| 1 |
Li_D_2019 |
Conserved microsatellites may contribute to stem-loop structures in 5′, 3′ terminals of Ebolavirus genomes |
Li, Douyue; Zhang, Hongxi; Peng, Shan; Pan, Saichao; Tan, Zhongyang |
2019 |
2019-06-30 |
PMC |
N |
PMC7092875 |
31078274.0 |
10.1016/j.bbrc.2019.04.192 |
n46p8acw |
0.955499 |
Auewarakul_2005, Lamb_1991, Hyde_2015, Rice_1992 |
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| 2 |
Zhang_2013 |
Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce |
Zhang, Boyu; Yehdego, Daniel T; Johnson, Kyle L; Leung, Ming-Ying; Taufer, Michela |
2013 |
2013-11-08 |
COMM-USE |
N |
PMC3952952 |
24564983.0 |
10.1186/1472-6807-13-s1-s3 |
p1i7bx94 |
0.925023 |
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Low_J_2010 |
| 3 |
Backofen_2013 |
Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures |
Backofen, Rolf; Fricke, Markus; Marz, Manja; Qin, Jing; Stadler, Peter F. |
2013 |
2013-01-01 |
PMC |
N |
PMC7114971 |
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10.1007/978-3-642-40453-5_10 |
p46abodr |
0.912465 |
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Qin_J_2014, Borodavka_2016, Fricke_2019 |
| 4 |
Qin_J_2014 |
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures |
Qin, Jing; Fricke, Markus; Marz, Manja; Stadler, Peter F; Backofen, Rolf |
2014 |
2014-09-11 |
None |
N |
PMC4181469 |
25285153.0 |
10.1186/1748-7188-9-19 |
bifebnwt |
0.905115 |
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Backofen_2013, Borodavka_2016, Fricke_2019 |
| 5 |
Low_J_2010 |
SHAPE-Directed RNA Secondary Structure Prediction |
Low, Justin T.; Weeks, Kevin M. |
2010 |
2010-10-01 |
PMC |
N |
PMC2941709 |
20554050.0 |
10.1016/j.ymeth.2010.06.007 |
tv8hi2wy |
0.826445 |
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Yang_2015, Kolchanov_1996 |
| 6 |
Gao_J_2010 |
Inverse folding of RNA pseudoknot structures |
Gao, James ZM; Li, Linda YM; Reidys, Christian M |
2010 |
2010-06-23 |
COMM-USE |
N |
PMC2909241 |
20573197.0 |
10.1186/1748-7188-5-27 |
1lojd0xa |
0.826148 |
Staple_2005, Dost_2006 |
Guo_Y_2013 |
| 7 |
Dost_2006 |
Structural Alignment of Pseudoknotted RNA |
Dost, Banu; Han, Buhm; Zhang, Shaojie; Bafna, Vineet |
2006 |
2006-01-01 |
PMC |
N |
PMC7121381 |
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10.1007/11732990_13 |
a5htfx76 |
0.779868 |
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| 8 |
Borodavka_2016 |
Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures |
Borodavka, Alexander; Singaram, Surendra W.; Stockley, Peter G.; Gelbart, William M.; Ben-Shaul, Avinoam; Tuma, Roman |
2016 |
2016-11-15 |
None |
N |
PMC5113152 |
27851933.0 |
10.1016/j.bpj.2016.10.014 |
7jdh882a |
0.769802 |
Staple_2005, Wu_B_2009, Stork_2011 |
Baric_1987 |
| 9 |
Rangan_2020 |
De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery |
Ramya Rangan; Andrew M. Watkins; Wipapat Kladwang; Rhiju Das |
2020 |
2020-04-15 |
BioRxiv |
Y |
|
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10.1101/2020.04.14.041962 |
7gm92gau |
0.757971 |
Morikawa_1992, Lamb_1991, Staple_2005, Hyde_2015 |
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| 10 |
Seemann_2008 |
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments |
Seemann, Stefan E.; Gorodkin, Jan; Backofen, Rolf |
2008 |
2008-10-04 |
None |
N |
PMC2582601 |
18836192.0 |
10.1093/nar/gkn544 |
wtvfow2f |
0.750948 |
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Fricke_2019 |
| 11 |
Limanskaya_2013 |
Search for the new potential RNA thermometers in the genome of Salmonella enterica |
Limanskaya, O. Yu.; Murtazaeva, L. A.; Limanskii, A. P. |
2013 |
2013-02-17 |
PMC |
N |
PMC7089039 |
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10.1134/s0026261713010062 |
gpz7giuv |
0.729715 |
Rice_1992, Staple_2005, Payne_2017, Stork_2011, Auewarakul_2005 |
Limanskaya_2013 |
| 12 |
Baranov_2009 |
Sequences Promoting Recoding Are Singular Genomic Elements |
Baranov, Pavel V.; Gurvich, Olga |
2009 |
2009-07-21 |
PMC |
N |
PMC7122551 |
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10.1007/978-0-387-89382-2_14 |
tzn5y0z2 |
0.726516 |
Li_D_2019 |
Firth_2011 |
| 13 |
Chen_2015 |
Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints |
Chen, Jonathan\nL.; Bellaousov, Stanislav; Tubbs, Jason D.; Kennedy, Scott D.; Lopez, Michael J.; Mathews, David H.; Turner, Douglas H. |
2015 |
2015-10-09 |
None |
N |
PMC4666457 |
26451676.0 |
10.1021/acs.biochem.5b00833 |
6mb9w76f |
0.702515 |
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Cornish_2006, Low_J_2010 |
| 14 |
Wu_T_2009 |
IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico |
Wu, Tzong-Yuan; Hsieh, Chi-Chun; Hong, Jun-Jie; Chen, Chung-Yung; Tsai, Yuh-Show |
2009 |
2009-05-27 |
COMM-USE |
N |
PMC2698906 |
19473520.0 |
10.1186/1471-2105-10-160 |
wt0lvhfl |
0.684492 |
Martínez-Salas_2008, Lamb_1991 |
Hong_2013, Fajardo_2012, Yang_2015 |
| 15 |
Limanskaya_2013 |
Potential thermosensitive riboswitches in the genome of Salmonella |
Limanskaya, O. Yu.; Murtazaeva, L. A.; Limanskii, A. P. |
2013 |
2013-10-11 |
PMC |
N |
PMC7089174 |
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10.3103/s009545271305006x |
7fbzbxa2 |
0.673653 |
Rice_1992, Staple_2005, Stork_2011, Liu_Y_2009, Gorbalenya_1988 |
Limanskaya_2013 |
| 16 |
Bartas_2020 |
In-depth Bioinformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles |
Martin Bartas; Václav Brázda; Natália Bohálová; Alessio Cantara; Adriana Volná; Tereza Stachurová; Kateřina Malachová; Eva B. Jagelská; Otília Porubiaková; Jiří Červeň; Petr Pečinka |
2020 |
2020-04-11 |
BioRxiv |
Y |
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10.1101/2020.04.09.031252 |
d3q0xel1 |
0.665517 |
Hyde_2015, Liu_Y_2009, Gorbalenya_1988, Krause_1987 |
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| 17 |
Hong_2013 |
Viral IRES Prediction System - a Web Server for Prediction of the IRES Secondary Structure In Silico |
Hong, Jun-Jie; Wu, Tzong-Yuan; Chang, Tsair-Yuan; Chen, Chung-Yung |
2013 |
2013-11-05 |
COMM-USE |
N |
PMC3818432 |
24223923.0 |
10.1371/journal.pone.0079288 |
7pdh7alh |
0.661155 |
Martínez-Salas_2008, Morikawa_1992, Wu_T_2009, Landry_2009 |
Wu_T_2009, Fajardo_2012 |
| 18 |
Taufer_2008 |
RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology |
Taufer, Michela; Leung, Ming-Ying; Solorio, Thamar; Licon, Abel; Mireles, David; Araiza, Roberto; Johnson, Kyle L. |
2008 |
2008-11-30 |
PMC |
N |
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10.1016/j.parco.2008.08.002 |
wouunr5s |
0.653512 |
Wu_B_2009, Martínez-Salas_2008 |
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| 19 |
Dedepsidis_2010 |
Correlation between recombination junctions and RNA secondary structure elements in poliovirus Sabin strains |
Dedepsidis, Evaggelos; Kyriakopoulou, Zaharoula; Pliaka, Vaia; Markoulatos, Panayotis |
2010 |
2010-07-17 |
PMC |
N |
PMC7089419 |
20640496.0 |
10.1007/s11262-010-0512-5 |
5hm0jr7u |
0.634349 |
Auewarakul_2005, Rice_1992 |
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| 20 |
Burton_2016 |
The elusive quest for RNA knots |
Burton, Aaron S.; Di Stefano, Marco; Lehman, Niles; Orland, Henri; Micheletti, Cristian |
2016 |
2016-02-01 |
NONCOMM |
N |
PMC4829277 |
26828280.0 |
10.1080/15476286.2015.1132069 |
s3tdllby |
0.601396 |
Staple_2005, Liu_Y_2009, Pleij_1994 |
Borodavka_2016 |
| 21 |
Czech_2019 |
Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes |
Czech, Andreas; Konarev, Petr V.; Goebel, Ingrid; Svergun, Dmitri I.; Wills, Peter R.; Ignatova, Zoya |
2019 |
2019-02-21 |
None |
N |
PMC6384910 |
30792490.0 |
10.1038/s41598-019-39213-2 |
xmgkpk0b |
0.579048 |
Morikawa_1992, Atkins_1999, Pong_2011, Krause_1987, Guo_Y_2013 |
Marcheschi_2007, Marczinke_1998 |
| 22 |
Yang_2019 |
G-Quadruplex DNA and RNA |
Yang, Danzhou |
2019 |
2019-08-23 |
PMC |
N |
PMC7121297 |
31444741.0 |
10.1007/978-1-4939-9666-7_1 |
9yj7j4ba |
0.542283 |
Staple_2005, Pleij_1994, Liu_Y_2009, Stork_2011 |
Masante_2015 |
| 23 |
Tengs_2013 |
A mobile genetic element with unknown function found in distantly related viruses |
Tengs, Torstein; Kristoffersen, Anja Bråthen; Bachvaroff, Tsvetan R; Jonassen, Christine Monceyron |
2013 |
2013-04-25 |
COMM-USE |
N |
PMC3653767 |
23618040.0 |
10.1186/1743-422x-10-132 |
zk18gi8x |
0.523546 |
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| 24 |
Kolchanov_1996 |
Chemical and Computer Probing of RNA Structure 1 |
Kolchanov, N.A.; Titov, I.I.; Vlassova, I.E.; Vlassov, V.V. |
1996 |
1996-12-31 |
PMC |
N |
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8650302.0 |
10.1016/s0079-6603(08)60144-0 |
xuxlw4c0 |
0.522855 |
Staple_2005, Wu_B_2009, Stork_2011, Martínez-Salas_2008 |
Byszewska_2015 |
| 25 |
Madhugiri_2018 |
Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions |
Madhugiri, Ramakanth; Karl, Nadja; Petersen, Daniel; Lamkiewicz, Kevin; Fricke, Markus; Wend, Ulrike; Scheuer, Robina; Marz, Manja; Ziebuhr, John |
2018 |
2018-04-30 |
None |
N |
PMC7112051 |
29223446.0 |
10.1016/j.virol.2017.11.025 |
a1sf3r5e |
0.522668 |
Rice_1992, Pong_2011, Stork_2011 |
Yang_2015 |
| 26 |
Opuu_2017 |
Computational design of fully overlapping coding schemes for protein pairs and triplets |
Opuu, Vaitea; Silvert, Martin; Simonson, Thomas |
2017 |
2017-11-20 |
COMM-USE |
N |
PMC5696523 |
29158504.0 |
10.1038/s41598-017-16221-8 |
d86hnox1 |
0.521853 |
Krause_1987, Morikawa_1992, Firth_2009 |
Firth_2009, Lin_T_2004, Goldberg_1991 |
| 27 |
Wilson_1988 |
Crossover regions in foot-and-mouth disease virus (FMDV) recombinants correspond to regions of high local secondary structure |
Wilson, Valerie; Taylor, P.; Desselberger, U. |
1988 |
1988-01-01 |
PMC |
N |
PMC7086634 |
2848475.0 |
10.1007/bf01315570 |
bcmli6gj |
0.505067 |
Luytjes_1988 |
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| 28 |
Liu_C_2017 |
Complemented palindrome small RNAs first discovered from SARS coronavirus |
Chang Liu; Ze Chen; Wenyuan Shen; Deshui Yu; Siyu Li; Yue Hu; Haishuo Ji; Wenjun Bu; Qingsong Wang; Shan Gao |
2017 |
2017-09-07 |
BioRxiv |
N |
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10.1101/185876 |
g55d5ijx |
0.504951 |
Rice_1992, Auewarakul_2005, Krause_1987 |
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| 29 |
Gibbs_2004 |
The phylogeny of SARS coronavirus |
Gibbs, A. J.; Gibbs, M. J.; Armstrong, J. S. |
2004 |
2004-01-05 |
PMC |
N |
PMC7086792 |
14991447.0 |
10.1007/s00705-003-0244-0 |
wr7vrild |
0.482950 |
Rice_1992 |
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| 30 |
Wu_B_2013 |
Global Organization of a Positive-strand RNA Virus Genome |
Wu, Baodong; Grigull, Jörg; Ore, Moriam O.; Morin, Sylvie; White, K. Andrew |
2013 |
2013-05-23 |
COMM-USE |
N |
PMC3662671 |
23717202.0 |
10.1371/journal.ppat.1003363 |
vx0nc8io |
0.482599 |
Wu_B_2009, Martínez-Salas_2008, Rice_1992 |
Adams_2003 |
| 31 |
Monceyron_2014 |
Molecular characterisation of the 3′-end of the astrovirus genome |
Monceyron, C.; Grinde, B.; Jonassen, T. Ø. |
2014 |
2014-04-02 |
PMC |
N |
PMC7087294 |
9170498.0 |
10.1007/s007050050112 |
a8g3hba9 |
0.471526 |
Luytjes_1988, Auewarakul_2005, Rice_1992, Gorbalenya_1988 |
Godeny_1990, Lapps_1987, Goldberg_1991, Lin_T_2004 |
| 32 |
De_Nova-Ocampo_2018 |
Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins |
De Nova-Ocampo, Mónica; Soliman, Mayra Cristina; Espinosa-Hernández, Wendy; Velez-del Valle, Cristina; Salas-Benito, Juan; Valdés-Flores, Jesús; García-Morales, Lorena |
2018 |
2018-11-17 |
PMC |
N |
PMC7089336 |
30448895.0 |
10.1007/s11033-018-4498-8 |
e99fw336 |
0.465828 |
Hyde_2015, Lamb_1991, Morikawa_1992 |
Gutiérrez-Escolano_2003 |
| 33 |
Kai_Z_2019 |
An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots |
Kai, Zhang; Yuting, Wang; Yulin, Lv; Jun, Liu; Juanjuan, He |
2019 |
2019-12-27 |
COMM-USE |
N |
PMC6933665 |
31881969.0 |
10.1186/s12864-019-6300-2 |
9z8z03rp |
0.452326 |
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Yang_2015 |
SHAPE analysis of the RNA secondary structure of the Mouse Hepatitis Virus 5’ untranslated region and N-terminal nsp1 coding sequences |
Yang, Dong; Liu, Pinghua; Wudeck, Elyse V.; Giedroc, David P.; Leibowitz, Julian L. |
2015 |
2015-01-15 |
PMC |
N |
PMC4280293 |
25462342.0 |
10.1016/j.virol.2014.11.001 |
cciyb05w |
0.420151 |
Stork_2011, Rice_1992, Pong_2011, Lin_X_2015, Banerjee_2001 |
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| 35 |
Le_S_1992 |
Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses |
Le, Shu-Yun; Chen, Jih-H.; Sonenberg, Nahum; Maizel, Jacob V. |
1992 |
1992-12-31 |
PMC |
N |
PMC7131026 |
1333125.0 |
10.1016/0042-6822(92)90261-m |
diwm1940 |
0.416935 |
Morikawa_1992, Krause_1987, Firth_2009, Luytjes_1988, Gorbalenya_1988 |
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Chastain_1991 |
Structural Elements in RNA |
Chastain, Michael; Tinoco, Ignacio |
1991 |
1991-12-31 |
PMC |
N |
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10.1016/s0079-6603(08)60008-2 |
4eu9v5d3 |
0.391925 |
Staple_2005, Liu_Y_2009, Martínez-Salas_2008 |
Kolchanov_1996 |
| 37 |
Marr_2003 |
Mismatch Extension During Strong Stop Strand Transfer and Minimal Homology Requirements for Replicative Template Switching During Moloney Murine Leukemia Virus Replication |
Marr, Sharon Fodor; Telesnitsky, Alice |
2003 |
2003-07-18 |
PMC |
N |
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12850138.0 |
10.1016/s0022-2836(03)00597-7 |
47okncdw |
0.386109 |
Morikawa_1992, Stork_2011, Masante_2015, Rice_1992 |
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Pillai-Nair_2003 |
Cis-acting Regulatory Elements in the Potato Virus X 3′ Non-translated Region Differentially Affect Minus-strand and Plus-strand RNA Accumulation |
Pillai-Nair, Neeta; Kim, Kook-Hyung; Hemenway, Cynthia |
2003 |
2003-02-21 |
PMC |
N |
PMC7126608 |
12581634.0 |
10.1016/s0022-2836(02)01369-4 |
ppjohov8 |
0.372487 |
Chen_2013, Banerjee_2001, Stork_2011, Chen_2017 |
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Fricke_2019 |
Global importance of RNA secondary structures in protein-coding sequences |
Fricke, Markus; Gerst, Ruman; Ibrahim, Bashar; Niepmann, Michael; Marz, Manja |
2019 |
2019-02-15 |
PMC |
N |
PMC7109657 |
30101307.0 |
10.1093/bioinformatics/bty678 |
213ly4xo |
0.372027 |
Morikawa_1992, Krause_1987, Firth_2009, Hatfield_1990 |
Samal_2013 |
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Li_L_2008 |
Structural Lability in Stem–Loop 1 Drives a 5′ UTR–3′ UTR Interaction in Coronavirus Replication |
Li, Lichun; Kang, Hyojeung; Liu, Pinghua; Makkinje, Nick; Williamson, Shawn T.; Leibowitz, Julian L.; Giedroc, David P. |
2008 |
2008-03-28 |
None |
N |
PMC2652258 |
18289557.0 |
10.1016/j.jmb.2008.01.068 |
lorveab5 |
0.370440 |
Morikawa_1992, Krause_1987, Brierley_1989, Lamb_1991 |
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Bekaert_2005 |
An Extended Signal Involved in Eukaryotic −1 Frameshifting Operates through Modification of the E Site tRNA |
Bekaert, Michaël; Rousset, Jean-Pierre |
2005 |
2005-01-07 |
PMC |
N |
PMC7129640 |
15629717.0 |
10.1016/j.molcel.2004.12.009 |
yf8fvx7k |
0.354125 |
Morikawa_1992, Hatfield_1990, Krause_1987, Lamb_1991, Gorbalenya_1988 |
Li_L_2001, Gopinath_2015 |
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King_1985 |
Multiple sites of recombination within the RNA genome of foot-and-mouth disease virus |
King, Andrew M.Q.; McCahon, David; Saunders, Keith; Newman, John W.I.; Slade, William R. |
1985 |
1985-11-30 |
PMC |
N |
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3000107.0 |
10.1016/0168-1702(85)90437-x |
6y452g44 |
0.344584 |
Rice_1992, Auewarakul_2005 |
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Jang_2008 |
Isolation of inhibitory RNA aptamers against severe acute respiratory syndrome (SARS) coronavirus NTPase/Helicase |
Jang, Kyoung Jin; Lee, Na-Ra; Yeo, Woon-Seok; Jeong, Yong-Joo; Kim, Dong-Eun |
2008 |
2008-02-15 |
PMC |
N |
PMC7092905 |
18082623.0 |
10.1016/j.bbrc.2007.12.020 |
98ebhx0b |
0.326576 |
Stork_2011, Banerjee_2001, Lin_X_2015, Pong_2011, Gorbalenya_1988 |
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Usui_2015 |
A design principle for a single-stranded RNA genome that replicates with less double-strand formation |
Usui, Kimihito; Ichihashi, Norikazu; Yomo, Tetsuya |
2015 |
2015-09-18 |
NONCOMM |
N |
PMC4652763 |
26202975.0 |
10.1093/nar/gkv742 |
znhvdtg8 |
0.325668 |
Stork_2011, Rice_1992, Payne_2017, Wu_B_2009 |
Adams_2003 |
| 45 |
Xu_J_2016 |
Genome Organization of the SARS-CoV |
Xu, Jing; Hu, Jianfei; Wang, Jing; Han, Yujun; Hu, Yongwu; Wen, Jie; Li, Yan; Ji, Jia; Ye, Jia; Zhang, Zizhang; Wei, Wei; Li, Songgang; Wang, Jun; Wang, Jian; Yu, Jun; Yang, Huanming |
2016 |
2016-11-28 |
None |
N |
PMC5172239 |
15629035.0 |
10.1016/s1672-0229(03)01028-3 |
i738t9lf |
0.316197 |
Morikawa_1992, Lamb_1991, Luytjes_1988, Firth_2009 |
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Goldsmith_2016 |
Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets |
Goldsmith, Gunaseelan; Rathinavelan, Thenmalarchelvi; Yathindra, Narayanarao |
2016 |
2016-03-24 |
COMM-USE |
N |
PMC4807104 |
27010368.0 |
10.1371/journal.pone.0152102 |
tqx420oa |
0.316047 |
Kierzek_2006, Guo_Y_2013, Brierley_1991 |
Cornish_2006 |
| 47 |
Chen_2010 |
Group-specific structural features of the 5′-proximal sequences of coronavirus genomic RNAs |
Chen, Shih-Cheng; Olsthoorn, René C.L. |
2010 |
2010-05-25 |
PMC |
N |
PMC7111916 |
20202661.0 |
10.1016/j.virol.2010.02.007 |
obes9kjl |
0.313012 |
Gorbalenya_1988, Morikawa_1992, Luytjes_1988, Firth_2009, Hyde_2015 |
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Robertson_2004 |
The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome |
Robertson, Michael P; Igel, Haller; Baertsch, Robert; Haussler, David; Ares, Manuel; Scott, William G |
2004 |
2004-12-28 |
COMM-USE |
N |
PMC539059 |
15630477.0 |
10.1371/journal.pbio.0030005 |
p7um7o87 |
0.303321 |
Pong_2011, Gorbalenya_1988, Wu_B_2009, Stork_2011, Rice_1992 |
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