Topic 04 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 47 - 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 Domingo_2016 Chapter 4 Interaction of Virus Populations with Their Hosts Domingo, Esteban 2016 2016-12-31 PMC N PMC7150142 10.1016/b978-0-12-800837-9.00004-6 bl5bagvg 0.978378 Domingo_2020 Domingo_2020
2 Domingo_2020 Chapter 4 Interaction of virus populations with their hosts Domingo, Esteban 2020 2020-12-31 PMC N PMC7153317 10.1016/b978-0-12-816331-3.00004-0 hsypln33 0.978378 Domingo_2016 Domingo_2016
3 Aris-Brosou_2019 Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation Aris-Brosou, Stéphane; Parent, Louis; Ibeh, Neke 2019 2019-07-24 COMM-USE N PMC6722887 31344814.0 10.3390/v11080677 qeao4ghg 0.940306 Aris-Brosou_2019
4 Aris-Brosou_2019 Episodic diversifying selection and intragenomic interactions shape the evolution of DNA and RNA viruses Stéphane Aris-Brosou; Louis Parent; Neke Ibeh 2019 2019-02-03 BioRxiv N 10.1101/539239 j1q96sli 0.940176 Aris-Brosou_2019
5 Fitzsimmons_2018 A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus Fitzsimmons, William J.; Woods, Robert J.; McCrone, John T.; Woodman, Andrew; Arnold, Jamie J.; Yennawar, Madhumita; Evans, Richard; Cameron, Craig E.; Lauring, Adam S. 2018 2018-06-28 COMM-USE N PMC6040757 29953453.0 10.1371/journal.pbio.2006459 9cx1gdze 0.911957 Simon-Loriere_2011 Fitzsimmons_2018, Van_Slyke_2015
6 Fitzsimmons_2018 A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus William Fitzsimmons; Robert J. Woods; John T. McCrone; Andrew Woodman; Jamie J. Arnold; Madhumita Yennawar; Richard Evans; Craig E. Cameron; Adam S. Lauring 2018 2018-04-27 BioRxiv N 10.1101/309880 8p24gszj 0.900766 Simon-Loriere_2011 Fitzsimmons_2018, Van_Slyke_2015
7 Zhao_2018 Existing host range mutations constrain further emergence of RNA viruses Lele Zhao; Mansha Seth Pasricha; Dragos Stemate; Alvin Crespo-Bellido; Jacqueline Gagnon; Siobain Duffy 2018 2018-08-17 BioRxiv N 10.1101/394080 zguy9ba7 0.897310 Ford_2014
8 Cervera_2017 Viral fitness predicts the magnitude and direction of perturbations in the infected host transcriptome Héctor Cervera; Silvia Ambrós; Guillermo P. Bernet; Guillermo Rodrigo; Santiago F. Elena 2017 2017-10-20 BioRxiv N 10.1101/206789 0qmsripp 0.872794 Cervera_2018
9 Cervera_2018 Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study Cervera, Héctor; Ambrós, Silvia; Bernet, Guillermo P; Rodrigo, Guillermo; Elena, Santiago F 2018 2018-03-19 NONCOMM N PMC5995217 29562354.0 10.1093/molbev/msy038 9uqa39j9 0.872794 Cervera_2017
10 Simon-Loriere_2011 Why do RNA viruses recombine? Simon-Loriere, Etienne; Holmes, Edward C. 2011 2011-07-04 None N PMC3324781 21725337.0 10.1038/nrmicro2614 53atdvlv 0.864194 Simon-Loriere_2009
11 Ford_2014 Frequency and Fitness Consequences of Bacteriophage Φ6 Host Range Mutations Ford, Brian E.; Sun, Bruce; Carpino, James; Chapler, Elizabeth S.; Ching, Jane; Choi, Yoon; Jhun, Kevin; Kim, Jung D.; Lallos, Gregory G.; Morgenstern, Rachelle; Singh, Shalini; Theja, Sai; Dennehy, John J. 2014 2014-11-19 COMM-USE N PMC4237377 25409341.0 10.1371/journal.pone.0113078 u97oem9c 0.826408 Zhao_2018
12 Sanjuán_2016 Mechanisms of viral mutation Sanjuán, Rafael; Domingo-Calap, Pilar 2016 2016-07-08 COMM-USE N PMC5075021 27392606.0 10.1007/s00018-016-2299-6 jdg8gsve 0.792054
13 Martens_2011 Interfering Waves of Adaptation Promote Spatial Mixing Martens, Erik A.; Hallatschek, Oskar 2011 2011-11-23 PMC N PMC3213383 21900264.0 10.1534/genetics.111.130112 hzu4c8ls 0.761709 Simon-Loriere_2011 Somovilla_2019, Hünemeier_2012
14 Bayer_2018 Adaptation by copy number variation in monopartite viruses Bayer, Avraham; Brennan, Greg; Geballe, Adam P 2018 2018-12-31 PMC N PMC6289852 30015083.0 10.1016/j.coviro.2018.07.001 20rm4o7c 0.752022
15 Sabath_2012 Evolution of Viral Proteins Originated De Novo by Overprinting Sabath, Niv; Wagner, Andreas; Karlin, David 2012 2012-07-19 None N PMC3494269 22821011.0 10.1093/molbev/mss179 629fwmgk 0.738727
16 Somovilla_2019 Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures Somovilla, Pilar; Manrubia, Susanna; Lázaro, Ester 2019 2019-06-18 COMM-USE N PMC6631425 31216651.0 10.3390/pathogens8020080 as3odkj7 0.708254 Simon-Loriere_2011 Tibayrenc_2015
17 Moncla_2016 Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus Moncla, Louise H.; Zhong, Gongxun; Nelson, Chase W.; Dinis, Jorge M.; Mutschler, James; Hughes, Austin L.; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C. 2016 2016-02-10 None N PMC4761429 26867176.0 10.1016/j.chom.2016.01.011 u3hz6sz1 0.674338
18 Moriones_2007 Recombination in the TYLCV Complex: a Mechanism to Increase Genetic Diversity. Implications for Plant Resistance Development Moriones, Enrique; García-Andrés, Susana; Navas-Castillo, Jesús 2007 2007-01-01 PMC N PMC7121651 10.1007/978-1-4020-4769-5_7 w2tlq6ho 0.662185 Harper_2013
19 Cuevas_2016 Human norovirus hyper-mutation revealed by ultra-deep sequencing Cuevas, José M.; Combe, Marine; Torres-Puente, Manoli; Garijo, Raquel; Guix, Susana; Buesa, Javier; Rodríguez-Díaz, Jesús; Sanjuán, Rafael 2016 2016-07-31 PMC N 27094861.0 10.1016/j.meegid.2016.04.017 0rdiosxd 0.642935
20 Barr_2016 Chapter 2 Genetic Instability of RNA Viruses Barr, J.N.; Fearns, R. 2016 2016-12-31 PMC N PMC7149711 10.1016/b978-0-12-803309-8.00002-1 f8ab7413 0.630603
21 von_Hahn_2015 Cyclophilin polymorphism and virus infection von Hahn, Thomas; Ciesek, Sandra 2015 2015-10-31 PMC N PMC7102842 26281011.0 10.1016/j.coviro.2015.07.012 6xm0b5el 0.618245
22 Voronin_2009 Genetic Drift of HIV Populations in Culture Voronin, Yegor; Holte, Sarah; Overbaugh, Julie; Emerman, Michael 2009 2009-03-20 COMM-USE N PMC2652835 19300501.0 10.1371/journal.pgen.1000431 z0y2og29 0.614761 Simon-Loriere_2009 Ngandu_2009
23 Hanada_2004 A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes Hanada, Kousuke; Suzuki, Yoshiyuki; Gojobori, Takashi 2004 2004-06-23 PMC N PMC7107514 15014142.0 10.1093/molbev/msh109 36qx1sy9 0.590041 Gu_W_2004, Zhang_2014
24 Szpara_2019 Mechanisms of DNA Virus Evolution Szpara, Moriah L.; Van Doorslaer, Koenraad 2019 2019-12-31 PMC N 10.1016/b978-0-12-809633-8.20993-x sx608o1u 0.585760 Simon-Loriere_2011
25 Gervasi_2015 The context of host competence: a role for plasticity in host–parasite dynamics Gervasi, Stephanie S.; Civitello, David J.; Kilvitis, Holly J.; Martin, Lynn B. 2015 2015-09-30 None N PMC4567474 26048486.0 10.1016/j.pt.2015.05.002 bj99uuqz 0.584260
26 Tian_2018 The adaptation of codon usage of +ssRNA viruses to their hosts Tian, Lin; Shen, Xuejuan; Murphy, Robert W.; Shen, Yongyi 2018 2018-09-30 PMC N PMC7106036 29864509.0 10.1016/j.meegid.2018.05.034 wgeuh1i2 0.554782 Gu_W_2004 Sheikh_2020, Liu_Y_2011
27 Ng_M_2015 Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats Ng, Melinda; Ndungo, Esther; Kaczmarek, Maria E; Herbert, Andrew S; Binger, Tabea; Kuehne, Ana I; Jangra, Rohit K; Hawkins, John A; Gifford, Robert J; Biswas, Rohan; Demogines, Ann; James, Rebekah M; Yu, Meng; Brummelkamp, Thijn R; Drosten, Christian; Wang, Lin-Fa; Kuhn, Jens H; Müller, Marcel A; Dye, John M; Sawyer, Sara L; Chandran, Kartik 2015 2015-12-23 COMM-USE N PMC4709267 26698106.0 10.7554/elife.11785 o0y4rn0z 0.551764
28 Weng_2007 Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity Weng, Ziming; Barthelson, Roger; Gowda, Siddarame; Hilf, Mark E.; Dawson, William O.; Galbraith, David W.; Xiong, Zhongguo 2007 2007-09-19 None N PMC1975466 17878952.0 10.1371/journal.pone.0000917 p5ff5u4l 0.551016
29 Harper_2013 Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups Harper, S. J. 2013 2013-04-23 COMM-USE N PMC3632782 23630519.0 10.3389/fmicb.2013.00093 jl3uah1i 0.497000 Tibayrenc_2015
30 Sola_1999 Chapter 6 Drift and Conservatism in RNA Virus Evolution Are They Adapting or Merely Changing? Sola, Monica; Wain-Hobson, Simon 1999 1999-12-31 PMC N 10.1016/b978-012220360-2/50007-6 w7z97wir 0.490613 Simon-Loriere_2011 Somovilla_2019
31 Lauring_2013 The role of mutational robustness in RNA virus evolution Lauring, Adam S.; Frydman, Judith; Andino, Raul 2013 2013-03-25 PMC N PMC3981611 23524517.0 10.1038/nrmicro3003 wqir1u0k 0.479004 Bayer_2018, Somovilla_2019
32 Munir_2014 Estimation of Evolutionary Dynamics and Selection Pressure in Coronaviruses Munir, Muhammad; Cortey, Martí 2014 2014-12-18 PMC N PMC7121324 25720469.0 10.1007/978-1-4939-2438-7_4 6ml54592 0.462438 Tibayrenc_2015, Bayer_2018
33 Simon-Loriere_2009 Molecular Mechanisms of Recombination Restriction in the Envelope Gene of the Human Immunodeficiency Virus Simon-Loriere, Etienne; Galetto, Roman; Hamoudi, Meriem; Archer, John; Lefeuvre, Pierre; Martin, Darren P.; Robertson, David L.; Negroni, Matteo 2009 2009-05-08 COMM-USE N PMC2671596 19424420.0 10.1371/journal.ppat.1000418 4tvrhpss 0.459958 Simon-Loriere_2011
34 Pérez-Losada_2015 Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences Pérez-Losada, Marcos; Arenas, Miguel; Galán, Juan Carlos; Palero, Ferran; González-Candelas, Fernando 2015 2015-03-31 PMC N PMC7106159 25541518.0 10.1016/j.meegid.2014.12.022 yzu4luz9 0.454898 Simon-Loriere_2009
35 Sanjuán_2019 Genetic Diversity and Evolution of Viral Populations ☆ Sanjuán, Rafael; Domingo-Calap, Pilar 2019 2019-12-31 PMC N PMC7157443 10.1016/b978-0-12-809633-8.20958-8 bk7lete2 0.443114 WILSON_2015, Bayer_2018
36 Domingo_1998 Quasispecies and the implications for virus persistence and escape Domingo, Esteban 1998 1998-07-15 PMC N PMC7135314 9741634.0 10.1016/s0928-0197(98)00032-4 mauzesor 0.402393 Tibayrenc_2015
37 Pavesi_2019 Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation Pavesi, Angelo 2019 2019-06-30 PMC N PMC7125799 31004987.0 10.1016/j.virol.2019.03.017 z8uecyl6 0.350264 Sheikh_2020
38 Lloyd_2014 The High Cost of Fidelity Lloyd, Sarah B.; Kent, Stephen J.; Winnall, Wendy R. 2014 2014-01-01 PMC N PMC3887412 24180375.0 10.1089/aid.2013.0153 tzc12gzh 0.345264 Smith_2012
39 Leuven_2020 ΦX174 Attenuation by Whole Genome Codon Deoptimization James T. Van Leuven; Martina M. Ederer; Katelyn Burleigh; LuAnn Scott; Randall A. Hughes; Vlad Codrea; Andrew D. Ellington; Holly Wichman; Craig Miller 2020 2020-02-11 BioRxiv N 10.1101/2020.02.10.942847 mpb4fy16 0.339130 Gu_W_2004, Zhang_2014
40 Domingo_2008 CHAPTER 4 Viral Quasispecies: Dynamics, Interactions, and Pathogenesis * * Dedicated to Manfred Eigen on the occasion of his 80th birthday, for the insights that his pioneer studies have represented for virology. Domingo, Esteban; Escarmís, Cristina; Menéndez-Arias, Luis; Perales, Celia; Herrera, Mónica; Novella, Isabel S.; Holland, John J. 2008 2008-12-31 PMC N PMC7149507 10.1016/b978-0-12-374153-0.00004-7 n57lfj6u 0.338260 Domingo_1998
41 Olson_2014 A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain Olson, C. Anders; Wu, Nicholas C.; Sun, Ren 2014 2014-11-01 PMC N PMC4254498 25455030.0 10.1016/j.cub.2014.09.072 gs7infqj 0.336448 Simon-Loriere_2011, Simon-Loriere_2009 Parera_2006, Evans_2020
42 Lemos_de_Matos_2013 Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals Lemos de Matos, Ana; McFadden, Grant; Esteves, Pedro J. 2013 2013-11-27 COMM-USE N PMC3842351 24312370.0 10.1371/journal.pone.0081864 gi2kswai 0.321304