updated references

weissmanlab · Jan 31, 2023 · 289028a · 289028a
1 parent 67695a0
commit 289028a
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/research/complex.md b/research/complex.md
@@ -20,7 +20,7 @@ What does our theory predict about this case?
 
 Papers:
 
-- [Ghafari et al (2022), Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern](https://www.biorxiv.org/content/10.1101/2022.05.09.491227)
+- [Ghafari et al (2022), Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern](http://dx.doi.org/10.3389/fviro.2022.942555)
 - [Ghafari and Weissman (2019), The expected time to cross extended fitness plateaus](https://doi.org/10.1016/j.tpb.2019.03.008)
 - [Trotter et al (2014), Cryptic genetic variation can make “irreducible complexity” a common mode of adaptation in sexual populations](http://onlinelibrary.wiley.com/doi/10.1111/evo.12517/pdf)
 - [Weissman, Feldman, and Fisher (2010), The rate of fitness-valley crossing in sexual populations](http://www.genetics.org/content/186/4/1389.short)

diff --git a/research/inference.md b/research/inference.md
@@ -14,7 +14,7 @@ Doing so will require new analytical tools that ask questions that are only now
 Papers:
 
 - [Mehta et al (2022), Detecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes](https://www.biorxiv.org/content/10.1101/2022.03.14.484367)
-- [Ghafari et al (2022), Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern](https://www.biorxiv.org/content/10.1101/2022.05.09.491227)
+- [Ghafari et al (2022), Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern](http://dx.doi.org/10.3389/fviro.2022.942555)
 - [Ghafari et al (2020), Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method](https://journals.asm.org/doi/full/10.1128/JVI.00014-20)
 - [Sobel Leonard et al (2017), Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus](http://jvi.asm.org/content/early/2017/04/27/JVI.00171-17.abstract), and see [correction](https://journals.asm.org/doi/full/10.1128/JVI.00936-19). [Try it out!](https://github.com/weissmanlab/BB_bottleneck)
 - [Weissman and Hallatschek (2017), Minimal-assumption inference from population-genomic data](https://elifesciences.org/articles/24836)---please [try it out](https://github.com/weissmanlab/magic) and let us know what you think!
diff --git a/research/space.md b/research/space.md
@@ -13,7 +13,7 @@ How does this spatial structure interact with adaptive evolution?
 
 Papers:
 
-- [Min et al (2022), Spatial structure alters the site frequency spectrum produced by hitchhiking](https://www.biorxiv.org/content/10.1101/2022.06.08.495311)
-- [Smith and Weissman (2020), Isolation by Distance in Populations with Long-Range Dispersal](https://www.biorxiv.org/content/10.1101/2020.06.24.168211)
+- [Smith and Weissman (2023), Isolation by distance in populations with power-law dispersal](http://dx.doi.org/10.1093/g3journal/jkad023)
+- [Min et al (2022), Spatial structure alters the site frequency spectrum produced by hitchhiking](http://dx.doi.org/10.1093/genetics/iyac139)
 - [Allman and Weissman (2018), Hitchhiking in space: Ancestry in adapting, spatially extended populations](http://dx.doi.org/10.1111/evo.13431)
 
diff --git a/research/viral.md b/research/viral.md
@@ -13,9 +13,9 @@ Papers:
 
 - [Koelle et al (2022), 
 Masks Do No More Than Prevent Transmission: Theory and Data Undermine the Variolation Hypothesis](https://www.medrxiv.org/content/10.1101/2022.06.28.22277028)
-- [Ghafari et al (2022), Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern](https://www.biorxiv.org/content/10.1101/2022.05.09.491227)
+- [Ghafari et al (2022), Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern](http://dx.doi.org/10.3389/fviro.2022.942555)
 - [Scherer et al (2022), SARS-CoV-2 Evolution and Immune Escape in Immunocompromised Patients](https://www.nejm.org/doi/full/10.1056/NEJMc2202861)
-- [Allman, Koelle, and Weissman (2021), Heterogeneity in viral infections increases the rate of deleterious mutation accumulation](https://www.biorxiv.org/content/10.1101/2021.05.07.443113)
+- [Allman, Koelle, and Weissman (2022), Heterogeneity in viral populations increases the rate of deleterious mutation accumulation](http://dx.doi.org/10.1093/genetics/iyac127)
 - [Ghafari et al (2020), Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method](https://journals.asm.org/doi/full/10.1128/JVI.00014-20)
 - [Li et al (2019), Why are CD8 T cell epitopes of human influenza A virus conserved?](https://journals.asm.org/doi/full/10.1128/JVI.01534-18)
 - [Sobel Leonard et al (2017), Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus](http://jvi.asm.org/content/early/2017/04/27/JVI.00171-17.abstract), and see [correction](https://journals.asm.org/doi/full/10.1128/JVI.00936-19)