Topic 01 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 37 - 15 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 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 0.988564 Viehweger_2019
2 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 0.988238 Viehweger_2018
3 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 0.809732
4 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 0.787036
5 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 0.719283 Brister_2015, Chang_2011, Deng_2015, Cheng_2013 Wang_2010, Harel_2019, Djikeng_2009, Yang_2018
6 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 0.713668
7 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 0.685702 Zhang_2017
8 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 0.670571 Chang_2011, Lee_C_2017
9 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 0.649237 Viehweger_2019
10 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 0.621346
11 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 0.617424 Chang_2011, Cheng_2013, Brister_2015, Lee_C_2017 Kames_2020
12 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 0.606137 Djikeng_2009, Brister_2015
13 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 0.606079 Chen_2018, Cheng_2013
14 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 0.572950 Lee_C_2017
15 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 0.561696 Chang_2011, Lee_C_2017
16 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 0.552560 Chang_2011, Cheng_2013, Lee_C_2017
17 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 0.546978 Djikeng_2009, Chang_2011, Brister_2015
18 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 0.546598 Chang_2011
19 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 0.539451 Chang_2011 Wang_2010
20 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 0.538479 Deng_2015, Phillippy_2009, Warren_2007, Chang_2011 Harel_2019, Viehweger_2019, Viehweger_2018
21 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 0.533586 Mizutani_2007, Chang_2011 Lewandowska_2017
22 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 0.529993 Whiteford_2005
23 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 0.528131
24 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 0.524319 Chang_2011, Phillippy_2009, Whiteford_2005, Francis_2016, Harel_2019 Vashee_2017
25 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 0.518973 Zhang_2020 Langelier_2017
26 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 0.518037 Endoh_2005
27 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 0.517647 Smith_2013 Viehweger_2019
28 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 0.517458 Cheng_2013 Cook_2013
29 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 0.505198
30 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 0.497352
31 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 0.496713
32 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 0.495517 Cheng_2013, Chang_2011, Deng_2015, Whiteford_2005 Wang_2010
33 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 0.493248
34 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 0.488896 Siridechadilok_2013, Djikeng_2009, Smith_2013, Brister_2015 Dacheux_2014, Alquezar-Planas_2013
35 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 0.483463
36 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 0.473295 Cheng_2013, Lee_C_2017, Brister_2015
37 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 0.470037
38 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 0.466589 Mizutani_2007, Smits_2014 Alquezar-Planas_2013
39 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 0.462816
40 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 0.460090 Chang_2011, Brister_2015, Harel_2019, Deng_2015, Cheng_2013 Wang_2010
41 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 0.459668 Grewelle_2020
42 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 0.449098 Chang_2011, Francis_2016, Lee_C_2017 Wang_2010
43 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 0.445672 Lee_C_2017, Cheng_2013, Chang_2011, Gardner_2004, Francis_2016 Wang_2010
44 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 0.445273 Chang_2011, Lee_C_2017, Brister_2015
45 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 0.443471 Cheng_2013, O'Leary_2016
46 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 0.443410 Cheng_2013, Smith_2013, Chang_2011 Wang_2010, Viehweger_2019
47 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 0.442760 Chang_2011, Gardner_2004
48 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 0.437163 Chang_2011 Wang_2003
49 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 0.434272
50 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 0.431824 Chang_2011, Francis_2016, Lee_C_2017 Francis_2016, Zhang_2017
51 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 0.430911 Djikeng_2009, Brister_2015 Warwick-Dugdale_2019, Smits_2014
52 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 0.429874
53 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 0.429287 Deng_2015, Whiteford_2005, Cheng_2013, Chang_2011 Viehweger_2019, Viehweger_2018, Harel_2019
54 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 0.429287
55 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 0.427246 Cheng_2013, Chang_2011, Lee_C_2017
56 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 0.426174
57 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 0.421933 Chang_2011, Deng_2015 Zhang_2017, Wang_2010
58 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 0.421052 Whiteford_2005, Chang_2011, Deng_2015, Warren_2007 Routh_2012
59 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 0.418640 Chang_2011, Deng_2015, Harel_2019, Cheng_2013 Phillippy_2009, Routh_2012, Wang_2010, Francis_2016
60 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 0.418334
61 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 0.417451
62 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 0.413951
63 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 0.412868 Cheng_2013, Lee_C_2017, Deng_2015, Chang_2011
64 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 0.411534 Taboada_2016 Shan_2011
65 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 0.410332 Cheng_2013, Whiteford_2005, Francis_2016
66 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 0.409488 Lee_C_2017, Chang_2011, Smits_2014
67 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 0.408613 Chang_2011, Gardner_2004, Francis_2016
68 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 0.407943 Cheng_2013, O'Leary_2016, Brister_2015 Paez-Espino_2017, Wang_2010
69 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 0.405667 Chang_2011, Lee_C_2017
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