Topic 02 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 01 - 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 Koonin_2013 A virocentric perspective on the evolution of life Koonin, Eugene V; Dolja, Valerian V 2013 2013-10-31 None N PMC4326007 23850169.0 10.1016/j.coviro.2013.06.008 kjyuxc3g 0.918345 Rodríguez_2020
2 Berman_2019 Chapter 7 Viruses Berman, Jules J. 2019 2019-12-31 PMC N PMC7149528 10.1016/b978-0-12-817576-7.00007-9 74nt6tyz 0.883240
3 Baranowski_2003 Evolution of Cell Recognition by Viruses: A Source of Biological Novelty with Medical Implications Baranowski, Eric; Ruiz-Jarabo, Carmen M; Pariente, Nonia; Verdaguer, Nuria; Domingo, Esteban 2003 2003-12-31 PMC N PMC7119103 14719364.0 10.1016/s0065-3527(03)62002-6 gbtyjkws 0.872235 Rodríguez_2020
4 Holmes_2011 The Evolution of Endogenous Viral Elements Holmes, Edward C. 2011 2011-10-20 PMC N 22018237.0 10.1016/j.chom.2011.09.002 nyb20mhi 0.867547
5 Kaján_2019 Virus–Host Coevolution with a Focus on Animal and Human DNA Viruses Kaján, Győző L.; Doszpoly, Andor; Tarján, Zoltán László; Vidovszky, Márton Z.; Papp, Tibor 2019 2019-10-10 COMM-USE N PMC6943099 31599342.0 10.1007/s00239-019-09913-4 33fs6exl 0.848640 Rodríguez_2020, Koonin_2013
6 Domingo_2020 Chapter 1 Introduction to virus origins and their role in biological evolution Domingo, Esteban 2020 2020-12-31 PMC N 10.1016/b978-0-12-816331-3.00001-5 v6ci69n0 0.820910
7 Cann_2016 Chapter 3 Genomes Cann, Alan J. 2016 2016-12-31 PMC N PMC7150238 10.1016/b978-0-12-801946-7.00003-1 47q0yaxr 0.805799
8 Fermin_2018 Chapter 2 Virion Structure, Genome Organization, and Taxonomy of Viruses Fermin, Gustavo 2018 2018-12-31 PMC N PMC7149880 10.1016/b978-0-12-811257-1.00002-4 nvo8jz9j 0.764939 Koonin_2013, Rodríguez_2020
9 Simmonds_2018 Prisoners of war — host adaptation and its constraints on virus evolution Simmonds, Peter; Aiewsakun, Pakorn; Katzourakis, Aris 2018 2018-12-05 PMC N PMC7097816 30518814.0 10.1038/s41579-018-0120-2 52lcpf0x 0.764939 Rodríguez_2020
10 Rodríguez_2020 Chapter 3 Viral Emerging Pathogen Evolution Rodríguez, Virginia; Lagares, Alfredo; Arteaga, Heiser; Mattar, Salim; Ruiz, Luis Carlos 2020 2020-12-31 PMC N PMC7149897 10.1016/b978-0-12-819400-3.00003-x f3g3ek5u 0.760961 Koonin_2013
11 Moelling_2019 Viruses and Evolution – Viruses First? A Personal Perspective Moelling, Karin; Broecker, Felix 2019 2019-03-19 COMM-USE N PMC6433886 30941110.0 10.3389/fmicb.2019.00523 wk1rg58s 0.758409 Koonin_2013, Rodríguez_2020
12 Nasir_2015 A phylogenomic data-driven exploration of viral origins and evolution Nasir, Arshan; Caetano-Anollés, Gustavo 2015 2015-09-25 NONCOMM N PMC4643759 26601271.0 10.1126/sciadv.1500527 49360l2a 0.758078 Rodríguez_2020
13 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 0.738054
14 Fermin_2018 Chapter 5 Host Range, Host–Virus Interactions, and Virus Transmission Fermin, Gustavo 2018 2018-12-31 PMC N 10.1016/b978-0-12-811257-1.00005-x kfx0qvkp 0.699691
15 Miller_2006 Long-Distance RNA-RNA Interactions in Plant Virus Gene Expression and Replication Miller, W. Allen; White, K. Andrew 2006 2006-09-01 PMC N PMC1894749 16704356.0 10.1146/annurev.phyto.44.070505.143353 avd20f45 0.691310
16 Woolhouse_2013 The diversity of human RNA viruses Woolhouse, Mark E.J.; Adair, Kyle 2013 2013-02-01 PMC N PMC5831953 29503665.0 10.2217/fvl.12.129 gmt0f9da 0.688968
17 Donato_2017 The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses Donato, Celeste; Vijaykrishna, Dhanasekaran 2017 2017-05-10 COMM-USE N PMC5454415 28489047.0 10.3390/v9050102 7j43yic1 0.658292
18 Meyerson_2011 Two-stepping through time: mammals and viruses Meyerson, Nicholas R.; Sawyer, Sara L. 2011 2011-06-01 PMC N PMC3567447 21531564.0 10.1016/j.tim.2011.03.006 bc8tyej7 0.653730 Rodríguez_2020, Simmonds_2018
19 Agol_2008 The Origin and Evolution of Viruses Agol, Vadim I. 2008 2008-01-01 PMC N PMC7121209 10.1007/978-1-4020-8761-5_7 gy8d8285 0.653499 Rodríguez_2020
20 Holmes_2003 Error thresholds and the constraints to RNA virus evolution Holmes, Edward C 2003 2003-12-31 PMC N 14659685.0 10.1016/j.tim.2003.10.006 lnydntaz 0.652655
21 Slingenbergh_2018 Animal virus ecology and evolution are shaped by the virus host-body infiltration and colonization pattern. Jan Slingenbergh 2018 2018-12-10 BioRxiv N 10.1101/492603 xkmouavc 0.651844 Rodríguez_2020
22 Nathanson_2016 Chapter 7 Patterns of Infection Unwanted Guests—Quick Visits and Extended Stays Nathanson, Neal; González-Scarano, Francisco 2016 2016-12-31 PMC N PMC7149623 10.1016/b978-0-12-800964-2.00007-0 e6jt1fi4 0.645476
23 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 0.630389 Simon-Loriere_2011 Somovilla_2019
24 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 0.629276 Simon-Loriere_2011
25 Longdon_2014 The Evolution and Genetics of Virus Host Shifts Longdon, Ben; Brockhurst, Michael A.; Russell, Colin A.; Welch, John J.; Jiggins, Francis M. 2014 2014-11-06 COMM-USE N PMC4223060 25375777.0 10.1371/journal.ppat.1004395 zfl7pb4t 0.627864
26 Cann_2016 Chapter 6 Infection Cann, Alan J. 2016 2016-12-31 PMC N 10.1016/b978-0-12-801946-7.00006-7 5at0rhqk 0.624964
27 Bull_2008 Invasion thresholds and the evolution of nonequilibrium virulence Bull, James J; Ebert, Dieter 2008 2008-01-09 PMC N PMC3352400 25567500.0 10.1111/j.1752-4571.2007.00003.x xfb94lq8 0.605777 Rodríguez_2020
28 Enard_2020 Ancient RNA virus epidemics through the lens of recent adaptation in human genomes David Enard; Dmitri A. Petrov 2020 2020-03-20 BioRxiv N 10.1101/2020.03.18.997346 wzjyv8k6 0.604659
29 Agol_2012 Cytopathic effects: virus-modulated manifestations of innate immunity? Agol, Vadim I. 2012 2012-12-31 PMC N PMC7126625 23072900.0 10.1016/j.tim.2012.09.003 7icslv2r 0.593801
30 Pulliam_2008 Viral Host Jumps: Moving toward a Predictive Framework Pulliam, Juliet R. C. 2008 2008-02-13 PMC N PMC7087992 18648800.0 10.1007/s10393-007-0149-6 m1dkkbq7 0.587676 Rodríguez_2020
31 Lythgoe_2017 Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections Lythgoe, Katrina A.; Gardner, Andy; Pybus, Oliver G.; Grove, Joe 2017 2017-04-01 None N PMC5405858 28377208.0 10.1016/j.tim.2017.03.003 t2vl0cw6 0.570247 Rodríguez_2020
32 Haven_2013 Superinfection reconciles host–parasite association and cross-species transmission Haven, James; Park, Andrew William 2013 2013-12-31 PMC N PMC7126234 24161558.0 10.1016/j.tpb.2013.09.015 pu9vd195 0.568511
33 Loker_2012 Macroevolutionary Immunology: A Role for Immunity in the Diversification of Animal life Loker, Eric S. 2012 2012-03-12 NONCOMM N PMC3342036 22566909.0 10.3389/fimmu.2012.00025 e0tcmzl2 0.564689 Matthews_2020, McCoy_2003
34 Nasir_2017 Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo 2017 2017-06-23 COMM-USE N PMC5481351 28690608.0 10.3389/fmicb.2017.01178 2zm8wk2c 0.560495 Nasir_2015
35 Novella_1995 Rapid viral quasispecies evolution: implications for vaccine and drug strategies Novella, Isabel S.; Domingo, Esteban; Holland, John J. 1995 1995-08-31 PMC N 17607887.0 10.1016/s1357-4310(95)91551-6 15zfvsur 0.559131
36 McCoy_2003 Sympatric speciation in parasites – what is sympatry? McCoy, Karen D. 2003 2003-09-30 PMC N PMC7129588 12957516.0 10.1016/s1471-4922(03)00194-6 gpdzxp63 0.551267
37 Domingo_2020 Chapter 2 Molecular basis of genetic variation of viruses error-prone replication Domingo, Esteban 2020 2020-12-31 PMC N PMC7153327 10.1016/b978-0-12-816331-3.00002-7 r8el8nqm 0.548120 Simon-Loriere_2011 Domingo_2016
38 FENNER_1987 CHAPTER 6 Pathogenesis: Virus-Induced Changes in Cells FENNER, FRANK; BACHMANN, PETER A.; GIBBS, E. PAUL J.; MURPHY, FREDERICK A.; STUDDERT, MICHAEL J.; WHITE, DAVID O. 1987 1987-12-31 PMC N 10.1016/b978-0-12-253055-5.50010-4 uvr4tktn 0.541784
39 Bell_1993 Pathogen evolution within host individuals as a primary cause of senescence Bell, Graham 1993 1993-01-01 PMC N PMC7087926 8125270.0 10.1007/bf01435985 wg2splyf 0.540287 Rodríguez_2020
40 Bujarski_2008 Recombination Bujarski, J.J. 2008 2008-12-31 PMC N PMC7148591 10.1016/b978-012374410-4.00545-8 31xmue1g 0.530944 Simon-Loriere_2011
41 André_2005 The effect of disease life history on the evolutionary emergence of novel pathogens André, Jean-Baptiste; Day, Troy 2005 2005-08-09 PMC N PMC1559879 16191602.0 10.1098/rspb.2005.3170 bjmvnmcc 0.492679 McCoy_2003 Rodríguez_2020
42 Wu_N_2016 Adaptation in protein fitness landscapes is facilitated by indirect paths Wu, Nicholas C; Dai, Lei; Olson, C Anders; Lloyd-Smith, James O; Sun, Ren 2016 2016-07-08 COMM-USE N PMC4985287 27391790.0 10.7554/elife.16965 7kwlteyr 0.489841 Somovilla_2019
43 Soueidan_2015 Finding and identifying the viral needle in the metagenomic haystack: trends and challenges Soueidan, Hayssam; Schmitt, Louise-Amélie; Candresse, Thierry; Nikolski, Macha 2015 2015-01-07 COMM-USE N PMC4285800 25610431.0 10.3389/fmicb.2014.00739 bkreu1s2 0.476518
44 Wain-Hobson_2008 CHAPTER 13 Retrovirus Evolution Wain-Hobson, Simon 2008 2008-12-31 PMC N PMC7149677 10.1016/b978-0-12-374153-0.00013-8 7w8oq2ej 0.475692
45 Reanney_1974 Viruses and Evolution Reanney, D.C. 1974 1974-12-31 PMC N 4600790.0 10.1016/s0074-7696(08)61356-x olzleh6a 0.466912
46 Benecke_2012 Critical Dynamics in Host–Pathogen Systems Benecke, Arndt G. 2012 2012-09-12 PMC N PMC7121065 22976347.0 10.1007/82_2012_260 hastu5yg 0.463243 Matthews_2020 Rodríguez_2020, Valdano_2019
47 Belshaw_2008 Pacing a small cage: mutation and RNA viruses Belshaw, Robert; Gardner, Andy; Rambaut, Andrew; Pybus, Oliver G. 2008 2008-04-30 None N PMC7125972 18295930.0 10.1016/j.tree.2007.11.010 ce0025xi 0.463138 Bocharov_2018
48 Domingo_2016 Chapter 2 Molecular Basis of Genetic Variation of Viruses Error-Prone Replication Domingo, Esteban 2016 2016-12-31 PMC N PMC7149591 10.1016/b978-0-12-800837-9.00002-2 wi21dksk 0.462008 Domingo_2020
49 Martin_2019 Extreme Competence: Keystone Hosts of Infections Martin, Lynn B.; Addison, BriAnne; Bean, Andrew G.D.; Buchanan, Katherine L.; Crino, Ondi L.; Eastwood, Justin R.; Flies, Andrew S.; Hamede, Rodrigo; Hill, Geoffrey E.; Klaassen, Marcel; Koch, Rebecca E.; Martens, Johanne M.; Napolitano, Constanza; Narayan, Edward J.; Peacock, Lee; Peel, Alison J.; Peters, Anne; Raven, Nynke; Risely, Alice; Roast, Michael J.; Rollins, Lee A.; Ruiz-Aravena, Manuel; Selechnik, Dan; Stokes, Helena S.; Ujvari, Beata; Grogan, Laura F. 2019 2019-04-30 PMC N PMC7114649 30704782.0 10.1016/j.tree.2018.12.009 quw1gyw7 0.460805 Haven_2013
50 Biebricher_1999 Chapter 4 Mutation, Competition and Selection as Measured with Small RNA Molecules Biebricher, Christof K. 1999 1999-12-31 PMC N 10.1016/b978-012220360-2/50005-2 vgltrkv7 0.459738 Simon-Loriere_2011
51 Danchin_2009 A challenge to vaccinology: Living organisms trap information Danchin, Antoine 2009 2009-12-30 PMC N PMC7115390 20006133.0 10.1016/j.vaccine.2009.10.071 6dwj3ex3 0.448259
52 Overstreet_2016 Host–Symbiont Relationships: Understanding the Change from Guest to Pest Overstreet, Robin M.; Lotz, Jeffrey M. 2016 2016-01-06 PMC N PMC7123458 10.1007/978-3-319-28170-4_2 3lta1tbp 0.447589 McCoy_2003
53 Matthews_2020 On biological evolution and environmental solutions Matthews, Blake; Jokela, Jukka; Narwani, Anita; Räsänen, Katja; Pomati, Francesco; Altermatt, Florian; Spaak, Piet; Robinson, Christopher T.; Vorburger, Christoph 2020 2020-07-01 PMC N PMC7118648 10.1016/j.scitotenv.2020.138194 vhjuus50 0.445074 Peterson_2008
54 Villarreal_2009 Persistence pays: how viruses promote host group survival Villarreal, Luis P 2009 2009-08-31 PMC N 19608458.0 10.1016/j.mib.2009.06.014 bdz01kch 0.439946 Roossinck_2011 Rodríguez_2020
55 Roossinck_2011 Changes in Population Dynamics in Mutualistic versus Pathogenic Viruses Roossinck, Marilyn J. 2011 2011-01-17 COMM-USE N PMC3187592 21994724.0 10.3390/v3010012 okdiyk1m 0.422072 Rodríguez_2020
56 Johnson_2011 Mechanisms for Env Glycoprotein Acquisition by Retroviruses Johnson, Marc C. 2011 2011-03-01 PMC N PMC3048835 21247353.0 10.1089/aid.2010.0350 3p5bsk93 0.420391
57 Burrell_2017 Chapter 2 Classification of Viruses and Phylogenetic Relationships Burrell, Christopher J.; Howard, Colin R.; Murphy, Frederick A. 2017 2017-12-31 PMC N PMC7149777 10.1016/b978-0-12-375156-0.00002-3 y8c60w4a 0.417493 Rodríguez_2020, Fermin_2018
58 San_Martín_2013 Structure and Assembly of Complex Viruses San Martín, Carmen 2013 2013-02-16 PMC N PMC7122652 23737057.0 10.1007/978-94-007-6552-8_11 0x3nt6si 0.415124
59 Lucía-Sanz_2017 Multipartite viruses: adaptive trick or evolutionary treat? Lucía-Sanz, Adriana; Manrubia, Susanna 2017 2017-11-09 COMM-USE N PMC5680193 29263796.0 10.1038/s41540-017-0035-y z2fpahsg 0.412638 Valdano_2019
60 Baker_2019 Chapter 17 Parasitic Diseases Baker, David G. 2019 2019-12-31 PMC N PMC7150290 10.1016/b978-0-12-811829-0.00017-0 d7m0s10o 0.412364
61 Sinkovics_2011 Horizontal Gene Transfers with or without Cell Fusions in All Categories of the Living Matter Sinkovics, Joseph G. 2011 2011-04-11 PMC N PMC7120942 21506007.0 10.1007/978-94-007-0782-5_2 b9z5yjcg 0.396503 Baranov_2009
62 Chiara_2020 Domestication reprogrammed the budding yeast life cycle Matteo De Chiara; Benjamin Barré; Karl Persson; Amadi Onyetuga Chioma; Agurtzane Irizar; Joseph Schacherer; Jonas Warringer; Gianni Liti 2020 2020-02-09 BioRxiv N 10.1101/2020.02.08.939314 hwvr0v8c 0.392596 McCoy_2003, Simon-Loriere_2011
63 Saberi_2018 A planarian nidovirus expands the limits of RNA genome size Saberi, Amir; Gulyaeva, Anastasia A.; Brubacher, John L.; Newmark, Phillip A.; Gorbalenya, Alexander E. 2018 2018-11-01 None N PMC6211748 30383829.0 10.1371/journal.ppat.1007314 pxf8piqm 0.376420
64 Pradeu_2016 Mutualistic viruses and the heteronomy of life Pradeu, Thomas 2016 2016-10-31 PMC N PMC7108282 26972872.0 10.1016/j.shpsc.2016.02.007 ymc31ckv 0.365878 Rodríguez_2020, Koonin_2013
65 Domingo_2020 Chapter 6 Virus population dynamics examined with experimental model systems Domingo, Esteban 2020 2020-12-31 PMC N PMC7153323 10.1016/b978-0-12-816331-3.00006-4 uvcdt42w 0.362246 Domingo_2016, Rodríguez_2020
66 Gorbalenya_2018 Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank Gorbalenya, Alexander E. 2018 2018-06-26 COMM-USE N PMC6132925 29942981.0 10.1007/s00705-018-3915-6 upi9ie6d 0.350084 Polverino_2017
67 Mehlhorn_2013 Introduction: The World of Bats Mehlhorn, Heinz 2013 2013-09-03 PMC N PMC7121961 10.1007/978-3-642-39333-4_1 nc9cyu2u 0.348230 Looker_2006
68 Purssell_2019 Antimicrobials Purssell, Edward 2019 2019-09-04 PMC N PMC7120529 10.1007/978-3-030-32004-1_6 wdhhl15j 0.343219
69 Domingo_2016 Chapter 8 Quasispecies Dynamics in Disease Prevention and Control Domingo, Esteban 2016 2016-12-31 PMC N PMC7149962 10.1016/b978-0-12-800837-9.00008-3 na5jqrpb 0.342830
70 Guy_C_2019 Phylogeny matters: revisiting ‘a comparison of bats and rodents as reservoirs of zoonotic viruses’ Guy, Cylita; Thiagavel, Jeneni; Mideo, Nicole; Ratcliffe, John M. 2019 2019-02-13 None N PMC6408376 30891262.0 10.1098/rsos.181182 2uwvbgzx 0.338647 McCoy_2003
71 Vannier-Santos_2011 Parasites or Cohabitants: Cruel Omnipresent Usurpers or Creative “Éminences Grises”? Vannier-Santos, Marcos A.; Lenzi, Henrique L. 2011 2011-07-18 COMM-USE N PMC3140032 21785696.0 10.1155/2011/214174 5omt75qr 0.334195 McCoy_2003, Looker_2006 Rupprecht_2015
72 Hatcher_2015 Trait-Mediated Effects of Parasites on Invader-Native Interactions Hatcher, Melanie J.; Dick, Jaimie T. A.; Paterson, Rachel A.; Alexander, Mhairi E.; Bunke, Mandy; Dunn, Alison M. 2015 2015-07-20 PMC N PMC7120441 10.1007/978-3-319-22936-2_3 x5n4dyxp 0.333892 McCoy_2003, Roossinck_2011
73 Valdano_2019 Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission Valdano, Eugenio; Manrubia, Susanna; Gómez, Sergio; Arenas, Alex 2019 2019-03-18 None N PMC6438571 30883545.0 10.1371/journal.pcbi.1006876 nro3cdm2 0.331506
74 Mishra_2020 Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis Mishra, Pushpendra Mani; Verma, Navneet Chandra; Rao, Chethana; Uversky, Vladimir N.; Nandi, Chayan Kanti 2020 2020-04-02 PMC N 10.1016/bs.pmbts.2020.03.001 qlglk6ly 0.330401
75 Aouacheria_2016 Evolution of the BCL-2-Regulated Apoptotic Pathway Aouacheria, Abdel; Le Goff, Emilie; Godefroy, Nelly; Baghdiguian, Stephen 2016 2016-05-24 PMC N PMC7123326 10.1007/978-3-319-41324-2_9 dao241jh 0.329030
76 Dietrich_2017 The bulky and the sweet: How neutralizing antibodies and glycan receptors compete for virus binding Dietrich, Melanie H.; Harprecht, Christina; Stehle, Thilo 2017 2017-10-24 PMC N PMC5699497 28986957.0 10.1002/pro.3319 hx6ys1t2 0.321316
77 Nor_M_2017 Pneumonia in the tropics: Report from the Task Force on tropical diseases by the World Federation of Societies of Intensive and Critical Care Medicine Nor, Mohd Basri Mat; Richards, Guy A.; McGloughlin, Steve; Amin, Pravin R. 2017 2017-12-31 PMC N PMC7138420 29129538.0 10.1016/j.jcrc.2017.11.004 4hn55wui 0.307290
78 Valle_1988 Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis Valle, Rosaura P.C.; Morch, Marie-Dominique 1988 1988-08-01 PMC N 3042454.0 10.1016/0014-5793(88)81225-0 qo74f00i 0.304937 Bocharov_2018