| 1 |
Bashir_2020 |
An efficient pattern growth approach for mining fault tolerant frequent itemsets |
Bashir, Shariq |
2020 |
2020-04-01 |
PMC |
N |
PMC7126664 |
|
10.1016/j.eswa.2019.113046 |
qndr28n6 |
0.677543 |
Lee_C_2017, Xu_Z_2009, Saw_A_2019, Saw_A_2019 |
Hu_Y_2006, Lee_G_2009, Wu_Y_2020, McCrae_2008 |
| 2 |
Isa_Irawan_2019 |
Application of Needleman-Wunch Algorithm to identify mutation in DNA sequences of Corona virus |
Isa Irawan, Mohammad; Mukhlash, Imam; Rizky, Abduh; Ririsati Dewi, Alfiana |
2019 |
2019-05-01 |
COMM-USE |
N |
PMC7106772 |
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10.1088/1742-6596/1218/1/012031 |
feq9grdc |
0.675180 |
Lee_C_2017, Chang_2011 |
|
| 3 |
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 |
0.663562 |
Montgomery_2004, Lee_C_2017 |
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| 4 |
Park_2018 |
Technological opportunity discovery for technological convergence based on the prediction of technology knowledge flow in a citation network |
Park, Inchae; Yoon, Byungun |
2018 |
2018-11-30 |
PMC |
N |
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10.1016/j.joi.2018.09.007 |
skmxrkhf |
0.641896 |
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| 5 |
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 |
0.631768 |
Chang_2011, Lee_C_2017 |
|
| 6 |
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 |
|
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10.1101/852657 |
besvz92f |
0.630349 |
UNKNOWN_2018, UNKNOWN_2016 |
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| 7 |
Mock_2019 |
VIDHOP, viral host prediction with Deep Learning |
Florian Mock; Adrian Viehweger; Emanuel Barth; Manja Marz |
2019 |
2019-03-12 |
BioRxiv |
N |
|
|
10.1101/575571 |
o4y8ci0n |
0.554193 |
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Lopez-Rincon_2020 |
| 8 |
Crossman_2020 |
Leverging Deep Learning to Simulate Coronavirus Spike proteins has the potential to predict future Zoonotic sequences |
Lisa Caroline Crossman |
2020 |
2020-04-20 |
BioRxiv |
N |
|
|
10.1101/2020.04.20.046920 |
x8jytnj6 |
0.543863 |
Lee_C_2017, Chang_2011 |
|
| 9 |
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 |
0.536707 |
Chang_2011, Montgomery_2004, Lee_C_2017 |
Morfopoulou_2014 |
| 10 |
Broseus_2020 |
TALC: Transcription Aware Long Read Correction |
Lucile Broseus; Aubin Thomas; Andrew J. Oldfield; Dany Severac; Emeric Dubois; William Ritchie |
2020 |
2020-01-11 |
BioRxiv |
N |
|
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10.1101/2020.01.10.901728 |
wtarrhf0 |
0.522036 |
Montgomery_2004 |
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| 11 |
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 |
0.511555 |
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| 12 |
Hatcher_2017 |
Virus Variation Resource – improved response to emergent viral outbreaks |
Hatcher, Eneida L.; Zhdanov, Sergey A.; Bao, Yiming; Blinkova, Olga; Nawrocki, Eric P.; Ostapchuck, Yuri; Schäffer, Alejandro A.; Brister, J. Rodney |
2017 |
2017-01-04 |
PMC |
N |
PMC5210549 |
27899678.0 |
10.1093/nar/gkw1065 |
worgd0xu |
0.508562 |
UNKNOWN_2018, UNKNOWN_2016 |
|
| 13 |
Shang_2020 |
CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning |
Jiayu Shang; Yanni Sun |
2020 |
2020-03-27 |
BioRxiv |
N |
|
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10.1101/2020.03.26.009001 |
pd0cmefo |
0.487917 |
Chang_2011, Lee_C_2017, Sen_D_2018, Montgomery_2004 |
Mock_2019, Lopez-Rincon_2020 |
| 14 |
Waagmeester_2020 |
A protocol for adding knowledge to Wikidata, a case report |
Andra Waagmeester; Egon L. Willighagen; Andrew I. Su; Martina Kutmon; Jose Emilio Labra Gayo; Daniel Fernández-Álvarez; Peter J. Schaap; Lisa M. Verhagen; Jasper J. Koehorst |
2020 |
2020-04-07 |
BioRxiv |
Y |
|
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10.1101/2020.04.05.026336 |
a0bbw3er |
0.483328 |
Lee_C_2017 |
Greenbaum_2009, Collier_2007, McCrae_2008 |
| 15 |
Morfopoulou_2014 |
Bayesian mixture analysis for metagenomic community profiling. |
Sofia Morfopoulou; Vincent Plagnol |
2014 |
2014-07-25 |
BioRxiv |
N |
|
|
10.1101/007476 |
058r9486 |
0.469642 |
Chang_2011, Liou_2013, Lee_C_2017, Saw_A_2019 |
Morfopoulou_2015 |
| 16 |
Li_H_2018 |
Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences |
Li, Han; Sun, Fengzhu |
2018 |
2018-07-03 |
COMM-USE |
N |
PMC6030160 |
29968780.0 |
10.1038/s41598-018-28308-x |
rxhygr8x |
0.462619 |
Lee_C_2017, Chang_2011 |
|
| 17 |
Bao_Y_2008 |
Virus Classification by Pairwise Sequence Comparison (PASC) |
Bao, Y.; Kapustin, Y.; Tatusova, T. |
2008 |
2008-12-31 |
PMC |
N |
|
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10.1016/b978-012374410-4.00710-x |
aa88gtzr |
0.451682 |
Chang_2011, Lee_C_2017 |
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| 18 |
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 |
0.443129 |
Chang_2011, Lee_C_2017 |
Lopez-Rincon_2020 |
| 19 |
Cho_M_2019 |
Prediction of cross-species infection propensities of viruses with receptor similarity |
Cho, Myeongji; Son, Hyeon Seok |
2019 |
2019-09-30 |
PMC |
N |
PMC7106226 |
31026604.0 |
10.1016/j.meegid.2019.04.016 |
55lkfivh |
0.442290 |
Chang_2011, Qi_Z_2018, Cheng_2012 |
|
| 20 |
Qiang_2020 |
Using the spike protein feature to predict infection risk and monitor the evolutionary dynamic of coronavirus |
Qiang, Xiao-Li; Xu, Peng; Fang, Gang; Liu, Wen-Bin; Kou, Zheng |
2020 |
2020-03-25 |
COMM-USE |
Y |
PMC7093988 |
32209118.0 |
10.1186/s40249-020-00649-8 |
llv3cvdr |
0.426641 |
Lee_C_2017, Chang_2011 |
|
| 21 |
Wu_Y_2020 |
NetNCSP: Nonoverlapping closed sequential pattern mining |
Wu, Youxi; Zhu, Changrui; Li, Yan; Guo, Lei; Wu, Xindong |
2020 |
2020-03-31 |
PMC |
Y |
|
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10.1016/j.knosys.2020.105812 |
pdf3i2tt |
0.418818 |
Chang_2011, Qi_Z_2018, Dai_Q_2012, Lee_C_2017 |
Bashir_2020, Lee_G_2009, Hu_Y_2006, McCrae_2008 |
| 22 |
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 |
0.418711 |
Lee_C_2017 |
|
| 23 |
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 |
0.413332 |
Lee_C_2017, Chang_2011, Saw_A_2019 |
|
| 24 |
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 |
0.399420 |
Montgomery_2004, Lu_Q_2006, Kurc_2006 |
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| 25 |
Zhou_2018 |
A generalized approach to predicting protein-protein interactions between virus and host |
Zhou, Xiang; Park, Byungkyu; Choi, Daesik; Han, Kyungsook |
2018 |
2018-08-13 |
COMM-USE |
N |
PMC6101077 |
30367586.0 |
10.1186/s12864-018-4924-2 |
4uvezfqm |
0.399118 |
Chang_2011 |
|
| 26 |
Wilm_2012 |
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets |
Wilm, Andreas; Aw, Pauline Poh Kim; Bertrand, Denis; Yeo, Grace Hui Ting; Ong, Swee Hoe; Wong, Chang Hua; Khor, Chiea Chuen; Petric, Rosemary; Hibberd, Martin Lloyd; Nagarajan, Niranjan |
2012 |
2012-10-12 |
NONCOMM |
N |
PMC3526318 |
23066108.0 |
10.1093/nar/gks918 |
bmcku2yb |
0.395284 |
Chang_2011, Montgomery_2004 |
|
| 27 |
Adetiba_2018 |
Alignment-Free Z-Curve Genomic Cepstral Coefficients and Machine Learning for Classification of Viruses |
Adetiba, Emmanuel; Olugbara, Oludayo O.; Taiwo, Tunmike B.; Adebiyi, Marion O.; Badejo, Joke A.; Akanle, Matthew B.; Matthews, Victor O. |
2018 |
2018-03-07 |
PMC |
N |
PMC7120486 |
|
10.1007/978-3-319-78723-7_25 |
ddu6yl8r |
0.395051 |
Lee_C_2017, Liou_2013, Chang_2011, Saw_A_2019, Liu_L_2012 |
Lopez-Rincon_2020, Mock_2019, AlMoammar_2018, Ozturk_2020 |
| 28 |
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 |
0.393667 |
Montgomery_2004, Xu_Z_2009, Kurc_2006 |
Shcherbina_2016, Morfopoulou_2015, Morfopoulou_2014 |
| 29 |
Fonseca_2019 |
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes |
Fonseca, Vagner; Libin, Pieter J. K.; Theys, Kristof; Faria, Nuno R.; Nunes, Marcio R. T.; Restovic, Maria I.; Freire, Murilo; Giovanetti, Marta; Cuypers, Lize; Nowé, Ann; Abecasis, Ana; Deforche, Koen; Santiago, Gilberto A.; de Siqueira, Isadora C.; San, Emmanuel J.; Machado, Kaliane C. B.; Azevedo, Vasco; Filippis, Ana Maria Bispo-de; da Cunha, Rivaldo Venâncio; Pybus, Oliver G.; Vandamme, Anne-Mieke; Alcantara, Luiz C. J.; de Oliveira, Tulio |
2019 |
2019-05-08 |
COMM-USE |
N |
PMC6527240 |
31067235.0 |
10.1371/journal.pntd.0007231 |
xn2wulnp |
0.389101 |
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| 30 |
Alguwaizani_2018 |
Predicting Interactions between Virus and Host Proteins Using Repeat Patterns and Composition of Amino Acids |
Alguwaizani, Saud; Park, Byungkyu; Zhou, Xiang; Huang, De-Shuang; Han, Kyungsook |
2018 |
2018-05-09 |
COMM-USE |
N |
PMC5966669 |
29854357.0 |
10.1155/2018/1391265 |
0dxrai3j |
0.362645 |
Lee_C_2017, Chang_2011, Sen_D_2018 |
Zhou_2018 |
| 31 |
Hu_Y_2006 |
Mining association rules with multiple minimum supports: a new mining algorithm and a support tuning mechanism |
Hu, Ya-Han; Chen, Yen-Liang |
2006 |
2006-10-31 |
PMC |
N |
PMC7127670 |
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10.1016/j.dss.2004.09.007 |
s96d3ust |
0.361892 |
Lee_C_2017, Liou_2013 |
Bashir_2020, Lee_G_2009, Wu_Y_2020, McCrae_2008 |
| 32 |
Lee_G_2009 |
Proportional fault-tolerant data mining with applications to bioinformatics |
Lee, Guanling; Peng, Sheng-Lung; Lin, Yuh-Tzu |
2009 |
2009-02-19 |
PMC |
N |
PMC7087812 |
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10.1007/s10796-009-9158-z |
kt9sbn40 |
0.344724 |
Lee_C_2017, Liou_2013, Saw_A_2019, Qi_Z_2018, Chang_2011 |
Bashir_2020, Wilson_2003, Hu_Y_2006, Wu_Y_2020 |
| 33 |
Moshiri_2020 |
ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes |
Niema Moshiri |
2020 |
2020-04-21 |
BioRxiv |
N |
|
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10.1101/2020.04.20.052068 |
l9a7upui |
0.320829 |
Montgomery_2004, Chang_2011, Lee_C_2017 |
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| 34 |
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 |
0.309025 |
Chang_2011, Saw_A_2019, Saw_A_2019, Dai_Q_2012 |
|
| 35 |
Weissenbacher_2017 |
Extracting geographic locations from the literature for virus phylogeography using supervised and distant supervision methods |
Weissenbacher, Davy; Sarker, Abeed; Tahsin, Tasnia; Scotch, Matthew; Gonzalez, Graciela |
2017 |
2017-07-26 |
PMC |
N |
PMC5543364 |
28815119.0 |
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g22ggyxb |
0.307808 |
Chang_2011, Lee_C_2017 |
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