| 1 |
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 |
0.921121 |
|
Lefkowitz_2018 |
| 2 |
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 |
0.911080 |
|
Fauquet_2008, Adams_2016 |
| 3 |
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 |
0.791288 |
Cheng_2013, O'Leary_2016 |
Shean_2019 |
| 4 |
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 |
0.781720 |
|
|
| 5 |
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 |
0.739155 |
O'Leary_2016, Cheng_2013, Brister_2015 |
|
| 6 |
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 |
0.610155 |
|
Pickett_2012 |
| 7 |
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 |
0.603970 |
Cheng_2013, Gardner_2008 |
Schäffer_2019 |
| 8 |
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 |
0.529679 |
Cheng_2013, O'Leary_2016, Brister_2015 |
Paez-Espino_2017, Wang_2010 |
| 9 |
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 |
0.528646 |
Cheng_2013, Brister_2015, O'Leary_2016 |
Wang_2010 |
| 10 |
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 |
0.501670 |
|
Wang_2010 |
| 11 |
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 |
0.478242 |
Cheng_2013, O'Leary_2016, Brister_2015 |
Pickett_2011 |
| 12 |
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 |
0.441662 |
Cheng_2013, Brister_2015, Chang_2011, O'Leary_2016 |
Wang_2010, Zhang_2017 |
| 13 |
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 |
0.400456 |
Lee_C_2017, Chang_2011, Cheng_2013 |
Shifman_2019 |
| 14 |
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 |
0.394932 |
Chang_2011, Lee_C_2017, Brister_2015 |
|
| 15 |
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 |
0.392188 |
Chang_2011 |
Ward_1993, Kuhn_2020 |
| 16 |
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 |
0.384784 |
Cheng_2013, Brister_2015, Smits_2014, Deng_2015 |
|
| 17 |
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 |
0.372648 |
Chang_2011, Cheng_2013, Lee_C_2017 |
Yu_Z_2010 |
| 18 |
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 |
0.371183 |
Cheng_2013, Deng_2015, Brister_2015, Chang_2011 |
|
| 19 |
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 |
0.363393 |
Cheng_2013, Smith_2013, Chang_2011 |
Wang_2010, Viehweger_2019 |
| 20 |
Kuhn_2020 |
Virus Taxonomy |
Kuhn, Jens H. |
2020 |
2020-12-31 |
PMC |
N |
PMC7157452 |
|
10.1016/b978-0-12-809633-8.21231-4 |
0ckt6f92 |
0.352232 |
Roux_2019 |
Ward_1993 |
| 21 |
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 |
0.341260 |
Cheng_2013, O'Leary_2016, Lee_C_2017 |
|
| 22 |
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 |
0.325633 |
Chang_2011, Lee_C_2017, Cheng_2013 |
Dacheux_2014 |