subcommunities paper

lasy · Nov 29, 2023 · b5210e0 · b5210e0
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diff --git a/_news/2023-09-01-uclouvain.md b/_news/2023-09-01-uclouvain.md
diff --git a/_news/2023-10-26-DurbanDSB.md b/_news/2023-10-26-DurbanDSB.md
diff --git a/_news/2199-01-01-future-post.md b/_news/2199-01-01-future-post.md
diff --git a/_posts/2023-11-29-Subcommunities-paper.md b/_posts/2023-11-29-Subcommunities-paper.md
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+---
+title: 'Our paper on "Subcommunities of the vaginal microbiota" is out in Proceedings B'
+date: 2023-11-29
+permalink: /posts/2023/11/Subcommunities-paper
+tags:
+  - research
+---
+
+In this [paper](http://lasy.github.io/publication/2023-Symul-VMRC-subcommunities), we show that mixed membership models - here, topic models (LDA) - better describe vaginal microbiota composition than "community (state) types" that are based on clustering approaches. 
+They also better predict the risk of transitioning to a sub-optimal state (loss of Lactobacillus dominance) and better describe longitudinal changes along menstrual cycles.
+
+![figure1](/images/publications/2023_Symul.png)
+
+
+The identification of the topics rely on a package ([alto](https://lasy.github.io/alto/index.html)) previously developed with Kris Sankaran and Julia Fukuyama and described [here](http://lasy.github.io/publication/2021-Fukuyama).
+
+
+So, if you're in need of a dimension reduction method for representing microbiota data, these described here might be a good option. Would love to discuss if you end up trying or finding something that better suit your neeeds.
+
+![figure2](/images/publications/2023_Symul_fig2.png)
+
+
+[Download pdf](http://lasy.github.io/files/papers/2023_Symul_subcommunities.pdf)
+
+I warmly thanks all my co-authors, the VMRC for their relentless efforts in understanding the vaginal microbiota and how to restore it to a healthy state, and the study participants who accepted a quite intensive collection of swabs.
+
+
diff --git a/_publications/2023-Symul-VMRC-subcommunities.md b/_publications/2023-Symul-VMRC-subcommunities.md
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+---
+title: "Sub-communities of the vaginal ecosystem in pregnant and non-pregnant women."
+collection: publications
+permalink: /publication/2023-Symul-VMRC-subcommunities
+date: 2023-11-29
+venue: 'Proceedings of the Royal Society B: Biological Sciences'
+paperurl: http://lasy.github.io/files/papers/2023_Symul_subcommunities.pdf
+---
+
+__L. Symul__, P. Jeganathan, E. K. Costello, M. France, S. Bloom, J. Ravel, D. Kwon, D. Relman, S. Holmes
+
+![figure1](/images/publications/2023_Symul.png)
+
+
+[Link to publication](https://royalsocietypublishing.org/doi/10.1098/rspb.2023.1461) |
+[Download pdf](http://lasy.github.io/files/papers/2023_Symul_subcommunities.pdf)
diff --git a/files/papers/2023_Symul_subcommunities.pdf b/files/papers/2023_Symul_subcommunities.pdf
diff --git a/images/publications/2023_Symul.png b/images/publications/2023_Symul.png
diff --git a/images/publications/2023_Symul_fig2.png b/images/publications/2023_Symul_fig2.png