Update paper link

README.md

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 # Deep mutational scanning of Lassa virus Josiah strain glycoprotein using a barcoded lentiviral platform
-See [Carr, Crawford, ..., Bloom](https://www.biorxiv.org/content/10.1101/2024.02.05.579020v1) for the paper describing this study. Note that this repository has been updated since the release of the pre-print posted above so there could be small differences between the paper and pipeline figures.  
+See [Carr, Crawford, ..., Bloom](https://www.cell.com/immunity/fulltext/S1074-7613(24)00319-4) for the paper describing this study. 
 
 For documentation of the analysis, see [https://dms-vep.github.io/LASV_Josiah_GP_DMS/](https://dms-vep.github.io/LASV_Josiah_GP_DMS/)
 

homepage/.vitepress/config.mjs

@@ -12,14 +12,14 @@ export default defineConfig({
     // https://vitepress.dev/reference/default-theme-config
     nav: [
       { text: "Home", link: "/" },
-      { text: 'Paper', link: "https://www.biorxiv.org/content/10.1101/2024.02.05.579020v1" },
+      { text: 'Paper', link: "https://www.cell.com/immunity/fulltext/S1074-7613(24)00319-4" },
       { text: 'Cell Entry', link: '/cell_entry' },
       { text: 'Antibody Escape', link: '/antibody_escape' },
       { text: "Appendix", link: "/appendix", target: "_self" },
     ],
     socialLinks: [{ icon: "github", link: "https://github.com/dms-vep/LASV_Josiah_GP_DMS.git" }],
     footer: {
-      message: 'Study by <a href="https://www.biorxiv.org/content/10.1101/2024.02.05.579020v1">Carr, Crawford, et al (2024), bioRxiv, DOI 10.1101/2024.02.05.579020</a>',
+      message: 'Study by <a href="https://www.cell.com/immunity/fulltext/S1074-7613(24)00319-4">Carr, Crawford, et al (2024), bioRxiv, DOI 10.1101/2024.02.05.579020</a>',
     },
   },
 });

homepage/experiments_and_biosafety.md

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 # Experiments and biosafety
 
-The paper describing this study is [Carr, Crawford, et al (2024)](https://www.biorxiv.org/content/10.1101/2024.02.05.579020v1). The measurements are all made using a pseudovirus-based deep mutational scanning system that was originally described in [Dadonaite et al (2023)](https://doi.org/10.1016/j.cell.2023.02.001).
+The paper describing this study is [Carr, Crawford, et al (2024)](https://www.cell.com/immunity/fulltext/S1074-7613(24)00319-4). The measurements are all made using a pseudovirus-based deep mutational scanning system that was originally described in [Dadonaite et al (2023)](https://doi.org/10.1016/j.cell.2023.02.001).
 
 A key aspect of this system is that it utilizes pseudotyped lentiviral virions that encode no viral genes other than the viral entry protein (in this case GPC).
 Pseudotyping is a [widely used and safe method](https://blog.addgene.org/viral-vectors-101-pseudotyping) to study viral entry proteins, since the pseudoviruses can only undergo a single cycle of infection and therefore pose no risk of transmission or replication in humans or any other animals.

homepage/index.md

@@ -29,7 +29,7 @@ features:
 ## About this site
 This website contains interactive plots and numerical results from [pseudovirus deep mutational scanning](https://www.sciencedirect.com/science/article/pii/S0092867423001034?via%3Dihub) experiments that measure the effects of mutations to the glycoprotein complex (GPC) of the lineage IV Lassa virus Josiah strain on cell entry and antibody escape.
 
-The paper describing this study is [Carr, Crawford, et al (2024)](https://www.biorxiv.org/content/10.1101/2024.02.05.579020v1).
+The paper describing this study is [Carr, Crawford, et al (2024)](https://www.cell.com/immunity/fulltext/S1074-7613(24)00319-4).
 
 The links in the boxes above take you to interactive plots or descriptions of different aspects of the study.
 For a high-level overview, see the [summary](summary){target="_self"} of how mutations affect cell entry and antibody escape.