2019
DOI: 10.1038/s41467-019-09879-3
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Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures

Abstract: Pathogens face varying microenvironments in vivo, but suitable experimental systems and analysis tools to dissect how three-dimensional (3D) tissue environments impact pathogen spread are lacking. Here we develop an Integrative method to Study Pathogen spread by Experiment and Computation within Tissue-like 3D cultures (INSPECT-3D), combining quantification of pathogen replication with imaging to study single-cell and cell population dynamics. We apply INSPECT-3D to analyze HIV-1 spread between primary human C… Show more

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Cited by 71 publications
(115 citation statements)
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References 68 publications
(85 reference statements)
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“…In order to help understand complex pathogenrelated processes, computational models were developed for viral 46,47 bacterial, 48 parasitic 49 and fungal pathogens. 50 The bioinformatics tools (Table 3) are used to identify possible epitopes for vaccine formulation.…”
Section: Immunoinformatics and Infectious Diseasementioning
confidence: 99%
“…In order to help understand complex pathogenrelated processes, computational models were developed for viral 46,47 bacterial, 48 parasitic 49 and fungal pathogens. 50 The bioinformatics tools (Table 3) are used to identify possible epitopes for vaccine formulation.…”
Section: Immunoinformatics and Infectious Diseasementioning
confidence: 99%
“…gene expression, signal transduction and multicellular systems (e.g. Imle et al , 2019 ; Lenive et al , 2016 ; Picchini, 2014 ).…”
Section: Introductionmentioning
confidence: 99%
“…Contrarily, in likelihood-free methods, particularly ABC, it is easy to disregard any noise due to the unnecessity of even formulating a likelihood and the various inherent approximation levels, so that error sources can be difficult to pinpoint from the result. In the past, it has repeatedly not been included in ABC analyses ( Eriksson et al , 2019 ; Imle et al , 2019 ; Jagiella et al , 2017 ; Lenive et al , 2016 ; Toni et al , 2009 ). Asymptotic unbiasedness of ABC is however granted only if the data-generation process is perfectly reproduced.…”
Section: Introductionmentioning
confidence: 99%
“…gene expression, signal transduction, and multi-cellular systems (e.g. Lenive et al (2016); Picchini (2014); Imle et al (2019)).…”
Section: Introductionmentioning
confidence: 99%
“…Contrarily, in likelihood-free methods, particularly ABC, it is easy to disregard any noise due to the unnecessity of even formulating a likelihood and the various inherent approximation levels, so that error sources can be difficult to pinpoint from the result. In the past, it has repeatedly not been included in ABC analyses (Toni et al, 2009;Lenive et al, 2016;Jagiella et al, 2017;Imle et al, 2019;Eriksson et al, 2019). Asymptotic unbiasedness of ABC is however granted only if the data-generation process is perfectly reproduced.…”
Section: Introductionmentioning
confidence: 99%