Topic 10 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 25 - 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 ponti_2018 A method for RNA structure prediction shows evidence for structure in lncRNAs Riccardo Delli ponti; Alexandros Armaos; Stefanie Marti; Gian Gaetano Tartaglia 2018 2018-04-16 BioRxiv N 10.1101/284869 jb447ndz 0.824928 Chang_2011, Saw_A_2019, Liao_2006, Qi_Z_2018, Dai_Q_2012 Delli_Ponti_2018, Sperschneider_2012
2 Delli_Ponti_2018 A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs Delli Ponti, Riccardo; Armaos, Alexandros; Marti, Stefanie; Tartaglia, Gian Gaetano 2018 2018-12-03 COMM-USE N PMC6286970 30560136.0 10.3389/fmolb.2018.00111 scn7b4c6 0.810154 Chang_2011, Saw_A_2019, Liao_2006, Qi_Z_2018, Dai_Q_2012 ponti_2018
3 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 0.793799 Liao_2006, Chang_2011, Dai_Q_2012, Dawson_2007
4 Tagashira_2020 PhyloFold: Precise and Swift Prediction of RNA Secondary Structures to Incorporate Phylogeny among Homologs Masaki Tagashira 2020 2020-03-06 BioRxiv N 10.1101/2020.03.05.975797 l72x4wn3 0.778935 Lee_C_2017, Chang_2011, Saw_A_2019, Qi_Z_2018, Dai_Q_2012 Sperschneider_2012, Zhang_2013, Choo_2009
5 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 0.737691 Wu_T_2009 Wu_T_2009
6 Sperschneider_2010 DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model Sperschneider, Jana; Datta, Amitava 2010 2010-01-31 NONCOMM N PMC2853144 20123730.0 10.1093/nar/gkq021 q26f8pv4 0.726748 Lee_C_2017, Dawson_2007, Dai_Q_2012, Song_2005 Sperschneider_2012, Reeder_2007, Kai_Z_2019
7 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 0.721104 Chang_2011, Saw_A_2019, Lee_C_2017, Dai_Q_2012, Qi_Z_2018 Suresh_2015, Sperschneider_2012
8 Vila_2018 (13)C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information Vila, Jorge A.; Arnautova, Yelena A. 2018 2018-07-20 PMC N PMC7123919 10.1007/978-3-319-95843-9_20 gytg4iku 0.686326 Qi_Z_2018, Kirillova_2009, Plewczyński_2008, Chang_2011 Vila_2014
9 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 0.683653 Lee_C_2017 Hong_2013
10 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 0.667477 Dawson_2007, Chang_2011, Qi_Z_2018
11 Janssen_2015 The RNA shapes studio Janssen, Stefan; Giegerich, Robert 2015 2015-02-01 COMM-USE N PMC4308662 25273103.0 10.1093/bioinformatics/btu649 5igorndt 0.645316 Montgomery_2004, Wang_2006, Lee_C_2017, Chang_2011 Gao_J_2010, Reeder_2007, Sperschneider_2012
12 Vila_2014 (13)C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information Vila, Jorge A.; Arnautova, Yelena A. 2014 2014-01-01 PMC N PMC7121069 10.1007/978-3-642-28554-7_19 jz2mrn4t 0.629744 Qi_Z_2018, Kirillova_2009, Plewczyński_2008, Chang_2011 Vila_2018
13 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 0.626505 Chang_2011, Saw_A_2019, Lee_C_2017, Qi_Z_2018, Dai_Q_2012
14 Liu_C_2005 Profiling and Searching for RNA Pseudoknot Structures in Genomes Liu, Chunmei; Song, Yinglei; Malmberg, Russell L.; Cai, Liming 2005 2005-01-01 PMC N PMC7120494 10.1007/11567752_2 jms7hrmp 0.618832 Chang_2011, Liu_C_2005, Dai_Q_2012, Saw_A_2019 Liu_C_2005
15 Jabbari_2014 A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures Jabbari, Hosna; Condon, Anne 2014 2014-05-18 COMM-USE N PMC4064103 24884954.0 10.1186/1471-2105-15-147 u14tj0so 0.604465 Saw_A_2019, Lee_C_2017, Qi_Z_2018, Chang_2011, Dai_Q_2012 Sperschneider_2012, Kai_Z_2019
16 Dawson_2007 Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding Dawson, Wayne K.; Fujiwara, Kazuya; Kawai, Gota 2007 2007-09-19 None N PMC1975678 17878940.0 10.1371/journal.pone.0000905 9zm4per4 0.583955 Chang_2011, Qi_Z_2018 Sperschneider_2012
17 Sadreyev_2003 Profile–profile comparisons by COMPASS predict intricate homologies between protein families Sadreyev, Ruslan I.; Baker, David; Grishin, Nick V. 2003 2003-10-23 PMC N PMC2366929 14500884.0 iomwwsud 0.571006 Saw_A_2019, Lee_C_2017, Chang_2011, Qi_Z_2018 Zemla_2011
18 Vila_2010 Sequential nearest-neighbor effects on computed (13)C(α) chemical shifts Vila, Jorge A.; Serrano, Pedro; Wüthrich, Kurt; Scheraga, Harold A. 2010 2010-07-20 None N PMC2970923 20644980.0 10.1007/s10858-010-9435-7 1t433pfu 0.562064 Liao_2006, Qi_Z_2018, Saw_A_2019
19 Sperschneider_2012 Predicting pseudoknotted structures across two RNA sequences Sperschneider, Jana; Datta, Amitava; Wise, Michael J. 2012 2012-12-01 COMM-USE N PMC3516145 23044552.0 10.1093/bioinformatics/bts575 iuglkdcp 0.555985 Wang_2006, Lee_C_2017, Dawson_2007, Montgomery_2004 Kai_Z_2019
20 Mead_2019 Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling Mead, Dylan J.T.; Lunagomez, Simón; Gatherer, Derek 2019 2019-11-30 PMC N PMC7110651 31377535.0 10.1016/j.jmgm.2019.07.014 azpg5yrh 0.552688 Chang_2011, Saw_A_2019, Lee_C_2017, Zheng_2008, Dai_Q_2012 Zemla_2011, Li_C_2018, Suresh_2015
21 Lu_C_2005 A memory-efficient algorithm for multiple sequence alignment with constraints Lu, Chin Lung; Huang, Yen Pin 2005 2005-01-01 PMC N PMC7109922 15374876.0 10.1093/bioinformatics/bth468 e9app2cv 0.547978 Lee_C_2017, Chang_2011, Saw_A_2019, Dai_Q_2012, Qi_Z_2018 Song_2005, Chung_2007, Pessia_2015, Kai_Z_2019
22 Li_M_2015 Predicting RNA Secondary Structures: One-grammar-fits-all Solution Li, Menglu; Cheng, Micheal; Ye, Yongtao; Hon, Wk; Ting, Hf; Lam, Tw; Tang, Cy; Wong, Thomas; Yiu, Sm 2015 2015-01-01 PMC N PMC7121278 10.1007/978-3-319-19048-8_18 p8puu1jk 0.546844 Lee_C_2017, Chang_2011, Qi_Z_2018, Saw_A_2019 Gao_J_2010
23 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 0.545533 Saw_A_2019, Chang_2011, Qi_Z_2018 Kai_Z_2018, Sperschneider_2012
24 Zhao_2013 SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P.; Marth, Gabor T. 2013 2013-12-04 COMM-USE N PMC3852983 24324759.0 10.1371/journal.pone.0082138 6f1vqkqm 0.540064 Lee_C_2017, Montgomery_2004, Lu_Q_2006 Lu_C_2005, Reeder_2007
25 Bendaña_2008 Colorstock, SScolor, Ratón: RNA alignment visualization tools Bendaña, Yuri R.; Holmes, Ian H. 2008 2008-02-15 PMC N PMC7109877 18218657.0 10.1093/bioinformatics/btm635 r9diwa8y 0.533783 UNKNOWN_2018, UNKNOWN_2016, Montgomery_2004 Reeder_2007
26 Delli Ponti_2017 A high-throughput approach to profile RNA structure Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano 2017 2017-03-17 NONCOMM N PMC5389523 27899588.0 10.1093/nar/gkw1094 k23xlzj0 0.533647 Saw_A_2019, Wang_2006, Dai_Q_2012
27 Reeder_2007 pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows Reeder, Jens; Steffen, Peter; Giegerich, Robert 2007 2007-05-03 NONCOMM N PMC1933184 17478505.0 10.1093/nar/gkm258 zgv4kd6j 0.518743 Lu_Q_2006, Montgomery_2004, UNKNOWN_2018, Wang_2006, Lee_C_2017 Sperschneider_2012
28 Liu_C_2005 Profiling and Searching for RNA Pseudoknot Structures in Genomes Liu, Chunmei; Song, Yinglei; Malmberg, Russell L.; Cai, Liming 2005 2005-01-01 PMC N PMC7122704 10.1007/11428848_123 egbkl2v2 0.515520 Liu_C_2005, Chang_2011, Dai_Q_2012, Saw_A_2019 Liu_C_2005
29 Kai_Z_2018 A Novel Efficient Simulated Annealing Algorithm for the RNA Secondary Structure Predicting with Pseudoknots Kai, Zhang; Yulin, Lv 2018 2018-07-06 PMC N PMC7121944 10.1007/978-3-319-95933-7_44 jxgd1yc4 0.504126 Qi_Z_2018, Chang_2011, Lee_C_2017, Saw_A_2019 Kai_Z_2019
30 Reeder_2006 Beyond Mfold: Recent advances in RNA bioinformatics Reeder, Jens; Höchsmann, Matthias; Rehmsmeier, Marc; Voss, Björn; Giegerich, Robert 2006 2006-06-25 PMC N PMC7125698 16530285.0 10.1016/j.jbiotec.2006.01.034 qgit5qqo 0.486719 Montgomery_2004, Dawson_2007
31 Song_2005 Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment Song, Yinglei; Liu, Chunmei; Huang, Xiuzhen; Malmberg, Russell L.; Xu, Ying; Cai, Liming 2005 2005-01-01 PMC N PMC7121179 10.1007/11557067_31 gjild96e 0.484580 Chang_2011, Qi_Z_2018, Dai_Q_2012, Saw_A_2019
32 Heal_2018 Applying graph theory to protein structures: an Atlas of coiled coils Heal, Jack W; Bartlett, Gail J; Wood, Christopher W; Thomson, Andrew R; Woolfson, Derek N 2018 2018-10-01 COMM-USE N PMC6157074 29722888.0 10.1093/bioinformatics/bty347 pq1vaknj 0.437459 Wang_2006, Montgomery_2004, Lee_C_2017, Qi_Z_2018, Lu_Q_2006 Song_2005, Munteanu_2008, van_Dijk_2008
33 Chung_2007 RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints Chung, Yun-Sheng; Lee, Wei-Hsun; Tang, Chuan Yi; Lu, Chin Lung 2007 2007-05-08 NONCOMM N PMC1933182 17488842.0 10.1093/nar/gkm275 cjcvm3x7 0.425949 Lee_C_2017, Chang_2011, Qi_Z_2018, Dai_Q_2012, Kirillova_2009 Lu_C_2005, Song_2005, Zemla_2011, Altschul_1991
34 Zemla_2011 StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L 2011 2011-06-02 COMM-USE N PMC3121648 21635786.0 10.1186/1471-2105-12-226 s7kzp795 0.364098 Chang_2011, Lee_C_2017, Qi_Z_2018, Saw_A_2019
35 Heo_L_2020 Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement Lim Heo; Michael Feig 2020 2020-03-28 BioRxiv Y 10.1101/2020.03.25.008904 9qv11m4f 0.335310 Saw_A_2019, Lee_C_2017, Chang_2011, Dai_Q_2012, Qi_Z_2018
36 Roy_R_2007 3.36 Application of Multivalent Mannosylated Dendrimers in Glycobiology Roy, R.; Touaibia, M. 2007 2007-12-31 PMC N PMC7152399 10.1016/b978-044451967-2/00112-4 zj1fvery 0.306352