1 |
Snyder_2006 |
PATRIC: The VBI PathoSystems Resource Integration Center |
Snyder, E. E.; Kampanya, N.; Lu, J.; Nordberg, E. K.; Karur, H. R.; Shukla, M.; Soneja, J.; Tian, Y.; Xue, T.; Yoo, H.; Zhang, F.; Dharmanolla, C.; Dongre, N. V.; Gillespie, J. J.; Hamelius, J.; Hance, M.; Huntington, K. I.; Jukneliene, D.; Koziski, J.; Mackasmiel, L.; Mane, S. P.; Nguyen, V.; Purkayastha, A.; Shallom, J.; Yu, G.; Guo, Y.; Gabbard, J.; Hix, D.; Azad, A. F.; Baker, S. C.; Boyle, S. M.; Khudyakov, Y.; Meng, X. J.; Rupprecht, C.; Vinje, J.; Crasta, O. R.; Czar, M. J.; Dickerman, A.; Eckart, J. D.; Kenyon, R.; Will, R.; Setubal, J. C.; Sobral, B. W. S. |
2006 |
2006-11-16 |
NONCOMM |
N |
PMC1669763 |
17142235.0 |
10.1093/nar/gkl858 |
3ulketgy |
0.849432 |
UNKNOWN_2018, UNKNOWN_2016 |
Zhang_2007 |
2 |
Aziz_2012 |
SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models |
Aziz, Ramy K.; Devoid, Scott; Disz, Terrence; Edwards, Robert A.; Henry, Christopher S.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Stevens, Rick L.; Vonstein, Veronika; Xia, Fangfang |
2012 |
2012-10-24 |
None |
N |
PMC3480482 |
23110173.0 |
10.1371/journal.pone.0048053 |
vret3sh1 |
0.839319 |
Montgomery_2004, Lu_Q_2006 |
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3 |
Kurc_2006 |
An XML-based System for Synthesis of Data from Disparate Databases |
Kurc, Tahsin; Janies, Daniel A.; Johnson, Andrew D.; Langella, Stephen; Oster, Scott; Hastings, Shannon; Habib, Farhat; Camerlengo, Terry; Ervin, David; Catalyurek, Umit V.; Saltz, Joel H. |
2006 |
2006-06-30 |
PMC |
N |
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16501185.0 |
10.1197/jamia.m1848 |
m0q52a2t |
0.826433 |
Montgomery_2004, Mendizabal-Ruiz_2018 |
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4 |
Peters_2007 |
Integrating epitope data into the emerging web of biomedical knowledge resources |
Peters, Bjoern; Sette, Alessandro |
2007 |
2007-01-01 |
PMC |
N |
PMC7097317 |
17479127.0 |
10.1038/nri2092 |
vvlsqy36 |
0.820696 |
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5 |
Aurrecoechea_2017 |
EuPathDB: the eukaryotic pathogen genomics database resource |
Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie |
2017 |
2017-01-04 |
NONCOMM |
N |
PMC5210576 |
27903906.0 |
10.1093/nar/gkw1105 |
t94aufs3 |
0.805256 |
UNKNOWN_2018, UNKNOWN_2016 |
Zhang_2007, Snyder_2006 |
6 |
Su_H_2012 |
Framing the structure of global open innovation research |
Su, Hsin-Ning; Lee, Pei-Chun |
2012 |
2012-04-30 |
PMC |
N |
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10.1016/j.joi.2011.12.001 |
xu4camqf |
0.771172 |
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Lee_P_2011 |
7 |
Kolatkar_2008 |
C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training |
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2008 |
2008-02-20 |
COMM-USE |
N |
PMC2229842 |
18286178.0 |
10.1371/journal.pone.0001621 |
pb1e2w7s |
0.770044 |
Lu_Q_2006, Montgomery_2004 |
Wang_2006, Montgomery_2004, Molodenskiy_2019, Asbury_2010 |
8 |
Wagner_2020 |
Real-time biomedical knowledge synthesis of the exponentially growing world wide web using unsupervised neural networks |
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2020 |
2020-04-04 |
BioRxiv |
N |
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10.1101/2020.04.03.020602 |
tnoybbfx |
0.759757 |
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Joshi_2020 |
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Weir_2017 |
Development of a microbial dose response visualization and modelling application for QMRA modelers and educators |
Weir, Mark H.; Mitchell, Jade; Flynn, William; Pope, Joanna M. |
2017 |
2017-02-01 |
PMC |
N |
PMC5665384 |
29104445.0 |
10.1016/j.envsoft.2016.11.011 |
wslu5fof |
0.751066 |
Lu_Q_2006, Kurc_2006 |
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10 |
Asbury_2010 |
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome |
Asbury, Thomas M; Mitman, Matt; Tang, Jijun; Zheng, W Jim |
2010 |
2010-09-02 |
COMM-USE |
N |
PMC2941692 |
20813045.0 |
10.1186/1471-2105-11-444 |
5pvln91x |
0.742121 |
Montgomery_2004, Chang_2011, Sen_D_2018 |
Montgomery_2004, Aziz_2012 |
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Stanstrup_2019 |
The metaRbolomics Toolbox in Bioconductor and beyond |
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2019 |
2019-09-23 |
COMM-USE |
N |
PMC6835268 |
31548506.0 |
10.3390/metabo9100200 |
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0.726300 |
Lu_Q_2006, Montgomery_2004, Kurc_2006 |
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Lefkowitz_2008 |
Virus Databases |
Lefkowitz, E.J.; Odom, M.R.; Upton, C. |
2008 |
2008-12-31 |
PMC |
N |
PMC7150036 |
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10.1016/b978-012374410-4.00719-6 |
60vrlrim |
0.723191 |
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Nakai_1992 |
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Finnie_2016 |
EpiJSON: A unified data-format for epidemiology |
Finnie, Thomas J.R.; South, Andy; Bento, Ana; Sherrard-Smith, Ellie; Jombart, Thibaut |
2016 |
2016-06-30 |
None |
N |
PMC7104924 |
27266846.0 |
10.1016/j.epidem.2015.12.002 |
8gyejoc5 |
0.708363 |
Lu_Q_2006 |
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SNAD: sequence name annotation-based designer |
Sidorov, Igor A; Reshetov, Denis A; Gorbalenya, Alexander E |
2009 |
2009-08-14 |
COMM-USE |
N |
PMC2739203 |
19682364.0 |
10.1186/1471-2105-10-251 |
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0.698929 |
Montgomery_2004, Wang_2006, Lu_Q_2006, UNKNOWN_2018 |
Pessia_2015, Choo_2009, Schäffer_2019 |
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Watson_2007 |
DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data |
Watson, Michael; Dukes, Juliet; Abu-Median, Abu-Bakr; King, Donald P; Britton, Paul |
2007 |
2007-09-14 |
COMM-USE |
N |
PMC2375028 |
17868443.0 |
10.1186/gb-2007-8-9-r190 |
rzzsmuoc |
0.671921 |
Montgomery_2004, Mendizabal-Ruiz_2018, Lee_C_2017 |
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Lee_P_2011 |
Quantitative mapping of scientific research—The case of electrical conducting polymer nanocomposite |
Lee, Pei-Chun; Su, Hsin-Ning |
2011 |
2011-01-31 |
PMC |
N |
PMC7126463 |
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10.1016/j.techfore.2010.06.002 |
vl6gkoin |
0.665538 |
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Su_H_2012 |
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Nagraj_2018 |
epicontacts: Handling, visualisation and analysis of epidemiological contacts |
Nagraj, VP; Randhawa, Nistara; Campbell, Finlay; Crellen, Thomas; Sudre, Bertrand; Jombart, Thibaut |
2018 |
2018-10-11 |
COMM-USE |
N |
PMC6572866 |
31240097.0 |
10.12688/f1000research.14492.2 |
82820j9a |
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UNKNOWN_2018, Lu_Q_2006, Montgomery_2004 |
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Zhang_2007 |
An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data |
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2007 |
2007-11-04 |
NONCOMM |
N |
PMC2239001 |
17984082.0 |
10.1093/nar/gkm903 |
0kkm0tgj |
0.641247 |
UNKNOWN_2016, UNKNOWN_2018, Wang_2006 |
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19 |
UNKNOWN_2018 |
Database resources of the National Center for Biotechnology Information |
None |
2018 |
2018-01-04 |
PMC |
N |
PMC5753372 |
29140470.0 |
10.1093/nar/gkx1095 |
ca6pff0p |
0.624145 |
UNKNOWN_2016 |
UNKNOWN_2016 |
20 |
UNKNOWN_2019 |
UniProt: a worldwide hub of protein knowledge |
None |
2019 |
2019-01-08 |
COMM-USE |
N |
PMC6323992 |
30395287.0 |
10.1093/nar/gky1049 |
pt7v3gb4 |
0.593089 |
UNKNOWN_2018, UNKNOWN_2016 |
Choo_2009, van_Dijk_2008 |
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Bauch_2020 |
Informing epidemic (research) responses in a timely fashion by knowledge management - a Zika virus use case |
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2020 |
2020-04-18 |
BioRxiv |
N |
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10.1101/2020.04.17.044743 |
tbx0ppu8 |
0.592183 |
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Lu_Q_2006 |
KDE Bioscience: Platform for bioinformatics analysis workflows |
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2006 |
2006-08-31 |
PMC |
N |
PMC7106075 |
16260186.0 |
10.1016/j.jbi.2005.09.001 |
ihh521ur |
0.589955 |
Montgomery_2004, Xu_Z_2009 |
Greenbaum_2009, Aziz_2012, Snyder_2006 |
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Araújo_2011 |
A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems |
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2011 |
2011-12-22 |
COMM-USE |
N |
PMC3287582 |
22369688.0 |
10.1186/1471-2164-12-s4-s13 |
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0.585227 |
Lu_Q_2006 |
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Montgomery_2004 |
Sockeye: A 3D Environment for Comparative Genomics |
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2004 |
2004-05-01 |
None |
N |
PMC479126 |
15123592.0 |
10.1101/gr.1890304 |
ts1eb8fk |
0.576977 |
Chang_2011, Wang_2006, Dai_Q_2012 |
Wang_2006, Song_2005 |
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Stokes_1993 |
Computer network for a diagnostic virology laboratory |
Stokes, K.Jerry; Morris, David J.; Klapper, Paul E.; Semple, A.David; Crosdale, Elaine; Corbitt, Gerald |
1993 |
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PMC |
N |
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8106601.0 |
10.1016/0166-0934(93)90113-6 |
eawmuuye |
0.568558 |
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26 |
Pathegama_2005 |
Interactive Real-time Image Analysis System for Distant Operation |
Pathegama, Mahinda P.; Göl, Özdemir |
2005 |
2005-01-01 |
PMC |
N |
PMC7121714 |
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10.1007/0-387-26325-x_3 |
5nc8f3a4 |
0.545885 |
Montgomery_2004, Mendizabal-Ruiz_2018 |
Kylberg_2009, Acar_2016 |
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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 |
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0.545630 |
UNKNOWN_2018 |
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28 |
Wilson_2003 |
Application of data mining techniques in pharmacovigilance |
Wilson, Andrew M; Thabane, Lehana; Holbrook, Anne |
2003 |
2003-09-30 |
PMC |
N |
PMC1884444 |
14748811.0 |
10.1046/j.1365-2125.2003.01968.x |
183n1lrf |
0.544123 |
Collier_2007 |
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Joshi_2020 |
deepMINE - Natural Language Processing based Automatic Literature Mining and Research Summarization for Early-Stage Comprehension in Pandemic Situations specifically for COVID-19 |
Bhrugesh Joshi; Vishvajit Bakarola; Parth Shah; Ramar Krishnamurthy |
2020 |
2020-04-02 |
BioRxiv |
Y |
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10.1101/2020.03.30.014555 |
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Bottomly_2015 |
plethy: management of whole body plethysmography data in R |
Bottomly, Daniel; Wilmot, Beth; McWeeney, Shannon K |
2015 |
2015-04-29 |
None |
N |
PMC4434826 |
25924931.0 |
10.1186/s12859-015-0547-7 |
ermuiujq |
0.529071 |
Lu_Q_2006, Montgomery_2004, Kurc_2006 |
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ViPR: an open bioinformatics database and analysis resource for virology research |
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2011 |
2011-10-17 |
NONCOMM |
N |
PMC3245011 |
22006842.0 |
10.1093/nar/gkr859 |
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0.522020 |
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Pickett_2012 |
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Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community |
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2012 |
2012-11-19 |
COMM-USE |
N |
PMC3509690 |
23202522.0 |
10.3390/v4113209 |
facjsy92 |
0.506552 |
UNKNOWN_2018, Montgomery_2004 |
Pickett_2011 |
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Wu_T_2020 |
Open-source analytics tools for studying the COVID-19 coronavirus outbreak |
Tianzhi Wu; Xijin Ge; Guangchuang Yu; Erqiang Hu |
2020 |
2020-02-27 |
BioRxiv |
N |
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10.1101/2020.02.25.20027433 |
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Santillana_2014 |
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Yang_2007 |
IDBD: Infectious Disease Biomarker Database |
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2007 |
2007-11-03 |
NONCOMM |
N |
PMC2238845 |
17982173.0 |
10.1093/nar/gkm925 |
8cixsjrf |
0.476340 |
Collier_2007, Lu_Q_2006 |
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MMDB: annotating protein sequences with Entrez's 3D-structure database |
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2006 |
2006-11-29 |
NONCOMM |
N |
PMC1751549 |
17135201.0 |
10.1093/nar/gkl952 |
6qpsxmgi |
0.474315 |
UNKNOWN_2016, Montgomery_2004, UNKNOWN_2018 |
Song_2005, Zemla_2011 |
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1984-12-31 |
PMC |
N |
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6380915.0 |
10.1016/0010-4825(84)90033-7 |
83f0ruku |
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UNKNOWN_2018 |
Stokes_1993, Chapman_2004 |
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Sturm_2020 |
Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data |
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2020 |
2020-04-13 |
BioRxiv |
Y |
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10.1101/2020.04.10.035865 |
q6w8zgc3 |
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Montgomery_2004, Kurc_2006 |
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Pérez_2016 |
Glyco3D: A Suite of Interlinked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies, and Glycosyltransferases |
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2016 |
2016-09-08 |
PMC |
N |
PMC7121943 |
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10.1007/978-4-431-56454-6_7 |
1c515h51 |
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Wang_2006, Montgomery_2004, UNKNOWN_2018 |
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A Bioinformatics View of Glycan–Virus Interactions |
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2019 |
2019-04-23 |
COMM-USE |
N |
PMC6521074 |
31018588.0 |
10.3390/v11040374 |
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0.417608 |
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UNKNOWN_2016 |
Database resources of the National Center for Biotechnology Information |
None |
2016 |
2016-01-04 |
PMC |
N |
PMC4702911 |
26615191.0 |
10.1093/nar/gkv1290 |
a564l6vs |
0.415323 |
UNKNOWN_2018 |
UNKNOWN_2018, Aurrecoechea_2017 |
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Spatial and temporal epidemiological analysis in the Big Data era |
Pfeiffer, Dirk U.; Stevens, Kim B. |
2015 |
2015-11-01 |
PMC |
N |
PMC7114113 |
26092722.0 |
10.1016/j.prevetmed.2015.05.012 |
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Coelho_2008 |
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Introduction to 3D Immersive and Interactive Learning |
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PMC |
N |
PMC7122101 |
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10.1007/978-981-4021-90-6_1 |
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Integration of the Gene Ontology into an object-oriented architecture |
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2005-05-10 |
COMM-USE |
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PMC1156866 |
15885145.0 |
10.1186/1471-2105-6-113 |
tv1fx7sy |
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Montgomery_2004, Sen_D_2018, Qi_Z_2018 |
Sathiamurthy_2005, Vella_2017, Nakai_1992 |
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Virus Variation Resource – improved response to emergent viral outbreaks |
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PMC |
N |
PMC5210549 |
27899678.0 |
10.1093/nar/gkw1065 |
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0.370095 |
UNKNOWN_2018, UNKNOWN_2016 |
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Small-angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls |
Jacques, David A; Trewhella, Jill |
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PMC |
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PMC2867006 |
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10.1002/pro.351 |
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Qi_Z_2018, Liou_2013, Chang_2011 |
Chou_2011 |
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NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data |
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COMM-USE |
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PMC3206854 |
22073191.0 |
10.1371/journal.pone.0026781 |
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Liou_2013, Montgomery_2004, Chang_2011 |
Choo_2009, Pessia_2015, Lee_B_2009, Shen_2018 |
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Group Argumentation and Its Analysis on a Highlighted Social Event — Practice of Qualitative Meta-synthesis |
TANG, Xi-jin; LIU, Yi-jun |
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PMC |
N |
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10.1016/s1874-8651(08)60023-x |
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Matsuzaw_2011 |
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COVID19-Tracker: A shiny app to produce comprehensive data visualization for SARS-CoV-2 epidemic in Spain |
Aurelio Tobias; Joan Valls; Pau Satorra; Cristian Tebe |
2020 |
2020-04-06 |
BioRxiv |
Y |
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10.1101/2020.04.01.20049684 |
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Web-based electronic patient records for collaborative medical applications |
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2005-04-30 |
PMC |
N |
PMC7126510 |
15755531.0 |
10.1016/j.compmedimag.2004.09.005 |
srtkqr13 |
0.352592 |
Lu_Q_2006 |
Lapinsky_2004, Freifeld_2008 |
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Chapter 5 The GRANCH Techniques for Analysis of DNA, RNA and Protein Sequences |
Nandy, Ashesh |
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PMC |
N |
PMC7151884 |
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10.1016/b978-1-68108-053-6.50005-3 |
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Sen_D_2018 |
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Viral Infections in Immunocompromised Patients |
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2011 |
2011-01-31 |
None |
N |
PMC3030455 |
21195305.0 |
10.1016/j.bbmt.2010.11.008 |
63ohetih |
0.340328 |
|
|
52 |
Xu_Z_2009 |
CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes |
Xu, Zhao; Hao, Bailin |
2009 |
2009-07-01 |
NONCOMM |
N |
PMC2703908 |
19398429.0 |
10.1093/nar/gkp278 |
02opdk0m |
0.339165 |
Montgomery_2004, Lee_C_2017, Chang_2011 |
Yu_Z_2010 |
53 |
Huang_2011 |
Bioinformatics Resources and Tools for Phage Display |
Huang, Jian; Ru, Beibei; Dai, Ping |
2011 |
2011-01-18 |
COMM-USE |
N |
PMC6259106 |
21245805.0 |
10.3390/molecules16010694 |
407bthqj |
0.333855 |
Lu_Q_2006, Sen_D_2018 |
Huang_2006 |
54 |
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 |
|
10.1007/s10796-009-9158-z |
kt9sbn40 |
0.327509 |
Lee_C_2017, Liou_2013, Saw_A_2019, Qi_Z_2018, Chang_2011 |
Bashir_2020, Wilson_2003, Hu_Y_2006, Wu_Y_2020 |
55 |
Greenbaum_2009 |
Ontology Development for the Immune Epitope Database |
Greenbaum, Jason A.; Vita, Randi; Zarebski, Laura M.; Sette, Alessandro; Peters, Bjoern |
2009 |
2009-08-08 |
PMC |
N |
PMC7121563 |
|
10.1007/978-1-4419-0540-6_4 |
hgxhyg46 |
0.326798 |
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Sathiamurthy_2005 |
56 |
Nooij_2018 |
Overview of Virus Metagenomic Classification Methods and Their Biological Applications |
Nooij, Sam; Schmitz, Dennis; Vennema, Harry; Kroneman, Annelies; Koopmans, Marion P. G. |
2018 |
2018-04-23 |
COMM-USE |
N |
PMC5924777 |
29740407.0 |
10.3389/fmicb.2018.00749 |
s5k59eq8 |
0.323204 |
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57 |
Bekaert_2009 |
Recode-2: new design, new search tools, and many more genes |
Bekaert, Michaël; Firth, Andrew E.; Zhang, Yan; Gladyshev, Vadim N.; Atkins, John F.; Baranov, Pavel V. |
2009 |
2009-09-25 |
NONCOMM |
N |
PMC2808893 |
19783826.0 |
10.1093/nar/gkp788 |
8y8ho2x5 |
0.314031 |
Lee_C_2017 |
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58 |
Huang_2006 |
MIMOX: a web tool for phage display based epitope mapping |
Huang, Jian; Gutteridge, Alex; Honda, Wataru; Kanehisa, Minoru |
2006 |
2006-10-12 |
COMM-USE |
N |
PMC1618411 |
17038191.0 |
10.1186/1471-2105-7-451 |
1ypgij14 |
0.309291 |
Montgomery_2004, Lee_C_2017, Lu_Q_2006, Chang_2011, Qi_Z_2018 |
Mayrose_2007 |
59 |
Bos_L_2014 |
How integration of global omics-data could help preparing for pandemics – a scent of influenza |
Bos, Lieuwe D. J.; de Jong, Menno D.; Sterk, Peter J.; Schultz, Marcus J. |
2014 |
2014-04-22 |
COMM-USE |
N |
PMC4000993 |
24795745.0 |
10.3389/fgene.2014.00080 |
kusjwue0 |
0.308722 |
Collier_2007, Vazquez_2020 |
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60 |
Brodie_2004 |
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments |
Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris |
2004 |
2004-07-14 |
PMC |
N |
PMC481056 |
15253776.0 |
10.1186/1471-2105-5-96 |
lwla5ugt |
0.306893 |
Montgomery_2004, Chang_2011, Lee_C_2017, Wang_2006 |
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61 |
John_2019 |
Shiny Framework Based Visualization and Analytics Tool for Middle East Respiratory Syndrome |
John, Maya; Shaiba, Hadil |
2019 |
2019-12-04 |
PMC |
N |
PMC7122755 |
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10.1007/978-3-030-36365-9_16 |
r7tg0s45 |
0.303885 |
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62 |
Collier_2007 |
A multilingual ontology for infectious disease surveillance: rationale, design and challenges |
Collier, Nigel; Kawazoe, Ai; Jin, Lihua; Shigematsu, Mika; Dien, Dinh; Barrero, Roberto A.; Takeuchi, Koichi; Kawtrakul, Asanee |
2007 |
2007-06-26 |
PMC |
N |
PMC7087677 |
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10.1007/s10579-007-9019-7 |
4524vg4x |
0.300365 |
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Keller_2009 |