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2000 Biocomputing 2001  
To explore how the genome of an organism defines its growth, we have developed a computer simulation for the intracellular growth of phage T7 on its E. coli host.  ...  Finally, we suggest how generalization of this work can lead to a knowledge-driven simulation for the growth of any virus.  ...  Acknowledgments We thank the Office of Naval Research (Grant# N00014-98-1-0226) and the National Science Foundation Presidential Early Career Award to J.Y.  ... 
doi:10.1142/9789814447362_0051 fatcat:lnpxvtjvqrghno5jtkn4vdslii

Effect of different modes of viral spread on the dynamics of multiply infected cells in human immunodeficiency virus infection

D. Wodarz, D. N. Levy
2010 Journal of the Royal Society Interface  
During the growth phase, the number of cells infected with i viruses scales linearly with the number of singly infected cells (figure 6b).  ...  For now, we assume that cells and viruses mix perfectly. The results during the growth phase of the virus population remain unaffected.  ... 
doi:10.1098/rsif.2010.0266 pmid:20659927 pmcid:PMC3033025 fatcat:6f44lmblijd4lgdmkuvkp3u5hu

A Cellular Automata Model of Oncolytic Virotherapy in Pancreatic Cancer

J. Chen, D. Weihs, F. J. Vermolen
2020 Bulletin of Mathematical Biology  
The migration of injected viruses (as therapy) is modeled by diffusion through the tissue.  ...  As we expected, our model is able to simulate the pancreatic cancer growth at early stages, which is calibrated with experimental results.  ...  Compliance with Ethical Standards Conflicts of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1007/s11538-020-00780-5 pmid:32737595 fatcat:sbulqwhrvnfnjlhwlyyfqfr6wa

Amplification and Spread of Viruses in a Growing Plaque

1999 Journal of Theoretical Biology  
Here we treat the ampli"cation of viruses during plaque growth as a reaction}di!  ...  The two-dimensional propagation of viruses through a &&lawn" of receptive hosts, commonly called plaque growth, re#ects the dynamics of interactions between viruses and host cells.  ...  Stewart for suggestions on the implementation of the numerical algorithm. Karen Duca and Drew Endy provided valuable comments and suggestions.  ... 
doi:10.1006/jtbi.1999.1001 pmid:10525396 fatcat:idodqo5cyzd7dkvqowwlzq6wme

Effect of stochasticity on coinfection dynamics of respiratory viruses

Lubna Pinky, Gilberto Gonzalez-Parra, Hana M. Dobrovolny
2019 BMC Bioinformatics  
We find that unlike the prediction of the ODE model, for similar initial growth rates stochasticity allows for a slower growing virus to out-compete a faster growing virus.  ...  Stochastic simulations of single virus infections have shown that there is an extinction probability that depends on the size of the initial viral inoculum and parameters that describe virus-cell interactions  ...  Availability of data and materials All data is contained within the manuscript. All code is available at https://doi. org/  ... 
doi:10.1186/s12859-019-2793-6 fatcat:2yfbh4bo6jhs3f5dejzbduxipe

Modelling the Effects of Traits and Abiotic Factors on Viral Lysis in Phytoplankton

Kevin J. Flynn, Susan A. Kimmance, Darren R. Clark, Aditee Mitra, Luca Polimene, William H. Wilson
2021 Frontiers in Marine Science  
However, the timing of the development of the interaction (relative abundance of virus to host at the start of rapid host population growth), overlain on the growth rate and physiological status of the  ...  Simulations show that the optimal performance of a virus (i.e., optimal trait characterisation) is a function of many factors relating to the virus, its host, and the environment.  ...  Mass conservation is tracked including the conversion (decay) of adhered viruses to ammonium (which is the N-source simulated by the model).  ... 
doi:10.3389/fmars.2021.667184 fatcat:m5yta2spr5aqnlzoz2csxwifty

Computational Fitness Landscape for All Gene-Order Permutations of an RNA Virus

Kwang-il Lim, John Yin, Lauren Ancel Meyers
2009 PLoS Computational Biology  
How does the growth of a virus depend on the linear arrangement of genes in its genome?  ...  We used a mathematical model for vesicular stomatitis virus (VSV), a prototype RNA virus that encodes five genes (N-P-M-G-L), to simulate the intracellular growth of all 120 possible gene-order variants  ...  Acknowledgments This work was supported by a National Institutes of Health Phased Innovation Award (AI071197) to JY.  ... 
doi:10.1371/journal.pcbi.1000283 pmid:19197345 pmcid:PMC2627932 fatcat:chk47pd2qnczxkxydfuw43qwwi

A Multiscale Mathematical Model for Oncolytic Virotherapy

L. R. Paiva, C. Binny, S. C. Ferreira, M. L. Martins
2009 Cancer Research  
This result suggests that the search for viruses able to destroy tumor cells very fast does not necessarily lead to a more effective control of tumor growth.  ...  A multiscale model for virotherapy of cancer is investigated through simulations.  ...  The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C.  ... 
doi:10.1158/0008-5472.can-08-2173 pmid:19176387 fatcat:piqzve4slbfjhnyxiqpkzj47ai

Cycling of marine dissolved organic matter. II. A model analysis

N Blackburn, UL Zweifel, Å Hagström
1996 Aquatic Microbial Ecology  
Important observations made from the experimental system included the production of viruses, the presence of dead bacterial cells (ghosts), and the production of detritus.  ...  Simulations predicted that phosphorus recycling occurred via nucleic acids released during cell lysis caused by viruses and that nitrogen was recycled via proteins released as a combined result of cell  ...  We thank Richard Keil and Hugh Ducklow for reviewing the manuscript.  ... 
doi:10.3354/ame011079 fatcat:xsu7iuivh5fydcyacu2r3cizyu

Questing for an optimal, universal viral agent for oncolytic virotherapy [article]

L R Paiva, M L Martins, S C Ferreira Jr
2011 arXiv   pre-print
However, the optimal traits for oncolytic viruses depends critically on the tumor growth dynamics and do not necessarily include rapid replication, cytolysis and spreading currently assumed as necessary  ...  The interaction among viruses and tumor cells involves cell infection, intracellular virus replication and release of new viruses in the tissue after cell lysis.  ...  In summary, the outcomes of oncolytic virotherapy on solid tumors were investigated through computer simulations of a multiscale model for cancer growth.  ... 
arXiv:1109.3614v1 fatcat:qxu23gq3p5bg7hjvg5nfyzztka

Kinetic Modeling of Virus Growth in Cells

John Yin, Jacob Redovich
2018 Microbiology and Molecular Biology Reviews  
Here we review the initial case studies, which include studies of the one-step growth behavior of viruses that infect bacteria (Qβ, T7, and M13), human immunodeficiency virus, influenza A virus, poliovirus  ...  , vesicular stomatitis virus, baculovirus, hepatitis B and C viruses, and herpes simplex virus.  ...  and understanding of viruses.  ... 
doi:10.1128/mmbr.00066-17 pmid:29592895 fatcat:bdk4cmugo5aqnae2sg2nqjobra

An Agent-Based Metapopulation Model Simulating Virus-Based Biocontrol of Heterodera Glycines

Safyre Anderson, Chinmay Soman, Sadia Bekal, Leslie Domier, Kris Lambert, Kaustubh Bhalerao
2018 Journal of nematology  
The simulation model suggested that virus-based biocontrol worked best when the nematodes were inundated with the viruses.  ...  This study explores the question of what kinds of viruses would make useful biocontrol agents, taking into account evolutionary and population dynamics.  ...  Acknowledgments The authors acknowledge the following institutions for grant support: University of Illinois support to S.A., K.B., K.L. and S.B., USDA Hatch support to K.B. and K.L., National Science  ... 
doi:10.21307/jofnem-2018-002 pmid:30451429 pmcid:PMC6909315 fatcat:rg4kuqlvajbfjofoug2phvyfeu

Targeting evolutionary conserved sequences circumvents the evolution of resistance in a viral gene drive against human cytomegalovirus [article]

Marius Walter, Rosalba Perrone, Eric Verdin
2021 bioRxiv   pre-print
We report that after an initial invasion of the wildtype population, a drive-resistant population is positively selected over time and outcompetes gene drive viruses.  ...  A common consequence of gene drives is the appearance and selection of drive-resistant sequences that are no longer recognized by CRISPR-Cas9.  ...  Acknowledgments We thank members of the Verdin laboratory for technical and conceptual help. This study was funded through institutional support from the Buck Institute for Research on Aging.  ... 
doi:10.1101/2021.01.08.425902 fatcat:d56zolrmsfc2bj7ec6c4y4toau

Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection [article]

Jesse Kreger, Josephine Garcia, Natalia L Komarova, Dominik Wodarz, David N Levy
2020 bioRxiv   pre-print
We investigate the contribution of these two transmission pathways to recombinant evolution, by applying mathematical models to in vitro experimental data on the growth of fluorescent reporter viruses  ...  For example, we estimate that during cell-to-cell transmission, an average of 3 viruses successfully integrated into the target cell, which can significantly raise the infection multiplicity compared to  ...  Using the estimated parameters, we can simulate growth of the virus population to the same population size in silico and compare the number of recombinants that have been generated for the different assumed  ... 
doi:10.1101/2020.08.28.272351 fatcat:tvuyhu5eyvggjb2musvasvj2ga

Competitive exclusion during co-infection as a strategy to prevent the spread of a virus: A computational perspective

Safar Vafadar, Maryam Shahdoust, Ata Kalirad, Pooya Zakeri, Mehdi Sadeghi, Bashar Ibrahim
2021 PLoS ONE  
To demonstrate the co-infection of two viruses, we first simulate the characteristics of two virus growth processes separately. Then, we examine their interactions until one can dominate the other.  ...  We use Co-Wish to explore how the model varies as the parameters of each virus growth process change when two viruses infect the host simultaneously.  ...  Co-Wish supports simulating both discrete and stochastic behaviors of each stage of viral growth. It explicitly simulates the behavior of each virus in each stage of its growth process.  ... 
doi:10.1371/journal.pone.0247200 pmid:33626106 fatcat:j7np76mltfehjg7xii5eofnqoq
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