.jinsphys.2004.10.010 f5hfssk5 0.333626 Gorbalenya_1988, Rice_1992, Dolja_2006, Firth_2009, Payne_2017 Goldberg_1991, Carmo_2012, Bhat_2011
372 Gong_2016 A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity Gong, Yu-Nong; Chen, Guang-Wu; Yang, Shu-Li; Lee, Ching-Ju; Shih, Shin-Ru; Tsao, Kuo-Chien 2016 2016-03-17 COMM-USE N PMC4795770 26986479.0 10.1371/journal.pone.0151495 f59mrabl 0.333592 Chieochansin_2010, Kamau_2019, Langelier_2017, Wang_2013, Zhang_2020 Anis_2018, Sazmand_2019, Zaher_2020
373 Tse_H_2012 Identification of a Novel Bat Papillomavirus by Metagenomics Tse, Herman; Tsang, Alan K. L.; Tsoi, Hoi-Wah; Leung, Andy S. P.; Ho, Chi-Chun; Lau, Susanna K. P.; Woo, Patrick C. Y.; Yuen, Kwok-Yung 2012 2012-08-24 COMM-USE N PMC3427170 22937142.0 10.1371/journal.pone.0043986 srsfkfq1 0.331917 Chieochansin_2010, Taboada_2016, Auewarakul_2005, Firth_2009, Whiteford_2005 Lachheb_2019, Ren_X_2008, Lee_D_2019, Di_Martino_2009
374 Moreno_2020 Limited SARS-CoV-2 diversity within hosts and following passage in cell culture Gage Kahl Moreno; Katarina M Braun; Peter J Halfmann; Trent M Prall; Kasen K Riemersma; Amelia K Haj; Joseph Lalli; Kelsey R Florek; Thomas C Friedrich; Yoshihiro Kawaoka; David H O'Connor 2020 2020-04-20 BioRxiv Y 10.1101/2020.04.20.051011 izu5x2d4 0.331545 Chieochansin_2010, Francis_2016, Smits_2014, Chang_2011, Gardner_2004
375 Tirosh_2018 Expanded skin virome in DOCK8-deficient patients Tirosh, Osnat; Conlan, Sean; Deming, Clay; Lee-Lin, Shih-Queen; Huang, Xin; Su, Helen C.; Freeman, Alexandra F.; Segre, Julia A.; Kong, Heidi H. 2018 2018-11-05 PMC N PMC6286253 30397357.0 10.1038/s41591-018-0211-7 bk4rt51m 0.331400 Potgieter_1986, Lester_2014, Trobaugh_2017, Berkhout_2006, Shi_J_2012 Ansuini_2013, Drago-Serrano_2017, Jiang_2014, Malmo_2016
376 Tan_S_2019 Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools Tan, Shaoyuan; Dvorak, Cheryl M.T.; Murtaugh, Michael P. 2019 2019-12-07 COMM-USE N PMC6950593 31817886.0 10.3390/v11121132 x7wy4ooh 0.331360 Rice_1992, Armesto_2007, Mizutani_2007, Smits_2014, Bickerton_2017 Ren_X_2008, Alquezar-Planas_2013
377 Li_L_2011 From orphan virus to pathogen: the path to the clinical lab Li, Linlin; Delwart, Eric 2011 2011-10-01 PMC N PMC3190133 22003378.0 10.1016/j.coviro.2011.07.006 9v0f1v8m 0.331182 Rice_1992, Karlsson_2012, Grewelle_2020, Wang_2018, Trobaugh_2017 Valle-Casuso_2020, Galmès_2012, Davidson_2019
378 Kohl_2015 Protocol for Metagenomic Virus Detection in Clinical Specimens Kohl, Claudia; Brinkmann, Annika; Dabrowski, Piotr W.; Radonić, Aleksandar; Nitsche, Andreas; Kurth, Andreas 2015 2015-01-23 None N PMC4285256 25532973.0 10.3201/eid2101.140766 gx9oexv8 0.330188 Rice_1992, Djikeng_2009, Wang_2018, Naito_2007, Mizutani_2007 Lachheb_2019, Davidson_2019
379 de_Miranda_2017 Characterization of a Novel RNA Virus Discovered in the Autumnal Moth Epirrita autumnata in Sweden de Miranda, Joachim R.; Hedman, Harald; Onorati, Piero; Stephan, Jörg; Karlberg, Olof; Bylund, Helena; Terenius, Olle 2017 2017-08-08 COMM-USE N PMC5580471 10.3390/v9080214 1baso3q2 0.330081 Lu_P_2016, Xu_L_2018, Roberton_2006, Kosoy_2010 de_Groof_2015, Pickering_2015
380 Delwart_2012 Animal virus discovery: improving animal health, understanding zoonoses, and opportunities for vaccine development Delwart, Eric 2012 2012-06-30 None N PMC3378828 22463981.0 10.1016/j.coviro.2012.02.012 dz6ez5mw 0.329966 Wang_2018, Rice_1992, Brucker_2020, Sawyer_2012 Wu_Z_2018, Ren_X_2008, Lachheb_2019, Patel_2009
381 Coutinho_2015 Homology-Independent Metrics for Comparative Genomics Coutinho, Tarcisio José Domingos; Franco, Glória Regina; Lobo, Francisco Pereira 2015 2015-05-04 COMM-USE N PMC4446528 26029354.0 10.1016/j.csbj.2015.04.005 flznxurb 0.329257 Chang_2011, Zheng_2008, Francis_2016, Lee_C_2017 Francis_2016, Zhang_2017, Narra_2008
382 Stremlau_2015 Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa Stremlau, Matthew H.; Andersen, Kristian G.; Folarin, Onikepe A.; Grove, Jessica N.; Odia, Ikponmwonsa; Ehiane, Philomena E.; Omoniwa, Omowunmi; Omoregie, Omigie; Jiang, Pan-Pan; Yozwiak, Nathan L.; Matranga, Christian B.; Yang, Xiao; Gire, Stephen K.; Winnicki, Sarah; Tariyal, Ridhi; Schaffner, Stephen F.; Okokhere, Peter O.; Okogbenin, Sylvanus; Akpede, George O.; Asogun, Danny A.; Agbonlahor, Dennis E.; Walker, Peter J.; Tesh, Robert B.; Levin, Joshua Z.; Garry, Robert F.; Sabeti, Pardis C.; Happi, Christian T. 2015 2015-03-17 COMM-USE N PMC4363514 25781465.0 10.1371/journal.pntd.0003631 nqz3haqq 0.328039 Karlsson_2012, Weaver_2004, Lu_P_2016, Ryu_W_2017, Wang_2018 Galmès_2012, Chua_2011, Lachheb_2019
383 Francis_2016 Similar ratios of introns to intergenic sequence across animal genomes Warren R. Francis; Gert Wörheide 2016 2016-08-09 BioRxiv N 10.1101/068627 tiyjmih7 0.327991 Chang_2011, Zheng_2008, Wang_2007, Auewarakul_2005 Walker_2015, Lauber_2013
384 Rose_2016 Challenges in the analysis of viral metagenomes Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam; Robertson, David L; Prosperi, Mattia 2016 2016-08-03 NONCOMM N PMC5822887 29492275.0 10.1093/ve/vew022 x3u9i1vq 0.326979 UNKNOWN_2004, Gupta_2009, Djikeng_2009, Brister_2015 Warwick-Dugdale_2019, Smits_2014
385 Yang_2012 Genome characterization of a novel porcine bocavirus Yang, Wan-zhu; Yu, Jie-mei; Li, Jin-song; Cheng, Wei-xia; Huang, Can-ping; Duan, Zhao-jun 2012 2012-07-21 PMC N PMC7087259 22821184.0 10.1007/s00705-012-1407-7 qjq5zsfo 0.326369 Chieochansin_2010, Taboada_2016, Luytjes_1988, Morozov_1995, Callison_1999 Ren_X_2008, Mohamed_2018, Sun_W_2020, Shan_2011
386 Hjelmsø_2019 Metagenomic analysis of viruses in toilet waste from long distance flights—A new procedure for global infectious disease surveillance Hjelmsø, Mathis Hjort; Mollerup, Sarah; Jensen, Randi Holm; Pietroni, Carlotta; Lukjancenko, Oksana; Schultz, Anna Charlotte; Aarestrup, Frank M.; Hansen, Anders Johannes 2019 2019-01-14 COMM-USE N PMC6331095 30640944.0 10.1371/journal.pone.0210368 fhqc0ty1 0.325721 Brucker_2020, Buseh_2015, Fielding_2014, Griffiths_2010, Zhou_2020 Rabaa_2015, Dacheux_2014, Kim_W_2016, Shi_W_2017
387 Saitou_2013 Eukaryote Genomes Saitou, Naruya 2013 2013-08-22 PMC N PMC7119937 10.1007/978-1-4471-5304-7_8 ef6svn8f 0.325589 Cheng_2013, Francis_2016, Zheng_2008, Li_D_2019 Francis_2016, Walker_2011, Walker_2015, Ogando_2019
388 Brisebois_2018 Human viral pathogens are pervasive in wastewater treatment center aerosols Brisebois, Evelyne; Veillette, Marc; Dion-Dupont, Vanessa; Lavoie, Jacques; Corbeil, Jacques; Culley, Alexander; Duchaine, Caroline 2018 2018-05-31 PMC N PMC7128102 29778173.0 10.1016/j.jes.2017.07.015 jgrl4okd 0.324971 Lu_P_2016, Karlsson_2012, Ryu_W_2017, Rice_1992, Tallmadge_2008 Bing-Yuan_2018, Park_2007, Zambon_2005, Korzeniewski_2014
389 Li_K_2012 Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing Li, Kelvin; Shrivastava, Susmita; Brownley, Anushka; Katzel, Dan; Bera, Jayati; Nguyen, Anh Thu; Thovarai, Vishal; Halpin, Rebecca; Stockwell, Timothy B 2012 2012-11-06 COMM-USE N PMC3548747 23131097.0 10.1186/1743-422x-9-261 xjfb83is 0.324163 Armesto_2007, Majerciak_2018, Phillippy_2009, Keep_2015 Satyanarayana_2003, Moser_2012
390 Basler_2005 A Novel Paramyxovirus? Basler, Christopher F.; García-Sastre, Adolfo; Palese, Peter 2005 2005-01-23 PMC N PMC3294354 15705331.0 10.3201/eid1101.040653 hhebiwca 0.324086 Rice_1992, Haasnoot_2010, Volmer_2010, Trobaugh_2017 Lian_2014, Jiang_2017, O'Connor_1999
391 Wylie_2013 Virome genomics: a tool for defining the human virome Wylie, Kristine M; Weinstock, George M; Storch, Gregory A 2013 2013-08-31 PMC N PMC3755052 23706900.0 10.1016/j.mib.2013.04.006 084o1dmp 0.323795 Rice_1992, Wang_2018, Trobaugh_2017, Conzelmann_1996 Meliopoulos_2012, Satyanarayana_2003, Giorda_2013
392 Vashee_2017 Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination Vashee, Sanjay; Stockwell, Timothy B.; Alperovich, Nina; Denisova, Evgeniya A.; Gibson, Daniel G.; Cady, Kyle C.; Miller, Kristofer; Kannan, Krishna; Malouli, Daniel; Crawford, Lindsey B.; Voorhies, Alexander A.; Bruening, Eric; Caposio, Patrizia; Früh, Klaus 2017 2017-10-04 COMM-USE N PMC5628293 28989973.0 10.1128/mspheredirect.00331-17 n5rhhzc9 0.323593 Rice_1992, Armesto_2007, Bickerton_2017, Keep_2015, Keep_2014 Zhao_2019, Usme-Ciro_2014, Mishin_2001
393 Swanson_2010 Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice Swanson, Kelly S; Dowd, Scot E; Suchodolski, Jan S; Middelbos, Ingmar S; Vester, Brittany M; Barry, Kathleen A; Nelson, Karen E; Torralba, Manolito; Henrissat, Bernard; Coutinho, Pedro M; Cann, Isaac KO; White, Bryan A; Fahey, George C 2010 2010-10-21 PMC N PMC3105739 20962874.0 10.1038/ismej.2010.162 nmmkkvaq 0.323271 Francis_2016, Chieochansin_2010, Zheng_2008, Li_D_2019, Bastien_2003 Selvin_2019, Tun_H_2012, McGuire_2012, De_Leon_2018
394 Fasolo_2009 Protein Microarrays Fasolo, Joseph; Snyder, Michael 2009 2009-04-01 PMC N PMC7122403 19521827.0 10.1007/978-1-59745-540-4_12 39ix21x1 0.322824 Hu_S_2010, Cox_E_2015, Stoevesandt_2014, Rice_1992 Ponchon_2013, Stoevesandt_2014, Kwon_2009
395 HENNIG_2004 The revolution of the biology of the genome HENNIG, Wolfgang 2004 2004-02-23 PMC N PMC7091781 15040884.0 10.1038/sj.cr.7290196 bmfdd0e2 0.322740 Trobaugh_2017, Rice_1992, Haasnoot_2010, Wang_2007 Walker_2015
396 Gardner_2014 Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes Gardner, Shea N.; Jaing, Crystal J.; Elsheikh, Maher M.; Peña, José; Hysom, David A.; Borucki, Monica K. 2014 2014-08-03 COMM-USE N PMC4137498 25157264.0 10.1155/2014/101894 1e44usl6 0.322675 Rice_1992, Armesto_2007, Bickerton_2017, Keep_2015, Keep_2014 Ren_X_2008
397 Uhlenhaut_2009 Use of a universal virus detection assay to identify human metapneumovirus in a hematopoietic stem cell transplant recipient with pneumonia of unknown origin Uhlenhaut, Christine; Cohen, Jeffrey I.; Fedorko, Daniel; Nanda, Santosh; Krause, Philip R. 2009 2009-04-01 PMC N PMC2663017 19250860.0 10.1016/j.jcv.2009.01.011 z5s7pmf7 0.320839 Dinh_2011, Majerciak_2018, Armesto_2007, Mizutani_2007, Bickerton_2017 Lee_H_2017, Ren_X_2008
398 Tse_H_2011 Discovery and Genomic Characterization of a Novel Ovine Partetravirus and a New Genotype of Bovine Partetravirus Tse, Herman; Tsoi, Hoi-Wah; Teng, Jade L. L.; Chen, Xin-Chun; Liu, Haiying; Zhou, Boping; Zheng, Bo-Jian; Woo, Patrick C. Y.; Lau, Susanna K. P.; Yuen, Kwok-Yung 2011 2011-09-27 COMM-USE N PMC3181347 21980506.0 10.1371/journal.pone.0025619 pjdogrs4 0.320066 Chieochansin_2010, Cheung_2010, Volmer_2010, Basler_2005, Auewarakul_2005 Ghazisaeedi_2017, Ren_X_2008
399 Grover_2010 Oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets Grover, Veenita; Pierce, Margaret L.; Hoyt, Peter; Zhang, Fengqiu; Melcher, Ulrich 2010 2010-01-31 PMC N PMC7112940 19850081.0 10.1016/j.jviromet.2009.08.023 vrab6okz 0.319478 Rice_1992, Armesto_2007, Majerciak_2018, Keep_2015, Bickerton_2017 Engel_2010
400 Yu_C_2010 A Novel Construction of Genome Space with Biological Geometry Yu, Chenglong; Liang, Qian; Yin, Changchuan; He, Rong L.; Yau, Stephen S.-T. 2010 2010-04-01 NONCOMM N PMC2885272 20360268.0 10.1093/dnares/dsq008 3c4dttrt 0.318603 Chang_2011, Zheng_2008, Lee_C_2017, Qi_Z_2018 Lauber_2013
401 Ganova-Raeva_2013 Application of mass spectrometry to molecular diagnostics of viral infections Ganova-Raeva, Lilia M; Khudyakov, Yury E 2013 2013-05-01 PMC N PMC5831079 23638820.0 10.1586/erm.13.24 qh2kuzdc 0.318603 Sharon_2010, Djikeng_2009, May_E_2016, Weinrich_2009, Yadav_2013 Jordana-Lluch_2014, Wolk_2012, Ng_E_2013, Camarasa_2018
402 Mihalov-Kovács_2014 The fecal virome of domesticated animals Mihalov-Kovács, Eszter; Fehér, Enikő; Martella, Vito; Bányai, Krisztián; Farkas, Szilvia L. 2014 2014-02-01 PMC N PMC4188178 25674581.0 10.1007/s13337-014-0192-1 k0fw3vr3 0.318195 Brucker_2020, Li_L_2014, Gupta_2009, Wolfe_2005 Wu_Z_2018, Knutson_2017, Carvalho_2014
403 Lewandowski_2019 Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples Kuiama Lewandowski; Yifei Xu; Steven T. Pullan; Sheila F. Lumley; Dona Foster; Nicholas Sanderson; Alison Vaughan; Marcus Morgan; Nicole Bright; James Kavanagh; Richard Vipond; Miles Carroll; Anthony C. Marriott; Karen E Gooch; Monique Andersson; Katie Jeffery; Timothy EA Peto; Derrick W. Crook; A Sarah Walker; Philippa C. Matthews 2019 2019-06-19 BioRxiv N 10.1101/676155 75j8jydo 0.318186 Taboada_2016, Chieochansin_2010, Dinh_2011, Whiteford_2005, Gardner_2004 Lewandowski_2019
404 Wylezich_2018 A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection Wylezich, Claudia; Papa, Anna; Beer, Martin; Höper, Dirk 2018 2018-08-30 None N PMC6117295 30166611.0 10.1038/s41598-018-31496-1 alkxz0g3 0.317437 Chang_2011, Liou_2013, Mendizabal-Ruiz_2018, Deng_2015, Lee_C_2017 Tausch_2018, Baldwin_2014, Li_C_2020
405 Conceição-Neto_2015 Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses Conceição-Neto, Nádia; Zeller, Mark; Heylen, Elisabeth; Lefrère, Hanne; Mesquita, João Rodrigo; Matthijnssens, Jelle 2015 2015-05-20 COMM-USE N PMC4459443 25986582.0 10.1186/s12985-015-0305-5 7x5dckk7 0.316275 Xu_L_2018, Karlsson_2012, Tong_2009, Wang_2018, de_Sales_Lima_2015 Maganga_2014, Lee_D_2019, Crawford_2019, Wray_2016
406 Kames_2020 Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design Jacob Kames; David Dillon Holcomb; Ofer Kimchi; Michael DiCuccio; Nobuko Hamasaki-Katagiri; Tony Wang; Anton A Komar; Aikaterini Alexaki; Chava Kimchi-Sarfaty 2020 2020-03-31 BioRxiv Y 10.1101/2020.03.30.016832 2fn25l6m 0.315719 Naito_2007, Rice_1992, Volmer_2010, Auewarakul_2005, Lee_C_2017 Niemeyer_2018, Anderson_2020, Wang_2009, Lachheb_2019
407 Wu_A_2020 Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China Wu, Aiping; Peng, Yousong; Huang, Baoying; Ding, Xiao; Wang, Xianyue; Niu, Peihua; Meng, Jing; Zhu, Zhaozhong; Zhang, Zheng; Wang, Jiangyuan; Sheng, Jie; Quan, Lijun; Xia, Zanxian; Tan, Wenjie; Cheng, Genhong; Jiang, Taijiao 2020 2020-03-11 None Y PMC7154514 32035028.0 10.1016/j.chom.2020.02.001 orqlbw9m 0.315603 Crowe_2014, Lu_P_2016, Kamau_2019, Pillaiyar_2020 Coutard_2020, Li_K_2018, Fahmi_2020, Chen_2020
408 Ai_Y_2013 GenomeFingerprinter: The Genome Fingerprint and the Universal Genome Fingerprint Analysis for Systematic Comparative Genomics Ai, Yuncan; Ai, Hannan; Meng, Fanmei; Zhao, Lei 2013 2013-10-29 COMM-USE N PMC3812135 24205026.0 10.1371/journal.pone.0077912 b8jlvkg7 0.315468 Chang_2011, Dai_Q_2012, Cheng_2013, Zheng_2008, Qi_Z_2018 Cheng_2013, Phillippy_2009, Walker_2015
409 Scheuch_2015 RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets Scheuch, Matthias; Höper, Dirk; Beer, Martin 2015 2015-03-03 COMM-USE N PMC4351923 25886935.0 10.1186/s12859-015-0503-6 p6075gva 0.315007 Cheng_2013, Montgomery_2004, Yu_H_2007, Xu_Z_2009, Kurc_2006 Twin_2013, Shcherbina_2016, Morfopoulou_2015, Morfopoulou_2014
410 Piantadosi_2017 Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis Piantadosi, Anne; Mukerji, Shibani S; Chitneni, Pooja; Cho, Tracey A; Cosimi, Lisa A; Hung, Deborah T; Goldberg, Marcia B; Sabeti, Pardis C; Kuritzkes, Daniel R; Grad, Yonatan H 2017 2017-07-28 NONCOMM N PMC5534216 28761901.0 10.1093/ofid/ofx138 e6rc8mvu 0.314628 Langelier_2017, Zhang_2020, Lu_P_2016, Li_L_2014 Ouattara_2011, Galmès_2012, Hammerschmitt_2020
411 Ward_1993 Progress towards a higher taxonomy of viruses Ward, C.W. 1993 1993-12-31 PMC N 8140287.0 10.1016/s0923-2516(06)80059-2 5xuh0960 0.314250 Rice_1992, Auewarakul_2005, Payne_2017, Ryu_W_2017, Modrow_2013 Rodríguez_2020, Tibayrenc_2015, Ren_X_2008
412 Zhang_2005 RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses Zhang, Tao; Breitbart, Mya; Lee, Wah Heng; Run, Jin-Quan; Wei, Chia Lin; Soh, Shirlena Wee Ling; Hibberd, Martin L; Liu, Edison T; Rohwer, Forest; Ruan, Yijun 2005 2005-12-20 COMM-USE N PMC1310650 16336043.0 10.1371/journal.pbio.0040003 rxbcuseq 0.314204 Rice_1992, Auewarakul_2005, Ryu_W_2017, Wang_2018, Wang_2015 Ren_X_2008, Mittelholzer_1997
413 Zheng_2017 Viral metagenomics of six bat species in close contact with humans in southern China Zheng, Xue-yan; Qiu, Min; Guan, Wei-jie; Li, Jin-ming; Chen, Shao-wei; Cheng, Ming-ji; Huo, Shu-ting; Chen, Zhong; Wu, Yi; Jiang, Li-na; Chen, Qing 2017 2017-10-05 PMC N PMC7086785 28983731.0 10.1007/s00705-017-3570-3 8tuenv8q 0.313530 Xu_L_2018, Tong_2009, Chieochansin_2010, Wang_2015, Liu_S_2013 Dacheux_2014, Lee_D_2019
414 Day_J_2015 Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms Day, J. Michael; Oakley, Brian B.; Seal, Bruce S.; Zsak, Laszlo 2015 2015-01-30 COMM-USE N PMC4311960 25635690.0 10.1371/journal.pone.0117210 xgnisa56 0.313439 Brucker_2020, Fauci_2006, Lu_P_2016, Webster_2006, Schountz_2013 Mon_K_2015, Villena_2018, Park_2007
415 Slezak_2011 Chapter 29 Design of Genomic Signatures for Pathogen Identification and Characterization Slezak, Tom; Gardner, Shea; Allen, Jonathan; Vitalis, Elizabeth; Torres, Marisa; Torres, Clinton; Jaing, Crystal 2011 2011-12-31 PMC N PMC7149865 10.1016/b978-0-12-382006-8.00029-3 7avs10yv 0.312859 Leiva-Torres_2017, Cullen_2009, Gamermann_2014, UNKNOWN_2004, Chang_2011 Lee_J_2017, Wu_Z_2011, Giles_2015
416 Kalantar_2020 IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring Katrina L. Kalantar; Tiago Carvalho; Charles F.A. de Bourcy; Boris Dimitrov; Greg Dingle; Rebecca Egger; Julie Han; Olivia B. Holmes; Yun-Fang Juan; Ryan King; Andrey Kislyuk; Maria Mariano; Lucia V. Reynoso; David Rissato Cruz; Jonathan Sheu; Jennifer Tang; James Wang; Mark A. Zhang; Emily Zhong; Vida Ahyong; Sreyngim Lay; Sophana Chea; Jennifer A. Bohl; Jessica E. Manning; Cristina M. Tato; Joseph L. DeRisi 2020 2020-04-09 BioRxiv Y 10.1101/2020.04.07.030551 oinumv1z 0.312761 Montgomery_2004, Lu_Q_2006, Kurc_2006, Cheng_2013, Brister_2015 Naccache_2014, Kilianski_2015, McGarvey_2009, Tausch_2018
417 Zoll_2015 Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information Zoll, Jan; Rahamat-Langendoen, Janette; Ahout, Inge; Jonge, Marien I.de; Jans, Jop; Huijnen, Martijn A.; Ferwerda, Gerben; Warris, Adilia; Melchers, Willem J.G. 2015 2015-05-31 PMC N 25866327.0 10.1016/j.jcv.2015.02.010 94zykdrh 0.312404 Zhang_2020, Lu_P_2016, Karlsson_2012, Coverstone_2019, Brucker_2020 Shirato_2007, Memish_2014
418 Szpara_2019 Mechanisms of DNA Virus Evolution Szpara, Moriah L.; Van Doorslaer, Koenraad 2019 2019-12-31 PMC N 10.1016/b978-0-12-809633-8.20993-x sx608o1u 0.312227 Auewarakul_2005, Simon-Loriere_2011, Longdon_2018, Longdon_2017
419 Pan_C_2018 Whole-Genome Sequence of Human Rhinovirus C47, Isolated from an Adult Respiratory Illness Outbreak in Butte County, California, 2017 Pan, Chao-Yang; Padilla, Tasha; Yagi, Shigeo; Lewis, Linda S.; Ng, Terry Fei Fan; Marine, Rachel L.; Nix, William Allan; Wadford, Debra A. 2018 2018-02-01 PMC N PMC5794959 29437112.0 10.1128/genomea.01579-17 0p7cdj5v 0.311926 Lim_T_2012, Zhang_2020, Kim_J_2018, Langelier_2017 Pan_C_2018, Langelier_2017, Ouattara_2011
420 Masuda_2014 Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer Masuda, Tsuneyuki; Nagai, Makoto; Yamasato, Hiroshi; Tsuchiaka, Shinobu; Okazaki, Sachiko; Katayama, Yukie; Oba, Mami; Nishiura, Naomi; Sassa, Yukiko; Omatsu, Tsutomu; Furuya, Tetsuya; Koyama, Satoshi; Shirai, Junsuke; Taniguchi, Koki; Fujii, Yoshiki; Todaka, Reiko; Katayama, Kazuhiko; Mizutani, Tetsuya 2014 2014-06-25 PMC N PMC7127257 24725447.0 10.1016/j.vetmic.2014.03.009 ymj5uwvg 0.311124 Lu_P_2016, Li_W_2012, Cheun-Arom_2015, Puranaveja_2009, Vui_D_2014 Yan_N_2019, Oem_J_2019, da_Silva_Medeiros_2014, Mohamed_2018
421 Clem_2007 Virus detection and identification using random multiplex (RT)-PCR with 3'-locked random primers Clem, Amy L; Sims, Jonathan; Telang, Sucheta; Eaton, John W; Chesney, Jason 2007 2007-06-28 COMM-USE N PMC1950496 17598900.0 10.1186/1743-422x-4-65 b8lesr2g 0.311120 Rice_1992, Majerciak_2018, Armesto_2007, Keep_2015, Bickerton_2017 Fallahi_2015, Majerciak_2018
422 Maurano_2020 Sequencing analysis of the spread of SARS-CoV2 in the Greater New York City region Matthew T Maurano; Sitharam Ramaswami; Gael Westby; Paul Zappile; Dacia Dimartino; Guomiao Shen; Xiaojun Feng; Andre M Ribeiro-dos-Santos; Nicholas A Vulpescu; Margaret Black; Megan Hogan; Christian Marier; Peter Meyn; Yutong Zhang; John Cadley; Raquel Ordonez; Raven Luther; Emily Huang; Emily Guzman; Antonio Serrano; Brendan Belovarac; Tatyana Gindin; Andrew Lytle; Jared Pinnell; Theodore Vougiouklakis; Ludovic Boytard; John Chen; Lawrence H Lin; Amy Rapkiewicz; Vanessa Raabe; Marie I Samanovic-Golden; George Jour; Iman Osman; Maria Aguero-Rosenfeld; Mark J Mulligan; Paolo Cotzia; Matija Snuderl; Adriana Heguy 2020 2020-04-21 BioRxiv Y 10.1101/2020.04.15.20064931 wzxcrwea 0.310068 Guery_2014, Griffiths_2010, Zhou_2020, Brister_2015, Fielding_2014
423 Kang_2020 A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome Kang, Minghui; Wu, Haolin; Yang, Qiao; Huang, Li; Hu, Quanjun; Ma, Tao; Li, Zaiyun; Liu, Jianquan 2020 2020-02-01 COMM-USE N PMC6994597 32025321.0 10.1038/s41438-020-0240-5 cxrjzva4 0.309031 Wang_2007, Zhang_2016, Francis_2016, Cheng_2013 Chen_2013, Rahman_2017, Lee_C_2020, YAO_R_2013
424 Greninger_2018 A decade of RNA virus metagenomics is (not) enough Greninger, Alexander L. 2018 2018-01-15 PMC N PMC7114529 29055712.0 10.1016/j.virusres.2017.10.014 048xo7jn 0.308996 UNKNOWN_2013, UNKNOWN_2020, UNKNOWN_2010, Mack_2007 Ogando_2019, García-López_2019, Shi_M_2018
425 Zhang_2020 Complete Genome Sequences of Five Human Coronavirus NL63 Strains Causing Respiratory Illness in Hospitalized Children in China Zhang, Lu; Gan, Mian; Zhang, Zhaoyong; Li, Xin; Liu, Wenkuan; Zhu, Airu; Sun, Jing; Li, Fang; Wang, Yanqun; Zhang, Fuchun; Zhao, Jingxian; Zhou, Rong; Zhao, Jincun 2020 2020-02-20 COMM-USE N PMC7033275 32079638.0 10.1128/mra.01597-19 mkc4g3jk 0.308862 Kamau_2019, Garcia–Moliner_2013, Pillaiyar_2020, Taboada_2016 Brandão_2016, Lu_R_2015, Minosse_2008
426 Ho_Y_2011 Advances in mass spectrometry for the identification of pathogens Ho, Yen‐Peng; Reddy, P. Muralidhar 2011 2011-05-09 PMC N PMC7168406 21557290.0 10.1002/mas.20320 ymw9avlm 0.308714 Hager_2003, Ng_E_2013, Camarasa_2018, Ho_Y_2010, May_E_2016
427 Wilkinson_2020 Partial RdRp sequences offer a robust method for Coronavirus subgenus classification David A Wilkinson; Lea Joffrin; Camille Lebarbenchon; Patrick Mavingui 2020 2020-03-06 BioRxiv N 10.1101/2020.03.02.974311 jjraqr85 0.308624 Chang_2011, Zheng_2008, Lee_C_2017, Gardner_2004, Wang_2013 Fahmi_2020, Niemeyer_2018, Zhou_2017
428 Monaco_2018 Deconvoluting Virome-Wide Antiviral Antibody Profiling Data Daniel R. Monaco; Sanjay V. Kottapalli; Tiezheng Yuan; Florian P. Breitwieser; Danielle E. Anderson; Limin Wijaya; Kevin Tan; Wan Ni Chia; Kai Kammers; Mario Caturegli; Kathleen Waugh; Marian Rewers; Lin-Fa Wang; H. Benjamin Larman 2018 2018-05-30 BioRxiv N 10.1101/333625 pc4je19g 0.308463 Castrignano_2015, Leiva-Torres_2017, Lumby_2018, Chang_2011, Li_L_2014 Case_2017, Anderson_2020, Phares_2013
429 Van_Borm_2014 Next-Generation Sequencing in Veterinary Medicine: How Can the Massive Amount of Information Arising from High-Throughput Technologies Improve Diagnosis, Control, and Management of Infectious Diseases? Van Borm, Steven; Belák, Sándor; Freimanis, Graham; Fusaro, Alice; Granberg, Fredrik; Höper, Dirk; King, Donald P.; Monne, Isabella; Orton, Richard; Rosseel, Toon 2014 2014-08-11 PMC N PMC7123048 25399113.0 10.1007/978-1-4939-2004-4_30 4wlxbbh4 0.308463 UNKNOWN_2004, Djikeng_2009, Johnson_2018, Sharon_2010, Yadav_2013 Shifman_2019, Ren_X_2008, Anis_2018
430 Niimi_2014 Virus purification and enrichment by hydroxyapatite chromatography on a chip Niimi, Miyako; Masuda, Taisuke; Kaihatsu, Kunihiro; Kato, Nobuo; Nakamura, Shota; Nakaya, Takaaki; Arai, Fumihito 2014 2014-10-01 PMC N PMC7111472 10.1016/j.snb.2014.04.011 wph0lnzk 0.308394 Djikeng_2009, Siridechadilok_2013, Rice_1992, Mizutani_2007 Nagano_1989, Loa_C_2004, Eshaghi_2005
431 Benders_2010 Cloning whole bacterial genomes in yeast Benders, Gwynedd A.; Noskov, Vladimir N.; Denisova, Evgeniya A.; Lartigue, Carole; Gibson, Daniel G.; Assad-Garcia, Nacyra; Chuang, Ray-Yuan; Carrera, William; Moodie, Monzia; Algire, Mikkel A.; Phan, Quang; Alperovich, Nina; Vashee, Sanjay; Merryman, Chuck; Venter, J. Craig; Smith, Hamilton O.; Glass, John I.; Hutchison, Clyde A. 2010 2010-03-07 NONCOMM N PMC2860123 20211840.0 10.1093/nar/gkq119 h2beosyr 0.308394 Rice_1992, Saitou_2013, Francis_2016, Li_D_2019 Vashee_2017, Almazán_2007, Chen_2020
432 Host_2016 Discovery of a Novel Bat Gammaherpesvirus Host, Kurtis M.; Damania, Blossom 2016 2016-02-17 COMM-USE N PMC4863598 27303690.0 10.1128/msphere.00016-16 mz1go5gr 0.308277 Ryu_W_2017, Lu_P_2016, Crowe_2014, Wang_2015, Xu_L_2018 Lee_D_2019, Lachheb_2019, Hammerschmitt_2020, Sun_H_2014
433 Zhang_2018 Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples Zhang, Dan; Lou, Xiuyu; Yan, Hao; Pan, Junhang; Mao, Haiyan; Tang, Hongfeng; Shu, Yan; Zhao, Yun; Liu, Lei; Li, Junping; Chen, Jiang; Zhang, Yanjun; Ma, Xuejun 2018 2018-10-25 COMM-USE N PMC6202819 30359242.0 10.1186/s12864-018-5152-5 1vo72gop 0.307570 Armesto_2007, Majerciak_2018, Chen_2018, Rice_1992, Keep_2014 Souza_2019
434 Lee_D_2019 Two novel adenoviruses found in Cave Myotis bats (Myotis velifer) in Oklahoma Lee, Dana N.; Angiel, Meagan 2019 2019-12-03 PMC N PMC7089485 31797220.0 10.1007/s11262-019-01719-2 umvk59dc 0.307382 Xu_L_2018, Liu_S_2013, Chieochansin_2010, Sonntag_2009, Tong_2009 Doysabas_2019, Yinda_2016, Hammerschmitt_2020
435 Hu_J_2016 Evolution and Variation of the SARS-CoV Genome Hu, Jianfei; Wang, Jing; Xu, Jing; Li, Wei; Han, Yujun; Li, Yan; Ji, Jia; Ye, Jia; Xu, Zhao; Zhang, Zizhang; Wei, Wei; Li, Songgang; Wang, Jun; Wang, Jian; Yu, Jun; Yang, Huanming 2016 2016-11-28 None N PMC5172238 15629034.0 10.1016/s1672-0229(03)01027-1 8oz6bgz4 0.307274 Chang_2011, Zheng_2008, Wang_2013, Gardner_2004, Rice_1992 Niemeyer_2018, Narayanan_2015, Zhu_Y_2005, Lachheb_2019
436 Wassenaar_2020 2019_nCoV/SARS‐CoV‐2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses Wassenaar, T.M.; Zou, Y. 2020 2020-02-28 NONCOMM Y PMC7165814 32060933.0 10.1111/lam.13285 rq9hmjsx 0.306970 Wang_2018, Tong_2009, Xu_L_2018, Ryu_W_2017, Grewelle_2020 Niemeyer_2018, Fahmi_2020, Jiang_2017, Wang_2019
437 Tausch_2018 PathoLive - Real-time pathogen identification from metagenomic Illumina datasets Simon H. Tausch; Tobias P. Loka; Jakob M. Schulze; Andreas Andrusch; Jeanette Klenner; Piotr Wojciech Dabrowski; Martin S. Lindner; Andreas Nitsche; Bernhard Y. Renard 2018 2018-08-31 BioRxiv Y 10.1101/402370 wk70iipl 0.306970 Lee_C_2017, Chang_2011, Cheng_2013, Deng_2015, Brister_2015 Hörster_2019, Zinter_2018, Li_C_2020
438 Taboada_2016 Complete Genome Sequence of Human Coronavirus OC43 Isolated from Mexico Taboada, B. T.; Isa, P.; Espinoza, M. A.; Aponte, F. E.; Arias-Ortiz, M. A.; Monge-Martínez, J.; Rodríguez-Vázquez, R.; Díaz-Hernández, F.; Zárate-Vidal, F.; Wong-Chew, R. M.; Firo-Reyes, V.; del Río-Almendárez, C. N.; Gaitán-Meza, J.; Villaseñor-Sierra, A.; Martínez-Aguilar, G.; García-Borjas, M.; Noyola, D. E.; Pérez-Gónzalez, L. F.; López, S.; Santos-Preciado, J. I.; Arias, C. F. 2016 2016-11-10 COMM-USE N PMC5105101 27834708.0 10.1128/genomea.01256-16 l44dytci 0.306819 Kamau_2019, Chieochansin_2010, Zhang_2020, Kin_N_2017 Brandão_2016, Langelier_2017, Ren_X_2008, Kin_N_2017
439 Jones_2006 A long distance RT-PCR able to amplify the Pestivirus genome Jones, Leandro R.; Zandomeni, Rubén O.; Weber, E. Laura 2006 2006-06-30 PMC N PMC7112918 16497393.0 10.1016/j.jviromet.2006.01.005 lx1i00wj 0.306161 Thiel_2002, Majerciak_2018, Endoh_2005, Armesto_2007, Thiel_1997 Lazouskaya_2014
440 Li_H_2019 The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites Li, Heng; Li, Hongzhe; Wang, Jingjing; Guo, Lei; Fan, Haitao; Zheng, Huiwen; Yang, Zening; Huang, Xing; Chu, Manman; Yang, Fengmei; He, Zhanlong; Li, Nan; Yang, Jinxi; Wu, Qiongwen; Shi, Haijing; Liu, Longding 2019 2019-08-19 COMM-USE N PMC6700990 31426820.0 10.1186/s12985-019-1211-z dwok857k 0.306150 Francis_2016, Wang_2018, Trobaugh_2017, Callison_1999, Auewarakul_2005 Sonawane_2019, Ochoa-Repáraz_2014, Selvin_2019, Mon_K_2015
441 Kang_2011 Improvement of the specificity of a pan‐viral microarray by using genus‐specific oligonucleotides and reduction of interference by host genomes Kang, Xiaoping; Qin, Chengfeng; Li, Yongqiang; Liu, Hong; Lin, Fang; Li, Yuchang; Li, Jing; Zhu, Qingyu; Yang, Yinhui 2011 2011-07-07 PMC N PMC7167123 21739454.0 10.1002/jmv.22157 kssigadb 0.305341 Rice_1992, Endoh_2005, Majerciak_2018, Chen_2018, Oba_M_2018
442 Tischer_2012 Viral Bacterial Artificial Chromosomes: Generation, Mutagenesis, and Removal of Mini-F Sequences Tischer, B. Karsten; Kaufer, Benedikt B. 2012 2012-02-23 PMC N PMC3303620 22496607.0 10.1155/2012/472537 r1qzmzfe 0.303976 Rice_1992, Armesto_2007, Bickerton_2017, Keep_2014, Keep_2015 Usme-Ciro_2014, Yun_S_2015, Nowak_1984
443 Twin_2013 The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis Twin, Jimmy; Bradshaw, Catriona S.; Garland, Suzanne M.; Fairley, Christopher K.; Fethers, Katherine; Tabrizi, Sepehr N. 2013 2013-09-27 COMM-USE N PMC3785445 24086764.0 10.1371/journal.pone.0076892 qg2r691d 0.303841 Phillippy_2009, Whiteford_2005, Cheng_2013, Francis_2016, Chang_2011 McGuire_2012, Selvin_2019, Sazmand_2019
444 González-Candelas_2018 Population Genomics of Human Viruses González-Candelas, Fernando; Patiño-Galindo, Juan Ángel; Valiente-Mullor, Carlos 2018 2018-06-04 PMC N PMC7123750 10.1007/13836_2018_31 8g8ppdxg 0.303761 Wang_2018, Fauci_2006, Conzelmann_1996, Holmes_2007, Grewelle_2020 Gutiérrez_2013, Barr_2016
445 Lojkić_2016 Faecal virome of red foxes from peri-urban areas Lojkić, Ivana; Biđin, Marina; Prpić, Jelena; Šimić, Ivana; Krešić, Nina; Bedeković, Tomislav 2016 2016-04-30 PMC N PMC7112549 27012914.0 10.1016/j.cimid.2016.01.005 neqj85xf 0.303488 Lim_T_2012, Lu_P_2016, Ye_F_2019, Ramsauer_2007, Wang_2014 Park_2007, Woo_P_2016, Lee_D_2019, Candela_2019
446 Vinatzer_2019 Cyberbiosecurity Challenges of Pathogen Genome Databases Vinatzer, Boris A.; Heath, Lenwood S.; Almohri, Hussain M. J.; Stulberg, Michael J.; Lowe, Christopher; Li, Song 2019 2019-05-15 COMM-USE N PMC6529814 31157218.0 10.3389/fbioe.2019.00106 x6s34z1s 0.301571 Mack_2007, Zhou_2020, Kruk_2008, Brucker_2020, Gupta_2009 Rabaa_2015, Shi_W_2017, Zhang_2007
447 Caddy_2018 New viruses associated with canine gastroenteritis Caddy, S.L. 2018 2018-02-28 PMC N PMC7110870 29428093.0 10.1016/j.tvjl.2017.12.009 sp45lrz5 0.301128 Lu_P_2016, Ryu_W_2017, Walker_2010, Wang_2015 Balasuriya_2013, Di_Martino_2019, Carvalho_2014, Ouattara_2011
448 Li_S_2014 System analysis of synonymous codon usage biases in archaeal virus genomes Li, Sen; Yang, Jie 2014 2014-08-21 PMC N PMC7094158 24685889.0 10.1016/j.jtbi.2014.03.022 kg53pbyw 0.301015 Wang_2018, Auewarakul_2005, Gu_W_2004, Francis_2016, Rice_1992 Sheikh_2020, Gu_W_2004, Gutiérrez_2013, Tibayrenc_2015
449 Holmes_2013 The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia Holmes, Kathryn V.; Dominguez, Samuel R. 2013 2013-01-08 NONCOMM N PMC3546555 23300251.0 10.1128/mbio.00548-12 krvei97r 0.300501 Rice_1992, Ryu_W_2017, Wang_2018, Lu_P_2016, Wang_2015 Ren_X_2008, Lachheb_2019
450 Mushegian_2018 Sequence analysis of malacoherpesvirus proteins: Pan-herpesvirus capsid module and replication enzymes with an ancient connection to “Megavirales” Mushegian, Arcady; Karin, Eli Levy; Pupko, Tal 2018 2018-01-01 PMC N 29065352.0 10.1016/j.virol.2017.10.009 elmqg45v 0.300501 den_Boon_2010, Rice_1992, Ryu_W_2017, Gorbalenya_1988
451 Kraberger_2019 Novel smacoviruses identified in the faeces of two wild felids: North American bobcat and African lion Kraberger, Simona; Serieys, Laurel; Fountain-Jones, Nicolas; Packer, Craig; Riley, Seth; Varsani, Arvind 2019 2019-06-22 PMC N PMC7086625 31240485.0 10.1007/s00705-019-04329-3 4ipimv1a 0.300501 Xu_L_2018, Kosoy_2010, Tong_2009, Wang_2015, Liu_S_2013 Ghazisaeedi_2017, Lee_D_2019, Maganga_2014, Di_Martino_2009
452 Tapinos_2019 The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences Tapinos, Avraam; Constantinides, Bede; Phan, My V. T.; Kouchaki, Samaneh; Cotten, Matthew; Robertson, David L. 2019 2019-04-26 COMM-USE N PMC6563281 31035503.0 10.3390/v11050394 y5xsf3ij 0.300375 Chang_2011, Deng_2015, Montgomery_2004, Liou_2013, Dai_Q_2012 Zhang_2017, Pessia_2015, Wang_2010
453 Khan_2008 Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers Khan, Haseeb A.; Arif, Ibrahim A.; Bahkali, Ali H.; Al Farhan, Ahmad H.; Al Homaidan, Ali A. 2008 2008-10-06 COMM-USE N PMC2614192 19204824.0 r97x0paz 0.300265 Zheng_2008, Chieochansin_2010, Saw_A_2019, Chang_2011 Banks_2006, Ghazisaeedi_2017, Ramírez_2014, Burger_2004
454 Tchitchek_2014 Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome Tchitchek, Nicolas; Safronetz, David; Rasmussen, Angela L.; Martens, Craig; Virtaneva, Kimmo; Porcella, Stephen F.; Feldmann, Heinz; Ebihara, Hideki; Katze, Michael G. 2014 2014-11-14 COMM-USE N PMC4232415 25398096.0 10.1371/journal.pone.0112617 4ueabl9p 0.300237 Cheng_2013, Francis_2016, Chang_2011, Zheng_2008 Neves_2015, Zhu_L_2008, Russell_2018, Zivcec_2011