Topic 10 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 08 - 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 Siva-Jothy_2019 Dissecting genetic and sex-specific host heterogeneity in pathogen transmission potential Jonathon A. Siva-Jothy; Pedro F. Vale 2019 2019-08-14 BioRxiv N 10.1101/733915 0v5q4kp9 0.645688
2 Valdazo-González_2015 The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus Valdazo-González, Begoña; Kim, Jan T.; Soubeyrand, Samuel; Wadsworth, Jemma; Knowles, Nick J.; Haydon, Daniel T.; King, Donald P. 2015 2015-06-30 PMC N PMC7106308 25861750.0 10.1016/j.meegid.2015.03.032 xb480fly 0.600893 Giardina_2017 Cottam_2008
3 Zheng_2009 A Poisson model of sequence comparison and its application to coronavirus phylogeny Zheng, Xiaoqi; Qin, Yufang; Wang, Jun 2009 2009-02-28 PMC N PMC7094598 19073197.0 10.1016/j.mbs.2008.11.006 8qnq02gd 0.594033
4 Campbell_2018 When are pathogen genome sequences informative of transmission events? Campbell, Finlay; Strang, Camilla; Ferguson, Neil; Cori, Anne; Jombart, Thibaut 2018 2018-02-08 COMM-USE N PMC5821398 29420641.0 10.1371/journal.ppat.1006885 ifbf7ttt 0.592341 O'Dea_2010
5 Elghafghuf_2014 A cross-classified and multiple membership Cox model applied to calf mortality data Elghafghuf, Adel; Stryhn, Henrik; Waldner, Cheryl 2014 2014-07-01 PMC N PMC7114250 24703248.0 10.1016/j.prevetmed.2014.03.012 vytal7tz 0.590915 Griette_2020, Höhle_2007, Zhao_2013
6 Plazzotta_2016 Effects of memory on the shapes of simple outbreak trees Plazzotta, Giacomo; Kwan, Christopher; Boyd, Michael; Colijn, Caroline 2016 2016-02-18 COMM-USE N PMC4758066 26888437.0 10.1038/srep21159 mcdfcc8v 0.588919 Giardina_2017, Welch_2011, O'Dea_2010, Li_C_2018 Giardina_2017, Campbell_2019, Kühnert_2011
7 Andraud_2014 Early-Life Hepatitis E Infection in Pigs: The Importance of Maternally-Derived Antibodies Andraud, Mathieu; Casas, Maribel; Pavio, Nicole; Rose, Nicolas 2014 2014-08-21 COMM-USE N PMC4140806 25144763.0 10.1371/journal.pone.0105527 ey5xmb8a 0.577034 Li_C_2018, Wu_Q_2014, Welch_2011
8 Baele_2016 Emerging Concepts of Data Integration in Pathogen Phylodynamics Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe 2016 2016-06-06 COMM-USE N PMC5837209 28173504.0 10.1093/sysbio/syw054 qv5zsleh 0.544674 Bocharov_2018, Lemey_2009 Lemey_2009
9 Blumberg_2013 Inference of R (0) and Transmission Heterogeneity from the Size Distribution of Stuttering Chains Blumberg, Seth; Lloyd-Smith, James O. 2013 2013-05-02 COMM-USE N PMC3642075 23658504.0 10.1371/journal.pcbi.1002993 yv9zv5u4 0.541943 Safi_2011, Blumberg_2014, Kretzschmar_2020, Kucharski_2015
10 Giardina_2017 Inference of Transmission Network Structure from HIV Phylogenetic Trees Giardina, Federica; Romero-Severson, Ethan Obie; Albert, Jan; Britton, Tom; Leitner, Thomas 2017 2017-01-13 None N PMC5279806 28085876.0 10.1371/journal.pcbi.1005316 3gj754dq 0.536319 Lemey_2009, Welch_2011, Bifolchi_2013 Velsko_2014, O'Dea_2010
11 Ratmann_2012 Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study Ratmann, Oliver; Donker, Gé; Meijer, Adam; Fraser, Christophe; Koelle, Katia 2012 2012-12-27 None N PMC3531293 23300420.0 10.1371/journal.pcbi.1002835 wubaahn2 0.535226 Lemey_2009, Giardina_2017, Bifolchi_2013, Lemey_2014 Lemey_2009, Kühnert_2011
12 Hilton_2018 Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence Hilton, Sarah K; Bloom, Jesse D 2018 2018-11-06 COMM-USE N PMC6220371 30425841.0 10.1093/ve/vey033 zw5kt090 0.533789
13 Gogineni_2015 Role of Marine Natural Products in the Genesis of Antiviral Agents Gogineni, Vedanjali; Schinazi, Raymond F.; Hamann, Mark T. 2015 2015-08-28 PMC N PMC4883660 26317854.0 10.1021/cr4006318 q1ggl78u 0.532228 Alqahtani_2016, Mao_H_2019
14 Alqahtani_2016 Camel exposure and knowledge about MERS-CoV among Australian Hajj pilgrims in 2014 Alqahtani, Amani Salem; Wiley, Kerrie Elizabeth; Tashani, Mohamed; Heywood, Anita Elizabeth; Willaby, Harold Wayne; BinDhim, Nasser Fahad; Booy, Robert; Rashid, Harunor 2016 2016-01-18 PMC N PMC7090863 26810660.0 10.1007/s12250-015-3669-1 a2e3f161 0.532228 Gogineni_2015, Mao_H_2019
15 Mok_W_2007 Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens Mok, Wendy; Seto, Kelly; Stone, Jon 2007 2007-09-26 COMM-USE N PMC2684125 19461973.0 23yi8so0 0.524518 Bocharov_2018, Zheng_2020, Chowell_2017
16 Knodel_2018 Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface Knodel, Markus M.; Nägel, Arne; Reiter, Sebastian; Vogel, Andreas; Targett-Adams, Paul; McLauchlan, John; Herrmann, Eva; Wittum, Gabriel 2018 2018-01-08 COMM-USE N PMC5795441 29316722.0 10.3390/v10010028 58xrrowk 0.512045
17 Campbell_2019 Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data Campbell, Finlay; Cori, Anne; Ferguson, Neil; Jombart, Thibaut 2019 2019-03-29 COMM-USE N PMC6457559 30925168.0 10.1371/journal.pcbi.1006930 ijw5bl20 0.503172 O'Dea_2010 Velsko_2014, Campbell_2018
18 Kraemer_2015 Big city, small world: Density, contact rates, and transmission of dengue across Pakistan. Moritz U. G. Kraemer; T. Alex Perkins; Derek A.T. Cummings; Rubeena Zakar; Simon I. Hay; David L. Smith; Robert C. Reiner 2015 2015-04-27 BioRxiv N 10.1101/018481 8ilzm51q 0.473267 O'Dea_2010, Bifolchi_2013, Li_C_2018, Welch_2011, Bocharov_2018 Kraemer_2015, Kretzschmar_2020
19 Lemey_2009 Bayesian Phylogeography Finds Its Roots Lemey, Philippe; Rambaut, Andrew; Drummond, Alexei J.; Suchard, Marc A. 2009 2009-09-25 COMM-USE N PMC2740835 19779555.0 10.1371/journal.pcbi.1000520 l0uya9dh 0.472799 Bocharov_2018, Giardina_2017 Baele_2016, Velsko_2014
20 Bandoy_2020 Pandemic dynamics of COVID-19 using epidemic stage, instantaneous reproductive number and pathogen genome identity (GENI) score: modeling molecular epidemiology DJ Darwin R Bandoy; Bart C Weimer 2020 2020-03-20 BioRxiv Y 10.1101/2020.03.17.20037481 sz26gchn 0.462473 Li_C_2018, Giardina_2017
21 Kraemer_2015 Big city, small world: density, contact rates, and transmission of dengue across Pakistan Kraemer, M. U. G.; Perkins, T. A.; Cummings, D. A. T.; Zakar, R.; Hay, S. I.; Smith, D. L.; Reiner, R. C. 2015 2015-10-06 COMM-USE N PMC4614486 26468065.0 10.1098/rsif.2015.0468 iw3bzy0m 0.456415 Li_C_2018, Bifolchi_2013, O'Dea_2010, Welch_2011, Giardina_2017 Kraemer_2015, White_2013, Kong_2018
22 Velsko_2014 Mapping a viral phylogeny onto outbreak trees to improve host transmission inference Stephen P Velsko; Jonathan E Allen 2014 2014-11-11 BioRxiv N 10.1101/010389 wich35l7 0.420374 Bocharov_2018, Giardina_2017 Cottam_2008
23 Campbell_2018 outbreaker2: a modular platform for outbreak reconstruction Campbell, Finlay; Didelot, Xavier; Fitzjohn, Rich; Ferguson, Neil; Cori, Anne; Jombart, Thibaut 2018 2018-10-22 COMM-USE N PMC6196407 30343663.0 10.1186/s12859-018-2330-z gk8ely05 0.416904 Bocharov_2018, Duan_2015, Grassly_2008 Velsko_2014
24 Volz_2020 Genomic epidemiology of a densely sampled COVID19 outbreak in China Erik Volz; Han Fu; Haowei Wang; Xiauoyue Xi; Wei Chen; Dehui Liu; Yingying Chen; Mengmeng Tian; Wei Tan; Junjie Zai; Wanying Zan; Xinguang Li; Qing Nie 2020 2020-03-13 BioRxiv Y 10.1101/2020.03.09.20033365 xckkdci1 0.415089 Li_C_2018, Lemey_2009, O'Dea_2010
25 O'Dea_2010 Contact Heterogeneity and Phylodynamics: How Contact Networks Shape Parasite Evolutionary Trees O'Dea, Eamon B.; Wilke, Claus O. 2010 2010-12-01 COMM-USE N PMC2995904 21151699.0 10.1155/2011/238743 i7navmbn 0.406913 Bocharov_2018, Giardina_2017 Giardina_2017
26 Cottam_2008 Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus Cottam, Eleanor M; Thébaud, Gaël; Wadsworth, Jemma; Gloster, John; Mansley, Leonard; Paton, David J; King, Donald P; Haydon, Daniel T 2008 2008-01-29 PMC N PMC2599933 18230598.0 10.1098/rspb.2007.1442 gctd950h 0.384305 O'Dea_2010, Giardina_2017 Velsko_2014, Valdazo-González_2015
27 Ahmed_2020 First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community Ahmed, Warish; Angel, Nicola; Edson, Janette; Bibby, Kyle; Bivins, Aaron; O'Brien, Jake W.; Choi, Phil M.; Kitajima, Masaaki; Simpson, Stuart L.; Li, Jiaying; Tscharke, Ben; Verhagen, Rory; Smith, Wendy J.M.; Zaugg, Julian; Dierens, Leanne; Hugenholtz, Philip; Thomas, Kevin V.; Mueller, Jochen F. 2020 2020-04-18 PMC Y 10.1016/j.scitotenv.2020.138764 4om2u914 0.367019 Li_C_2018
28 Velsko_2014 Forensic interpretation of molecular variation on networks of disease transmission and genetic inheritance Velsko, Stephan P.; Osburn, Joanne; Allen, Jonathan 2014 2014-10-07 PMC N PMC7159361 25137141.0 10.1002/elps.201400205 7we3q5an 0.360733
29 Ray_B_2016 Network inference from multimodal data: A review of approaches from infectious disease transmission Ray, Bisakha; Ghedin, Elodie; Chunara, Rumi 2016 2016-12-31 PMC N PMC7106161 27612975.0 10.1016/j.jbi.2016.09.004 yzwsqlb2 0.353203 Bocharov_2018, Duan_2015 Campbell_2019, Yin_W_2015
30 Chong_2020 A Novel Method for the Estimation of a Dynamic Effective Reproduction Number (Dynamic-R) in the CoViD-19 Outbreak Yi Chen Chong 2020 2020-02-25 BioRxiv Y 10.1101/2020.02.22.20023267 o3hytzwu 0.349328 Zheng_2020, Bocharov_2018 Kucharski_2015, Tang_2020
31 Yin_W_2015 From genome-scale data to models of infectious disease: a Bayesian network-based strategy to drive model development Yin, Weiwei; Kissinger, Jessica C.; Moreno, Alberto; Galinski, Mary R.; Styczynski, Mark P. 2015 2015-12-01 PMC N PMC4679518 26093035.0 10.1016/j.mbs.2015.06.006 e89d3r95 0.339388 Bocharov_2018 Campbell_2019, Baele_2016, Cottam_2008
32 Dearlove_2013 Coalescent inference for infectious disease: meta-analysis of hepatitis C Dearlove, Bethany; Wilson, Daniel J. 2013 2013-03-19 COMM-USE N PMC3678333 23382432.0 10.1098/rstb.2012.0314 x7y81ss1 0.336581 Lemey_2009, Bifolchi_2013, Giardina_2017, Chowell_2017, Bocharov_2018 Kucharski_2015, Safi_2011
33 Eberhardt_2020 Multi-Stage Group Testing Optimizes COVID-19 Mass Population Testing Jens Niklas Eberhardt; Nikolas Peter Breuckmann; Christiane Sigrid Eberhardt 2020 2020-04-14 BioRxiv Y 10.1101/2020.04.10.20061176 ztsvzysq 0.334248 Bocharov_2018
34 Nannyonga_2012 The Dynamics, Causes and Possible Prevention of Hepatitis E Outbreaks Nannyonga, Betty; Sumpter, David J. T.; Mugisha, Joseph Y. T.; Luboobi, Livingstone S. 2012 2012-07-24 COMM-USE N PMC3404073 22911752.0 10.1371/journal.pone.0041135 5b936n3g 0.330151 Ng_T_2003, Chowell_2014
35 Duchêne_2015 Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations Duchêne, David A.; Duchêne, Sebastian; Holmes, Edward C.; Ho, Simon Y.W. 2015 2015-07-10 PMC N PMC7107558 26163668.0 10.1093/molbev/msv154 l9wrrapv 0.329203 Bocharov_2018, Chowell_2017 Hilton_2018
36 Blumberg_2014 Detecting Differential Transmissibilities That Affect the Size of Self-Limited Outbreaks Blumberg, Seth; Funk, Sebastian; Pulliam, Juliet R. C. 2014 2014-10-30 None N PMC4214794 25356657.0 10.1371/journal.ppat.1004452 uxq43me8 0.312053 Kucharski_2015, Kretzschmar_2020, Safi_2011
37 Kühnert_2011 Phylogenetic and epidemic modeling of rapidly evolving infectious diseases Kühnert, Denise; Wu, Chieh-Hsi; Drummond, Alexei J. 2011 2011-12-31 PMC N PMC7106223 21906695.0 10.1016/j.meegid.2011.08.005 7zbvgvk8 0.305912 Duan_2015, Bauer_2009, Grassly_2008 Baele_2016