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COVID answers in Scientific Journals all over the world

Public Library of Science: PLoS Computational Biology
  original article Date Title Authors   All Authors
1 [GO] 2022―Jan―12 Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff Le Khanh Ngan Nguyen, Itamar Megiddo, Susan Howick, Claudio José Struchiner
2 [GO] 2022―Jan―04 Microsimulation based quantitative analysis of COVID-19 management strategies István Z. Reguly, Dávid Csercsik, János Juhász, Kálmán Tornai, Zsófia Bujtár, Gergely Horváth, et al. (+9)
3 [GO] 2021―Dec―23 Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection Melanie E. Moses, Steven Hofmeyr, Judy L. Cannon, Akil Andrews, Rebekah Gridley, Monica Hinga, et al. (+6)
4 [GO] 2021―Dec―16 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant Joseph R. Larsen, Margaret R. Martin, John D. Martin, James B. Hicks, Peter Kuhn, Bard Ermentrout
5 [GO] 2021―Dec―13 Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization Fuminari Miura, Ka Yin Leung, Don Klinkenberg, Kylie E. C. Ainslie, Jacco Wallinga, Claudio José Struchiner
6 [GO] 2021―Dec―13 Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure Assaf Amitai, Becca Asquith
7 [GO] 2021―Dec―13 Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies Sarah A. Robinson, Matthew I. J. Raybould, Constantin Schneider, Wing Ki Wong, Claire Marks, Charlotte M. Deane, Franca Fraternali
8 [GO] 2021―Nov―24 Data-driven multi-scale mathematical modeling of SARS-CoV-2 infection reveals heterogeneity among COVID-19 patients Shun Wang, Mengqian Hao, Zishu Pan, Jinzhi Lei, Xiufen Zou, Amber M Smith
9 [GO] 2021―Nov―18 Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections Sean B. King, Mona Singh, Teresa M. Przytycka
10 [GO] 2021―Oct―28 Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing Emily Howerton, Matthew J. Ferrari, Ottar N. Bjørnstad, Tiffany L. Bogich, Rebecca K. Borchering, Chris P. Jewell, et al. (+7)
11 [GO] 2021―Oct―25 OutbreakFlow: Model-based Bayesian inference of disease outbreak dynamics with invertible neural networks and its application to the COVID-19 pandemics in Germany Stefan T. Radev, Frederik Graw, Simiao Chen, Nico T. Mutters, Vanessa M. Eichel, Till Bärnighausen, et al. (+2)
12 [GO] 2021―Oct―19 Factors affecting aerosol SARS-CoV-2 transmission via HVAC systems; a modeling study Zachary J. Cotman, Michael J. Bowden, Barrett P. Richter, Joseph H. Phelps, Christopher J. Dibble, Alison L. Marsden
13 [GO] 2021―Oct―14 Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts Yi Huang, Ishanu Chattopadhyay, Benjamin Muir Althouse
14 [GO] 2021―Oct―14 Interplay between mobility, multi-seeding and lockdowns shapes COVID-19 local impact Mattia Mazzoli, Emanuele Pepe, David Mateo, Ciro Cattuto, Laetitia Gauvin, Paolo Bajardi, et al. (+5)
15 [GO] 2021―Sep―20 Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys Siyu Chen, Jennifer A. Flegg, Lisa J. White, Ricardo Aguas, Claudio José Struchiner
16 [GO] 2021―Sep―17 Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model Federica Gugole, Luc E. Coffeng, Wouter Edeling, Benjamin Sanderse, Sake J. de Vlas, Daan Crommelin, Don Klinkenberg
17 [GO] 2021―Sep―13 Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2 Abhisek Dwivedy, Richard Mariadasse, Mohammed Ahmad, Sayan Chakraborty, Deepsikha Kar, Satish Tiwari, et al. (+8)
18 [GO] 2021―Sep―10 The importance of non-pharmaceutical interventions during the COVID-19 vaccine rollout Nicolò Gozzi, Paolo Bajardi, Nicola Perra, Roger Dimitri Kouyos
19 [GO] 2021―Sep―08 An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City Sheng Zhang, Joan Ponce, Zhen Zhang, Guang Lin, George Karniadakis, Sergei L. Kosakovsky Pond
20 [GO] 2021―Sep―07 Using test positivity and reported case rates to estimate state-level COVID-19 prevalence and seroprevalence in the United States Weihsueh A. Chiu, Martial L. Ndeffo-Mbah, Benjamin Muir Althouse
21 [GO] 2021―Sep―07 Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants Rui Yin, Johnathan D. Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush, et al. (+2)
22 [GO] 2021―Sep―02 Relaxing restrictions at the pace of vaccination increases freedom and guards against further COVID-19 waves Simon Bauer, Sebastian Contreras, Jonas Dehning, Matthias Linden, Emil Iftekhar, Sebastian B. Mohr, et al. (+3)
23 [GO] 2021―Aug―30 Targeted pandemic containment through identifying local contact network bottlenecks Shenghao Yang, Priyabrata Senapati, Di Wang, Chris T. Bauch, Kimon Fountoulakis, Benjamin Muir Althouse
24 [GO] 2021―Aug―12 Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic Ritabrata Dutta, Susana N. Gomes, Dante Kalise, Lorenzo Pacchiardi, Matthew (Matt) Ferrari
25 [GO] 2021―Aug―05 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants Natália Teruel, Olivier Mailhot, Rafael J. Najmanovich, Roland L. Dunbrack
26 [GO] 2021―Jul―26 Covasim: An agent-based model of COVID-19 dynamics and interventions Cliff C. Kerr, Robyn M. Stuart, Dina Mistry, Romesh G. Abeysuriya, Katherine Rosenfeld, Gregory R. Hart, et al. (+21)
27 [GO] 2021―Jul―26 A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic Bernard Cazelles, Clara Champagne, Benjamin Nguyen-Van-Yen, Catherine Comiskey, Elisabeta Vergu, Benjamin Roche, Roger Dimitri Kouyos
28 [GO] 2021―Jul―26 Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies, Alex R. Cook, et al. (+2)
29 [GO] 2021―Jul―22 Optimizing testing for COVID-19 in India Philip Cherian, Sandeep Krishna, Gautam I. Menon, Benjamin Muir Althouse
30 [GO] 2021―Jul―20 Spatially resolved simulations of the spread of COVID-19 in three European countries Andrea Parisi, Samuel P. C. Brand, Joe Hilton, Rabia Aziza, Matt J. Keeling, D. James Nokes, Alex Perkins
31 [GO] 2021―Jul―14 COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity Vladimir Naumov, Evgeny Putin, Stefan Pushkov, Ekaterina Kozlova, Konstantin Romantsov, Alexander Kalashnikov, et al. (+18)
32 [GO] 2021―Jul―12 Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19 Hamish Gibbs, Emily Nightingale, Yang Liu, James Cheshire, Leon Danon, Liam Smeeth, et al. (+5)
33 [GO] 2021―Jul―12 OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing Robert Hinch, William J. M. Probert, Anel Nurtay, Michelle Kendall, Chris Wymant, Matthew Hall, et al. (+21)
34 [GO] 2021―Jul―12 Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic Tenglong Li, Laura F. White, Alex Perkins
35 [GO] 2021―Jul―08 COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission Paul Tupper, Caroline Colijn, Philip K. Maini
36 [GO] 2021―Jul―08 COVID-19 modeling and non-pharmaceutical interventions in an outpatient dialysis unit Hankyu Jang, Philip M. Polgreen, Alberto M. Segre, Sriram V. Pemmaraju, Roger Dimitri Kouyos
37 [GO] 2021―Jul―08 The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins Lukasz Jaroszewski, Mallika Iyer, Arghavan Alisoltani, Mayya Sedova, Adam Godzik, Marco Punta
38 [GO] 2021―Jun―23 Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values Massimo Cavallaro, Haseeb Moiz, Matt J. Keeling, Noel D. McCarthy, Benjamin Muir Althouse
39 [GO] 2021―Jun―17 Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics Billy J. Gardner, A. Marm Kilpatrick, Sebastian Funk
40 [GO] 2021―Jun―17 Estimating the cumulative incidence of COVID-19 in the United States using influenza surveillance, virologic testing, and mortality data: Four complementary approaches Fred S. Lu, Andre T. Nguyen, Nicholas B. Link, Mathieu Molina, Jessica T. Davis, Matteo Chinazzi, et al. (+5)
41 [GO] 2021―Jun―16 A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2 Edward M. Hill, Benjamin D. Atkins, Matt J. Keeling, Louise Dyson, Michael J. Tildesley, Mercedes Pascual
42 [GO] 2021―May―27 Estimating direct and spill-over impacts of political elections on COVID-19 transmission using synthetic control methods Jue Tao Lim, Kenwin Maung, Sok Teng Tan, Suan Ee Ong, Jane Mingjie Lim, Joel Ruihan Koo, et al. (+7)
43 [GO] 2021―May―06 Modelling optimal vaccination strategy for SARS-CoV-2 in the UK Sam Moore, Edward M. Hill, Louise Dyson, Michael J. Tildesley, Matt J. Keeling, Alex Perkins
44 [GO] 2021―Apr―09 Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection Piyush Nanda, Amit Ghosh, Anders Wallqvist
45 [GO] 2021―Apr―01 Computational epitope map of SARS-CoV-2 spike protein Mateusz Sikora, Sören von Bülow, Florian E. C. Blanc, Michael Gecht, Roberto Covino, Gerhard Hummer, Alexander MacKerell
46 [GO] 2021―Mar―29 Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model Gregory L. Watson, Di Xiong, Lu Zhang, Joseph A. Zoller, John Shamshoian, Phillip Sundin, et al. (+5)
47 [GO] 2021―Mar―29 On realized serial and generation intervals given control measures: The COVID-19 pandemic case Andrea Torneri, Peter Libin, Gianpaolo Scalia Tomba, Christel Faes, James G. Wood, Niel Hens, Alex Perkins
48 [GO] 2021―Mar―17 Gene variants of coagulation related proteins that interact with SARS-CoV-2 David Holcomb, Aikaterini Alexaki, Nancy Hernandez, Ryan Hunt, Kyle Laurie, Jacob Kames, et al. (+5)
49 [GO] 2021―Mar―17 SARS-CoV-2 viral dynamics in non-human primates Antonio Gonçalves, Pauline Maisonnasse, Flora Donati, Mélanie Albert, Sylvie Behillil, Vanessa Contreras, et al. (+22)
50 [GO] 2021―Mar―09 Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics Pieter J. K. Libin, Lander Willem, Timothy Verstraeten, Andrea Torneri, Joris Vanderlocht, Niel Hens, Alex Perkins
51 [GO] 2021―Mar―08 A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes’ interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19 Jun Ding, David Earl Hostallero, Mohamed Reda El Khili, Gregory Joseph Fonseca, Simon Milette, Nuzha Noorah, et al. (+8)
52 [GO] 2021―Mar―04 Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic Quentin Richard, Samuel Alizon, Marc Choisy, Mircea T. Sofonea, Ramsès Djidjou-Demasse, Gabor Balazsi
53 [GO] 2021―Mar―04 Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance Vincent Brault, Bastien Mallein, Jean-François Rupprecht, Jingyi Jessica Li
54 [GO] 2021―Mar―01 Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action Peter Czuppon, Florence Débarre, Antonio Gonçalves, Olivier Tenaillon, Alan S. Perelson, Jérémie Guedj, et al. (+2)
55 [GO] 2021―Feb―26 Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches Judith A. Bouman, Julien Riou, Sebastian Bonhoeffer, Roland R. Regoes, James Lloyd-Smith
56 [GO] 2021―Feb―11 The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children Itai Dattner, Yair Goldberg, Guy Katriel, Rami Yaari, Nurit Gal, Yoav Miron, et al. (+5)
57 [GO] 2021―Feb―08 SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19 Giulia Fiscon, Federica Conte, Lorenzo Farina, Paola Paci, Manja Marz
58 [GO] 2021―Feb―03 Dynamics of COVID-19 under social distancing measures are driven by transmission network structure Anjalika Nande, Ben Adlam, Justin Sheen, Michael Z. Levy, Alison L. Hill, Alex Perkins
59 [GO] 2021―Feb―03 ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways Agatha Treveil, Balazs Bohar, Padhmanand Sudhakar, Lejla Gul, Luca Csabai, Marton Olbei, et al. (+7)
60 [GO] 2021―Jan―29 Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19 Burcu Tepekule, Anthony Hauser, Viacheslav N. Kachalov, Sara Andresen, Thomas Scheier, Peter W. Schreiber, et al. (+3)
61 [GO] 2021―Jan―29 Estimating the time-varying reproduction number of COVID-19 with a state-space method Shinsuke Koyama, Taiki Horie, Shigeru Shinomoto, Roger Dimitri Kouyos
62 [GO] 2021―Jan―22 Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies Matt J. Keeling, Edward M. Hill, Erin E. Gorsich, Bridget Penman, Glen Guyver-Fletcher, Alex Holmes, et al. (+6)
63 [GO] 2021―Jan―21 Post-lockdown abatement of COVID-19 by fast periodic switching Michelangelo Bin, Peter Y. K. Cheung, Emanuele Crisostomi, Pietro Ferraro, Hugo Lhachemi, Roderick Murray-Smith, et al. (+6)
64 [GO] 2021―Jan―19 Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar, Sahar Arbabi Moghadam, Jack A. Tuszynski, Michael T. Woodside, Alexander MacKerell
65 [GO] 2021―Jan―07 The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection Bruce Y. Lee, Sarah M. Bartsch, Marie C. Ferguson, Patrick T. Wedlock, Kelly J. O’Shea, Sheryl S. Siegmund, et al. (+3)
66 [GO] 2020―Dec―31 A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro Haiping Zhang, Yang Yang, Junxin Li, Min Wang, Konda Mani Saravanan, Jinli Wei, et al. (+12)
67 [GO] 2020―Dec―28 The COVID-19 outbreak in Sichuan, China: Epidemiology and impact of interventions Quan-Hui Liu, Ana I. Bento, Kexin Yang, Hang Zhang, Xiaohan Yang, Stefano Merler, et al. (+7)
68 [GO] 2020―Dec―18 Ten simple rules for creating a brand-new virtual academic meeting (even amid a pandemic) Scott Rich, Andreea O. Diaconescu, John D. Griffiths, Milad Lankarany, Scott Markel
69 [GO] 2020―Dec―09 Empirical model for short-time prediction of COVID-19 spreading Martí Català, Sergio Alonso, Enrique Alvarez-Lacalle, Daniel López, Pere-Joan Cardona, Clara Prats, Benjamin Muir Althouse
70 [GO] 2020―Dec―08 Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection Pranesh Padmanabhan, Rajat Desikan, Narendra M. Dixit, Miles P. Davenport
71 [GO] 2020―Dec―07 In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species Javier Delgado Blanco, Xavier Hernandez-Alias, Damiano Cianferoni, Luis Serrano, Rachel Kolodny
72 [GO] 2020―Dec―03 Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing Sean C. Anderson, Andrew M. Edwards, Madi Yerlanov, Nicola Mulberry, Jessica E. Stockdale, Sarafa A. Iyaniwura, et al. (+7)
73 [GO] 2020―Dec―03 Insights on cross-species transmission of SARS-CoV-2 from structural modeling João P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, João M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, et al. (+2)
74 [GO] 2020―Oct―29 Ten simple rules for women principal investigators during a pandemic Pamela K. Kreeger, Amy Brock, Holly C. Gibbs, K. Jane Grande-Allen, Alice H. Huang, Kristyn S. Masters, et al. (+4)
75 [GO] 2020―Oct―15 A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies Audrey McCombs, Claus Kadelka, James Lloyd-Smith
76 [GO] 2020―Oct―08 Use of Angiotensin-Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers During the COVID-19 Pandemic: A Modeling Analysis Mehrshad Sadria, Anita T. Layton, Daniel A. Beard
77 [GO] 2020―Sep―17 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization Zhengqiao Zhao, Bahrad A. Sokhansanj, Charvi Malhotra, Kitty Zheng, Gail L. Rosen, Nicola Segata
78 [GO] 2020―Jul―02 Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices Joe Hilton, Matt J. Keeling, Jennifer A. Flegg
79 [GO] 2020―Jun―25 Ten simple rules for researchers while in isolation from a pandemic Hoe-Han Goh, Philip E. Bourne, Scott Markel
80 [GO] 2020―Feb―07 Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic Susanne Reimering, Sebastian Muñoz, Alice C. McHardy, Cecile Viboud


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