Topic 01 -- 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 Duan_2015 Mathematical and computational approaches to epidemic modeling: a comprehensive review Duan, Wei; Fan, Zongchen; Zhang, Peng; Guo, Gang; Qiu, Xiaogang 2015 2015-10-09 PMC N PMC7133607 10.1007/s11704-014-3369-2 mh30ocvo 0.959564 Bauer_2009 Li_K_2011, Shang_2013, Li_C_2018
2 Leach_2010 Modelling Emerging Viral Epidemics for Public Health Protection Leach, Steve; Hall, Ian 2010 2010-08-16 PMC N PMC7120695 21116814.0 10.1007/978-1-60761-817-1_23 cx3ex9ru 0.902212 Citron_2020
3 Bauer_2009 Agent-based modeling of host–pathogen systems: The successes and challenges Bauer, Amy L.; Beauchemin, Catherine A.A.; Perelson, Alan S. 2009 2009-04-29 PMC N 10.1016/j.ins.2008.11.012 qlypp5z6 0.900319 Duan_2015
4 Lloyd-Smith_2015 Nine challenges in modelling the emergence of novel pathogens Lloyd-Smith, James O.; Funk, Sebastian; McLean, Angela R.; Riley, Steven; Wood, James L.N. 2015 2015-03-23 PMC N PMC4715032 25843380.0 10.1016/j.epidem.2014.09.002 w08xqf1g 0.895668 Bauer_2009, Duan_2015
5 Roche_2017 Chapter 14 Individual-Based Models for Public Health Roche, Benjamin; Duboz, Raphaël 2017 2017-12-31 PMC N PMC7148902 10.1016/bs.host.2017.08.008 lwxnx854 0.894595 Bocharov_2018, Duan_2015, Leach_2010 Leach_2010, Safi_2011
6 Fitzpatrick_2019 Modelling microbial infection to address global health challenges Fitzpatrick, Meagan C.; Bauch, Chris T.; Townsend, Jeffrey P.; Galvani, Alison P. 2019 2019-09-20 PMC N PMC6800015 31541212.0 10.1038/s41564-019-0565-8 j8iawzp8 0.889685
7 Ezanno_2011 Modelling the Dynamics of Host-Parasite Interactions: Basic Principles Ezanno, Pauline; Vergu, Elisabeta; Langlais, Michel; Gilot-Fromont, Emmanuelle 2011 2011-06-28 PMC N PMC7122337 10.1007/978-94-007-2114-2_5 2ueghyvv 0.869433 Bocharov_2018, Duan_2015 Remais_2010, Alexander_2009, Dimitrov_2008
8 LaDeau_2011 Data–model fusion to better understand emerging pathogens and improve infectious disease forecasting LaDeau, Shannon L.; Glass, Gregory E.; Hobbs, N. Thompson; Latimer, Andrew; Ostfeld, Richard S. 2011 2011-07-01 PMC N PMC7163730 21830694.0 10.1890/09-1409.1 meusb794 0.860171 Bocharov_2018
9 Brauer_2009 Mathematical epidemiology is not an oxymoron Brauer, Fred 2009 2009-11-18 COMM-USE N PMC2779504 19922686.0 10.1186/1471-2458-9-s1-s2 vufephkg 0.843887 Duan_2015, Grassly_2008, Bocharov_2018
10 Grassly_2008 Mathematical models of infectious disease transmission Grassly, Nicholas C.; Fraser, Christophe 2008 2008-05-13 PMC N PMC7097581 18533288.0 10.1038/nrmicro1845 iwwgfh9y 0.841002 Bocharov_2018, Duan_2015 Hanage_2016, Real_2007, Hollingsworth_2009
11 Johansson_2011 On the Treatment of Airline Travelers in Mathematical Models Johansson, Michael A.; Arana-Vizcarrondo, Neysarí; Biggerstaff, Brad J.; Staples, J. Erin; Gallagher, Nancy; Marano, Nina 2011 2011-07-25 COMM-USE N PMC3143116 21799782.0 10.1371/journal.pone.0022151 q9nlwflu 0.812525 Leach_2010 Yong_2016, Safi_2011
12 Wang_2014 Spatial epidemiology of networked metapopulation: an overview Wang, Lin; Li, Xiang 2014 2014-07-19 PMC N PMC7088704 10.1007/s11434-014-0499-8 c9d51iea 0.798854 WANG_2014, Voinson_2018
13 Liu_S_2016 epiDMS: Data Management and Analytics for Decision-Making From Epidemic Spread Simulation Ensembles Liu, Sicong; Poccia, Silvestro; Candan, K. Selçuk; Chowell, Gerardo; Sapino, Maria Luisa 2016 2016-12-01 PMC N PMC7107328 28830107.0 10.1093/infdis/jiw305 uk0dqnes 0.792368 Duan_2015, Brockmann_2014 Chowell_2017, Pyne_2015, Neri_2014
14 Chowell_2014 Transmission dynamics and control of Ebola virus disease (EVD): a review Chowell, Gerardo; Nishiura, Hiroshi 2014 2014-10-10 COMM-USE N PMC4207625 25300956.0 10.1186/s12916-014-0196-0 7skgb6eu 0.783170 Chowell_2015
15 Wu_J_2011 The use of mathematical models to inform influenza pandemic preparedness and response Wu, Joseph T; Cowling, Benjamin J 2011 2011-08-01 PMC N PMC3178755 21727183.0 10.1258/ebm.2010.010271 v932f5ni 0.774565 McVernon_2007
16 Wang_2018 Characterizing the dynamics underlying global spread of epidemics Wang, Lin; Wu, Joseph T. 2018 2018-01-15 COMM-USE N PMC5768765 29335536.0 10.1038/s41467-017-02344-z cvuvont8 0.768776 Zheng_2015, Colizza_2007
17 McVernon_2007 Model answers or trivial pursuits? The role of mathematical models in influenza pandemic preparedness planning McVernon, J; McCaw, CT; Mathews, JD 2007 2007-05-25 PMC N PMC4634556 19432634.0 10.1111/j.1750-2659.2007.00008.x ntub7gnw 0.764317 Wu_J_2011, Bucini_2019
18 Lessler_2016 Trends in the Mechanistic and Dynamic Modeling of Infectious Diseases Lessler, Justin; Azman, Andrew S.; Grabowski, M. Kate; Salje, Henrik; Rodriguez-Barraquer, Isabel 2016 2016-07-02 PMC N PMC7100697 10.1007/s40471-016-0078-4 yltc6wpv 0.763303 Duan_2015 Real_2007, Raja_Sekhara_Rao_2015, Citron_2020
19 WANG_2014 Spatial epidemiology of networked metapopulation: An overview Lin WANG; Xiang Li 2014 2014-06-04 BioRxiv N 10.1101/003889 i9tbix2v 0.761572 Wang_2014, Voinson_2018
20 Brockmann_2014 Understanding and predicting the global spread of emergent infectious diseases Brockmann, Dirk 2014 2014-09-30 PMC N PMC7148725 10.1016/j.phf.2014.07.001 o02505rt 0.758836 Lavine_2008
21 Cremin_2018 An infectious way to teach students about outbreaks Cremin, Íde; Watson, Oliver; Heffernan, Alastair; Imai, Natsuko; Ahmed, Norin; Bivegete, Sandra; Kimani, Teresia; Kyriacou, Demetris; Mahadevan, Preveina; Mustafa, Rima; Pagoni, Panagiota; Sophiea, Marisa; Whittaker, Charlie; Beacroft, Leo; Riley, Steven; Fisher, Matthew C. 2018 2018-06-23 None N PMC5971212 29289499.0 10.1016/j.epidem.2017.12.002 3st8912e 0.758007 Bocharov_2018, Zheng_2020, Duan_2015 Safi_2011, Daughton_2017
22 Cauchemez_2019 How Modelling Can Enhance the Analysis of Imperfect Epidemic Data Cauchemez, Simon; Hoze, Nathanaël; Cousien, Anthony; Nikolay, Birgit; ten bosch, Quirine 2019 2019-05-31 PMC N PMC7106457 30738632.0 10.1016/j.pt.2019.01.009 tysa2b5x 0.757273 Bocharov_2018 Cauchemez_2012, Real_2007, Citron_2020
23 Cori_2017 Key data for outbreak evaluation: building on the Ebola experience Cori, Anne; Donnelly, Christl A.; Dorigatti, Ilaria; Ferguson, Neil M.; Fraser, Christophe; Garske, Tini; Jombart, Thibaut; Nedjati-Gilani, Gemma; Nouvellet, Pierre; Riley, Steven; Van Kerkhove, Maria D.; Mills, Harriet L.; Blake, Isobel M. 2017 2017-05-26 COMM-USE N PMC5394647 28396480.0 10.1098/rstb.2016.0371 12t247bn 0.757207 Chowell_2014
24 Woolhouse_2011 How to make predictions about future infectious disease risks Woolhouse, Mark 2011 2011-07-12 COMM-USE N PMC3130384 21624924.0 10.1098/rstb.2010.0387 x6bvjkbk 0.742026 Bucini_2019, Leach_2010
25 Perrings_2014 Merging Economics and Epidemiology to Improve the Prediction and Management of Infectious Disease Perrings, Charles; Castillo-Chavez, Carlos; Chowell, Gerardo; Daszak, Peter; Fenichel, Eli P.; Finnoff, David; Horan, Richard D.; Kilpatrick, A. Marm; Kinzig, Ann P.; Kuminoff, Nicolai V.; Levin, Simon; Morin, Benjamin; Smith, Katherine F.; Springborn, Michael 2014 2014-09-19 PMC N PMC4366543 25233829.0 10.1007/s10393-014-0963-6 xm57cnw9 0.733601 Real_2007, Raja_Sekhara_Rao_2015, Loberg_2020
26 Chowell_2017 Fitting dynamic models to epidemic outbreaks with quantified uncertainty: A primer for parameter uncertainty, identifiability, and forecasts Chowell, Gerardo 2017 2017-08-12 NONCOMM N PMC5726591 29250607.0 10.1016/j.idm.2017.08.001 3aa8wgr0 0.720087 Bocharov_2018, Bifolchi_2013, Lemey_2009 Zimmer_2017, Lloyd_2009
27 Pyne_2015 Chapter 8 Big Data Applications in Health Sciences and Epidemiology Pyne, Saumyadipta; Vullikanti, Anile Kumar S.; Marathe, Madhav V. 2015 2015-12-31 PMC N PMC7152243 10.1016/b978-0-444-63492-4.00008-3 2u7r00s1 0.718946 Colizza_2007, Kim_L_2019, Chowell_2014, Chowell_2015
28 Arino_2017 Spatio-temporal spread of infectious pathogens of humans Arino, Julien 2017 2017-05-17 None N PMC6001966 29928738.0 10.1016/j.idm.2017.05.001 pghkmxds 0.718073 Grassly_2008, Bauer_2009, Duan_2015
29 Chisholm_2018 Implications of asymptomatic carriers for infectious disease transmission and control Chisholm, Rebecca H.; Campbell, Patricia T.; Wu, Yue; Tong, Steven Y. C.; McVernon, Jodie; Geard, Nicholas 2018 2018-02-14 None N PMC5830799 29515909.0 10.1098/rsos.172341 zf9bwk1y 0.701344 Leach_2010, Bocharov_2018
30 Sun_G_2016 Pattern transitions in spatial epidemics: Mechanisms and emergent properties Sun, Gui-Quan; Jusup, Marko; Jin, Zhen; Wang, Yi; Wang, Zhen 2016 2016-12-31 PMC N PMC7105263 27567502.0 10.1016/j.plrev.2016.08.002 qcesepj6 0.699843 Krause_2007 Kubiak_2010, Chowell_2015
31 Gomez_2020 INFEKTA: A General Agent-based Model for Transmission of Infectious Diseases: Studying the COVID-19 Propagation in Bogota - Colombia Jonatan Gomez; Jeisson Prieto; Elizabeth Leon; Arles Rodriguez 2020 2020-04-11 BioRxiv Y 10.1101/2020.04.06.20056119 vfr4pvmz 0.698330 Bifolchi_2013, Li_C_2018, Duan_2015, Grassly_2008, Lemey_2009 Yong_2016, Kretzschmar_2020, Imran_2018
32 Walters_2018 Modelling the global spread of diseases: A review of current practice and capability Walters, Caroline E.; Meslé, Margaux M.I.; Hall, Ian M. 2018 2018-12-31 PMC N PMC6227252 29853411.0 10.1016/j.epidem.2018.05.007 cbl9xds3 0.696330 Bocharov_2018, Zheng_2020, Chowell_2017 Safi_2011, Colizza_2007, Chowell_2014
33 Herrmann_2020 Using network science to propose strategies for effectively dealing with pandemics: The COVID-19 example Helena A Herrmann; Jean-Marc Schwartz 2020 2020-04-06 BioRxiv Y 10.1101/2020.04.02.20050468 ztl54g6q 0.689687 Bocharov_2018
34 Grad_2012 Cholera Modeling: Challenges to Quantitative Analysis and Predicting the Impact of Interventions Grad, Yonatan H.; Miller, Joel C.; Lipsitch, Marc 2012 2012-07-01 PMC N PMC3380087 22659546.0 10.1097/ede.0b013e3182572581 urzyn2ct 0.682878 Bocharov_2018 Park_2017, Chin_2019, Remais_2010
35 Clements_2009 Emerging viral zoonoses: Frameworks for spatial and spatiotemporal risk assessment and resource planning Clements, Archie C.A.; Pfeiffer, Dirk U. 2009 2009-10-31 PMC N PMC7110545 18718800.0 10.1016/j.tvjl.2008.05.010 28mhhwol 0.681707 Neri_2014
36 Wiratsudakul_2018 Dynamics of Zika virus outbreaks: an overview of mathematical modeling approaches Wiratsudakul, Anuwat; Suparit, Parinya; Modchang, Charin 2018 2018-03-22 COMM-USE N PMC5866925 29593941.0 10.7717/peerj.4526 9ftas3a5 0.679070 Duan_2015 Imran_2018
37 Carrasco_2013 Trends in parameterization, economics and host behaviour in influenza pandemic modelling: a review and reporting protocol Carrasco, Luis R; Jit, Mark; Chen, Mark I; Lee, Vernon J; Milne, George J; Cook, Alex R 2013 2013-05-07 COMM-USE N PMC3666982 23651557.0 10.1186/1742-7622-10-3 fhn8psco 0.670900 Duan_2015, Bauer_2009 Bucini_2019, Uribe-Sánchez_2011, Wu_J_2011
38 Donnelly_2004 Epidemiological and genetic analysis of severe acute respiratory syndrome Donnelly, Christl A; Fisher, Matthew C; Fraser, Christophe; Ghani, Azra C; Riley, Steven; Ferguson, Neil M; Anderson, Roy M 2004 2004-11-30 PMC N PMC7106498 15522679.0 10.1016/s1473-3099(04)01173-9 imvbkt69 0.668680
39 Kawashima_2016 Disease Outbreaks: Critical Biological Factors and Control Strategies Kawashima, Kent; Matsumoto, Tomotaka; Akashi, Hiroshi 2016 2016-05-31 PMC N PMC7122892 10.1007/978-3-319-39812-9_10 zd4v222b 0.665139 Bucini_2019, Chowell_2014
40 Neuberger_2013 Modelling in infectious diseases: between haphazard and hazard Neuberger, A.; Paul, M.; Nizar, A.; Raoult, D. 2013 2013-11-30 PMC N PMC7128462 23879334.0 10.1111/1469-0691.12309 doxr6yvv 0.661995 Leach_2010
41 Rizzo_2017 Toward a Realistic Modeling of Epidemic Spreading with Activity Driven Networks Rizzo, Alessandro; Porfiri, Maurizio 2017 2017-10-05 PMC N PMC7123080 10.1007/978-981-10-5287-3_14 y3c4uzmv 0.657948 Bocharov_2018, Chowell_2017, Bifolchi_2013, Duan_2015, He_D_2010 Han_X_2014, Bioglio_2016, Bifolchi_2013, Roy_M_2006
42 He_D_2010 Plug-and-play inference for disease dynamics: measles in large and small populations as a case study He, Daihai; Ionides, Edward L.; King, Aaron A. 2010 2010-02-06 COMM-USE N PMC2842609 19535416.0 10.1098/rsif.2009.0151 bze6g6jx 0.654046 Bocharov_2018, Chowell_2017, Zheng_2020, Leach_2010 Dearlove_2013, Park_2017, Citron_2020
43 Gubar_2017 Optimal Control of Multi-strain Epidemic Processes in Complex Networks Gubar, Elena; Zhu, Quanyan; Taynitskiy, Vladislav 2017 2017-09-05 PMC N PMC7120795 10.1007/978-3-319-67540-4_10 r2zazddg 0.642520 Sherborne_2015, Lv_W_2019, Wu_Q_2014, Raja_Sekhara_Rao_2015
44 Bocharov_2018 Modelling of Experimental Infections Bocharov, Gennady; Volpert, Vitaly; Ludewig, Burkhard; Meyerhans, Andreas 2018 2018-06-13 PMC N PMC7123718 10.1007/978-3-319-72317-4_4 zjnlibu4 0.641840 Zheng_2020, Chowell_2017, Grassly_2008
45 Hanage_2016 Pathogen Epidemiology Hanage, W.P. 2016 2016-12-31 PMC N PMC7148661 10.1016/b978-0-12-800049-6.00228-6 9xxhljpf 0.639387
46 Ferguson_2003 Planning for smallpox outbreaks Ferguson, Neil M.; Keeling, Matt J.; John Edmunds, W.; Gani, Raymond; Grenfell, Bryan T.; Anderson, Roy M.; Leach, Steve 2003 2003-01-01 PMC N PMC7095314 14562094.0 10.1038/nature02007 u69o55bs 0.633993
47 Kamvar_2019 Epidemic curves made easy using the R package incidence Kamvar, Zhian N.; Cai, Jun; Pulliam, Juliet R.C.; Schumacher, Jakob; Jombart, Thibaut 2019 2019-01-31 COMM-USE N PMC6509961 31119031.0 10.12688/f1000research.18002.1 uiqk356j 0.622959 Bocharov_2018 Song_2020, Loberg_2020, Daughton_2017
48 Hollingsworth_2009 Controlling infectious disease outbreaks: Lessons from mathematical modelling Hollingsworth, T Déirdre 2009 2009-10-05 PMC N PMC7099230 19806073.0 10.1057/jphp.2009.13 qpmeyqwf 0.621082 Raja_Sekhara_Rao_2015, Grassly_2008
49 Matthews_2005 New approaches to quantifying the spread of infection Matthews, Louise; Woolhouse, Mark 2005 2005-01-01 PMC N PMC7096817 15995653.0 10.1038/nrmicro1178 awvpfgum 0.616560 Yong_2016
50 House_2016 Bayesian uncertainty quantification for transmissibility of influenza, norovirus and Ebola using information geometry House, Thomas; Ford, Ashley; Lan, Shiwei; Bilson, Samuel; Buckingham-Jeffery, Elizabeth; Girolami, Mark 2016 2016-08-23 None N PMC5014059 27558850.0 10.1098/rsif.2016.0279 3eepsy3v 0.612793 Bifolchi_2013, Lemey_2009, Giardina_2017, O'Dea_2010 Akhmetzhanov_2019
51 Smirnova_2017 A primer on stable parameter estimation and forecasting in epidemiology by a problem-oriented regularized least squares algorithm Smirnova, Alexandra; Chowell, Gerardo 2017 2017-05-25 None N PMC6002070 29928741.0 10.1016/j.idm.2017.05.004 3fwla5ox 0.610794 Loberg_2020, Chowell_2017, Lega_2016, Bucini_2019
52 Bhatia_2019 Using Digital Surveillance Tools for Near Real-Time Mapping of the Risk of International Infectious Disease Spread: Ebola as a Case Study Sangeeta Bhatia; Britta Lassmann; Emily Cohn; Malwina Carrion; Moritz U.G. Kraemer; Mark Herringer; John Brownstein; Larry Madoff; Anne Cori; Pierre Nouvellet 2019 2019-11-15 BioRxiv N 10.1101/19011940 jwesa12u 0.605262
53 Daddar_2015 The potential of recurrent epidemics and pandemics in a highly mobile global society Daddar, Sabrina; Nirupama, N. 2015 2015-01-28 PMC N PMC7089195 10.1007/s11069-015-1628-7 tk7cl55p 0.601058 Chowell_2014, Ng_T_2003
54 Daughton_2017 An approach to and web-based tool for infectious disease outbreak intervention analysis Daughton, Ashlynn R.; Generous, Nicholas; Priedhorsky, Reid; Deshpande, Alina 2017 2017-04-18 COMM-USE N PMC5394686 28417983.0 10.1038/srep46076 2z32ln7g 0.600737 Kim_L_2019, Song_2020
55 Cauchemez_2012 Methods to infer transmission risk factors in complex outbreak data Cauchemez, Simon; Ferguson, Neil M. 2012 2012-03-07 COMM-USE N PMC3262428 21831890.0 10.1098/rsif.2011.0379 zdft23q8 0.592084 Bocharov_2018, Chowell_2017, Zheng_2020 Safi_2011, Campbell_2019
56 Lavine_2008 Directly transmitted viral diseases: modeling the dynamics of transmission Lavine, Jennie S.; Poss, Mary; Grenfell, Bryan T. 2008 2008-04-30 PMC N PMC7127822 18356058.0 10.1016/j.tim.2008.01.007 bwc8zjf2 0.589125
57 Remais_2010 Modelling Environmentally-Mediated Infectious Diseases of Humans: Transmission Dynamics of Schistosomiasis in China Remais, Justin 2010 2010-12-20 PMC N PMC7123861 20632531.0 10.1007/978-1-4419-6064-1_6 emxgbnvg 0.586439 Bifolchi_2013 Akhmetzhanov_2019
58 Dimitrov_2008 Adaptive modeling of viral diseases in bats with a focus on rabies Dimitrov, Dobromir T.; Hallam, Thomas G.; Rupprecht, Charles E.; McCracken, Gary F. 2008 2008-11-07 PMC N PMC7126102 18761020.0 10.1016/j.jtbi.2008.08.007 q2o71o4d 0.584707
59 Nguyen_2019 Simulation models for transmission of health care–associated infection: A systematic review Nguyen, Le Khanh Ngan; Megiddo, Itamar; Howick, Susan 2019 2019-12-18 PMC N 10.1016/j.ajic.2019.11.005 5ktlba3p 0.580337 Raja_Sekhara_Rao_2015, Safi_2011
60 Mitchell_2016 A data-driven model for influenza transmission incorporating media effects Mitchell, Lewis; Ross, Joshua V. 2016 2016-10-26 COMM-USE N PMC5098988 27853563.0 10.1098/rsos.160481 xrk8h85z 0.577810 Bocharov_2018, O'Dea_2010 Kim_L_2019, Dawson_2015, Tizzoni_2020, Tizzoni_2018
61 Vincenot_2011 Impact of the topology of metapopulations on the resurgence of epidemics rendered by a new multiscale hybrid modeling approach Vincenot, Christian Ernest; Moriya, Kazuyuki 2011 2011-07-31 PMC N 10.1016/j.ecoinf.2011.04.002 fmc5fwf3 0.577800 Bocharov_2018, Chowell_2017, Bifolchi_2013, Lemey_2009 Feng_2018, Roy_M_2006, Citron_2020
62 Lega_2016 Data-driven outbreak forecasting with a simple nonlinear growth model Lega, Joceline; Brown, Heidi E. 2016 2016-12-31 None N PMC5159251 27770752.0 10.1016/j.epidem.2016.10.002 6vty0pmk 0.571960 Bocharov_2018, Zheng_2020, Chowell_2017, Leach_2010, He_D_2010 Cauchemez_2012, Loberg_2020, Safi_2011, Chowell_2017
63 Brett_2017 Anticipating the emergence of infectious diseases Brett, Tobias S.; Drake, John M.; Rohani, Pejman 2017 2017-07-05 COMM-USE N PMC5550966 28679666.0 10.1098/rsif.2017.0115 ewooc2am 0.566243 Bocharov_2018, Bauer_2009, Chowell_2017 Dimitrov_2008, Chen_2019
64 Wang_2015 Coupled disease–behavior dynamics on complex networks: A review Wang, Zhen; Andrews, Michael A.; Wu, Zhi-Xi; Wang, Lin; Bauch, Chris T. 2015 2015-12-31 PMC N PMC7105224 26211717.0 10.1016/j.plrev.2015.07.006 i37v602u 0.554902 Bocharov_2018, Krause_2007, Leach_2010 Van_Segbroeck_2010, Chen_2014, Zhan_2018
65 Cook_2008 Constructing the effect of alternative intervention strategies on historic epidemics Cook, A.R; Gibson, G.J; Gottwald, T.R; Gilligan, C.A 2008 2008-02-26 PMC N PMC3227033 18302995.0 10.1098/rsif.2008.0030 0oygp21v 0.554802 Bocharov_2018, Zheng_2020, Chowell_2017, Cauchemez_2012 Loberg_2020, Kim_L_2019, Chen_2018, Safi_2011
66 Kwok_2019 Epidemic Models of Contact Tracing: Systematic Review of Transmission Studies of Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome Kwok, Kin On; Tang, Arthur; Wei, Vivian W.I.; Park, Woo Hyun; Yeoh, Eng Kiong; Riley, Steven 2019 2019-01-26 None N PMC6376160 30809323.0 10.1016/j.csbj.2019.01.003 d7lvxtxy 0.550134 Kretzschmar_2020
67 Bettencourt_2007 Towards Real Time Epidemiology: Data Assimilation, Modeling and Anomaly Detection of Health Surveillance Data Streams Bettencourt, Luís M. A.; Ribeiro, Ruy M.; Chowell, Gerardo; Lant, Timothy; Castillo-Chavez, Carlos 2007 2007-01-01 PMC N PMC7122958 10.1007/978-3-540-72608-1_8 cf2bbn3p 0.549621 Bocharov_2018, Chowell_2017 Chowell_2017, Southall_2020, Lega_2016, Cauchemez_2012
68 Chowell_2008 Quantifying the transmission potential of pandemic influenza Chowell, Gerardo; Nishiura, Hiroshi 2008 2008-03-31 PMC N PMC7105222 10.1016/j.plrev.2007.12.001 omq1atsu 0.548712 Bocharov_2018, Chowell_2017 Safi_2011, Chowell_2014, Kucharski_2015
69 Engbert_2020 Sequential data assimilation of the stochastic SEIR epidemic model for regional COVID-19 dynamics Ralf Engbert; Maximilian M. Rabe; Reinhold Kliegl; Sebastian Reich 2020 2020-04-17 BioRxiv Y 10.1101/2020.04.13.20063768 855am0mv 0.547944 Bifolchi_2013, Chowell_2017, Lemey_2009, Li_C_2018, Bocharov_2018
70 Lu_J_2020 A New, Simple Projection Model for COVID-19 Pandemic Jian Lu 2020 2020-03-24 BioRxiv Y 10.1101/2020.03.21.20039867 1y0pl31i 0.547415 Yong_2016
71 Tildesley_2009 Impact of spatial clustering on disease transmission and optimal control Tildesley, Michael J.; House, Thomas A.; Bruhn, Mark C.; Curry, Ross J.; O’Neil, Maggie; Allpress, Justine L. E.; Smith, Gary; Keeling, Matt J. 2009 2009-12-01 None N PMC2824282 19955428.0 10.1073/pnas.0909047107 mc751rwj 0.541721 Bocharov_2018 White_2013, Bjørnstad_2019, Safi_2011
72 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 0.539090 Bocharov_2018 Campbell_2019, Baele_2016, Cottam_2008
73 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 0.529348 Duan_2015, Bauer_2009, Grassly_2008 Baele_2016
74 Getz_2019 A quantitative narrative on movement, disease and patch exploitation in nesting agent groups Wayne M. Getz; Richard Salter; Krti Tallam 2019 2019-10-03 BioRxiv N 10.1101/791400 5gzgfudh 0.528159 Bocharov_2018
75 Real_2007 Infectious Disease Modeling and the Dynamics of Transmission Real, L. A.; Biek, R. 2007 2007-01-01 PMC N PMC7121613 17848059.0 10.1007/978-3-540-70962-6_2 7k3i3eio 0.523676 Bocharov_2018, Leach_2010 Kucharski_2015, Safi_2011, Wendelboe_2010
76 Bettencourt_2008 Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases Bettencourt, Luís M. A.; Ribeiro, Ruy M. 2008 2008-05-14 None N PMC2366072 18478118.0 10.1371/journal.pone.0002185 nmmimc71 0.521650 Thompson_2019, Voinson_2018, Neri_2014
77 Wearing_2005 Appropriate Models for the Management of Infectious Diseases Wearing, Helen J; Rohani, Pejman; Keeling, Matt J 2005 2005-07-26 COMM-USE N PMC1181873 16013892.0 10.1371/journal.pmed.0020174 ff7dg890 0.508810 Bocharov_2018, Chowell_2017 Safi_2011, Citron_2020, Real_2007
78 Southall_2020 Prospects for detecting early warning signals in discrete event sequence data: application to epidemiological incidence data Emma Southall; Michael J. Tildesley; Louise Dyson 2020 2020-04-02 BioRxiv N 10.1101/2020.04.02.021576 dp4qv77q 0.504119 Bocharov_2018, Zheng_2020, O'Dea_2010 Bucini_2019, Brett_2018
79 Kwong_2010 Spatial Components in Disease Modelling Kwong, Kim-hung; Lai, Poh-chin 2010 2010-01-01 PMC N PMC7122710 10.1007/978-3-642-12156-2_30 azqjvxtu 0.499517 Bocharov_2018 Citron_2020, Real_2007
80 Verelst_2016 Behavioural change models for infectious disease transmission: a systematic review (2010–2015) Verelst, Frederik; Willem, Lander; Beutels, Philippe 2016 2016-12-23 COMM-USE N PMC5221530 28003528.0 10.1098/rsif.2016.0820 de0y745b 0.491922 Bocharov_2018, Chowell_2017 Safi_2011
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185 Zhigljavsky_2020 Comparison of different exit scenarios from the lock-down for COVID-19 epidemic in the UK and assessing uncertainty of the predictions Anatoly Zhigljavsky; Roger Whitaker; Ivan Fesenko; Yakov Kremnitzer; Jack Noonan 2020 2020-04-14 BioRxiv Y 10.1101/2020.04.09.20059451 mipdahk4 0.318419 Zhigljavsky_2020, Ghaffarzadegan_2020, Kretzschmar_2020, Caccavo_2020
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188 Liu_Z_2020 Government Responses Matter: Predicting Covid-19 cases in US under an empirical Bayesian time series framework Ziyue Liu; Wensheng Guo 2020 2020-03-30 BioRxiv Y 10.1101/2020.03.28.20044578 boa0n9dz 0.311570 Li_C_2018 Distante_2020, Lopez_2020, Loberg_2020
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190 Hickmann_2015 Forecasting the 2013–2014 Influenza Season Using Wikipedia Hickmann, Kyle S.; Fairchild, Geoffrey; Priedhorsky, Reid; Generous, Nicholas; Hyman, James M.; Deshpande, Alina; Del Valle, Sara Y. 2015 2015-05-14 COMM-USE N PMC4431683 25974758.0 10.1371/journal.pcbi.1004239 9sgrw1qp 0.309403 Mondor_2012
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192 Mangiarotti_2020 Chaos theory applied to the outbreak of Covid-19: an ancillary approach to decision-making in pandemic context Sylvain Mangiarotti; Marisa Peyre; Yan Zhang; Mireille Huc; Francois Roger; Yann Kerr 2020 2020-04-06 BioRxiv Y 10.1101/2020.04.02.20051441 gnk3m0b8 0.306413 Ghaffarzadegan_2020, Loberg_2020, Caccavo_2020
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195 Cori_2013 A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics Cori, Anne; Ferguson, Neil M.; Fraser, Christophe; Cauchemez, Simon 2013 2013-09-15 PMC N PMC3816335 24043437.0 10.1093/aje/kwt133 itr3b63z 0.304320 Höhle_2007, Bocharov_2018, Lloyd_2009, Cauchemez_2012 Safi_2011, Thompson_2019, Chong_2020, Kucharski_2015
196 Cotta_2020 Modelling the COVID-19 epidemics in Brasil: Parametric identification and public health measures influence Renato Machado Cotta; Carolina Palma Naveira-Cotta; pierre magal 2020 2020-04-03 BioRxiv Y 10.1101/2020.03.31.20049130 3rmrkzuq 0.302906 Li_C_2018, Wu_Q_2014, Lloyd_2009, O'Dea_2010, Bifolchi_2013 Safi_2011, Kretzschmar_2020
197 Black_2013 Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic Black, Andrew J.; Ross, Joshua V. 2013 2013-08-30 None N PMC3758268 24023679.0 10.1371/journal.pone.0073420 ecxcw96m 0.302759 Bocharov_2018, Lloyd_2009, Chowell_2017 Safi_2011, Zimmer_2017, Cotta_2020
198 Parag_2019 Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models Kris V Parag; Christl A Donnelly 2019 2019-07-16 BioRxiv N 10.1101/703751 uboq3ofm 0.300817 Bocharov_2018, Chowell_2017, Bifolchi_2013, Lemey_2009 Lemey_2009, Baele_2016, Neri_2014
199 Viboud_2016 A generalized-growth model to characterize the early ascending phase of infectious disease outbreaks Viboud, Cécile; Simonsen, Lone; Chowell, Gerardo 2016 2016-06-30 PMC N PMC4903879 27266847.0 10.1016/j.epidem.2016.01.002 u7a1as7b 0.300623 Li_C_2018 Safi_2011, Chen_2019, Kretzschmar_2020
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