diff --git a/README.md b/README.md
index 0ce5cca..c450f8f 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,32 @@
-# lnsc-cell-browser
-LNSC cell browser
+## lnsc-cell-browser
+
+### Adding a new publication
+
+* Add a new entry to pubs.yml, the only information needed for the entry is
+ the pubmed URL which is added as the "pubmed" field
+* Optional links can also be added under the "links" field,
+ this includes "github", "atlas", and "geo"
+* Run pre-build.R to scrape the remaining information for the publication and
+ to update authors.yml
+* Rebuild site
+
+### Adding a new cell atlas
+
+* Add the atlas link to the associated publication listed in pubs.yml
+* Rebuild site
+
+### Adding a new project
+
+* Add project information to projects.yml
+* Required fields include, "title", "short", "hypothesis", and "abstract"
+* An optional image can also be included
+* Edit authors.yml to add authors to the new project
+* Run pre-build.R to automatically associate publications with the new project
+* Rebuild site
+
+### Building site
+
+* Remove directories from previous build (_site, .quarto)
+* Run pre-build.R and commit changes
+* Render site
+
diff --git a/atlases/2021-carpentier-34618370/index.qmd b/atlases/2021-carpentier-34618370/index.qmd
index 56c1a8a..12c135c 100644
--- a/atlases/2021-carpentier-34618370/index.qmd
+++ b/atlases/2021-carpentier-34618370/index.qmd
@@ -2,9 +2,9 @@
title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination
image: /images/2021-carpentier-34618370.jpg
-subtitle: '[ Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
+subtitle: '[ Atlas](http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com){.link-box-large}'
date: 'November 15, 2021'
-categories: [Project-1, Project-2, Core-C, Core-D, 2021]
+categories: [Project-1, Project-2, Project-3, Core-C, 2021]
about:
id: about
template: jolla
diff --git a/atlases/2021-walsh-33843587/index.qmd b/atlases/2021-walsh-33843587/index.qmd
index d9dad0e..cf44955 100644
--- a/atlases/2021-walsh-33843587/index.qmd
+++ b/atlases/2021-walsh-33843587/index.qmd
@@ -4,7 +4,7 @@ title: Molecular tracking devices quantify antigen distribution and archiving in
image: /images/2021-walsh-33843587.jpg
subtitle: '[ Atlas](https://d3898ys7yh3545.cloudfront.net/){.link-box-large}'
date: 'April 12, 2021'
-categories: [Project-2, Core-C, Core-D, 2021]
+categories: [Project-2, Project-3, Core-C, 2021]
about:
id: about
template: jolla
diff --git a/atlases/2024-lucas-38194268/index.qmd b/atlases/2024-lucas-38194268/index.qmd
index 3019af4..d1569b3 100644
--- a/atlases/2024-lucas-38194268/index.qmd
+++ b/atlases/2024-lucas-38194268/index.qmd
@@ -2,9 +2,9 @@
title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
image: /images/2024-lucas-38194268.jpg
-subtitle: '[ Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
+subtitle: '[ Atlas](http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com){.link-box-large}'
date: 'January 09, 2024'
-categories: [Project-1, Project-2, Core-C, Core-D, 2024]
+categories: [Project-1, Project-2, Project-3, Core-C, 2024]
about:
id: about
template: jolla
diff --git a/authors.yml b/authors.yml
index e746160..afda258 100644
--- a/authors.yml
+++ b/authors.yml
@@ -44,36 +44,6 @@ Beth Tamburini:
to be well suited for the training and success of the graduate students and post-docs
in my laboratory.
image: /images/beth-tamburini.jpg
-Jenna Guthmiller:
- suffix: PhD
- links:
- publications: https://scholar.google.com/citations?user=4arwbfMAAAAJ&hl=en&oi=ao
- website: https://guthmillerlab.weebly.com/
- email: mailto:jenna.guthmiller@cuanschutz.edu
- project: project-3
- bio: My long-term scientific goals are to understand the complex interactions between
- pathogens and the immune response mounted against them, with the objective of
- identifying and developing interventions to limit global infectious disease burdens.
- Fitting within these goals, my independent laboratory studies how preexisting
- immunity influences future immune responses against rapidly evolving viruses.
- My major contributions to science are understanding how protective humoral immunity
- is generated following infection and vaccination and how vaccination can harness
- broadly protective humoral immunity. During my postdoctoral studies, I investigated
- how preexisting immunity against influenza viruses shapes the recall of memory
- B cells in humans. I found that in the absence of preexisting immunity against
- the variable epitopes of the hemagglutinin (HA) head domain, humans could recall
- memory B cells against broadly protective epitopes of HA. These studies identified
- several novel classes of broadly neutralizing antibodies and a new highly conserved
- epitope where HA 'anchors' itself into the viral membrane. My research also identified
- that the first in-human universal influenza vaccine, which is intended to circumvent
- preexisting antibodies, robustly induced antibodies against broadly protective
- epitopes, including the anchor epitope. Lastly, I identified influenza vaccination
- and infection in humans differentially recalled discrete memory B cell specificities,
- with infection recalling memory B cells primed during childhood against highly
- conserved, albeit non-protective antigens. Together, these studies highlight the
- importance of understanding how preexisting antibodies influence the generation
- of broadly protective immunity.
- image: /images/jenna-guthmiller.jpeg
Jay Hesselberth:
suffix: PhD
links:
@@ -81,8 +51,8 @@ Jay Hesselberth:
website: https://hesselberthlab.org/
email: mailto:jay.hesselberth@cuanschutz.edu
project:
+ - project-3
- core-c
- - core-d
bio: I am an RNA biochemist and computational biologist with extensive experience
in developing new high- throughput methods and associated bioinformatic analysis
software. My RNA biology program spans classical and modern approaches to address
@@ -102,7 +72,7 @@ Ryan Sheridan:
publications: https://orcid.org/0000-0003-4012-3147
website: https://github.com/sheridar
email: mailto:ryan.sheridan@cuanschutz.edu
- project: core-d
+ project: core-c
Jennifer Matsuda:
suffix: PhD
links:
diff --git a/docs/2024-sheridan-38617225.pdf b/docs/2024-sheridan-38617225.pdf
new file mode 100644
index 0000000..ac97272
Binary files /dev/null and b/docs/2024-sheridan-38617225.pdf differ
diff --git a/images/2024-sheridan-38617225.jpg b/images/2024-sheridan-38617225.jpg
new file mode 100644
index 0000000..2079c37
Binary files /dev/null and b/images/2024-sheridan-38617225.jpg differ
diff --git a/images/jenna-guthmiller.jpeg b/images/jenna-guthmiller.jpeg
deleted file mode 100644
index bba0b04..0000000
Binary files a/images/jenna-guthmiller.jpeg and /dev/null differ
diff --git a/projects.qmd b/projects.qmd
index 86af2e7..a86ea0a 100644
--- a/projects.qmd
+++ b/projects.qmd
@@ -31,7 +31,7 @@ proj_yml <- proj_yml %>%
# Create page text
text <- proj_yml %>%
imap(~ {
- ttl <- str_c("# ", .y, "\n\n")
+ ttl <- str_c("\n\n# ", .y, "\n\n")
.x %>%
imap(~ {
diff --git a/projects.yml b/projects.yml
index 54c52a7..1fd8d42 100644
--- a/projects.yml
+++ b/projects.yml
@@ -43,26 +43,11 @@ project-2:
infection of LNSCs to vaccine immunity."
project-3:
- title: Investigate the role of immune complexes in antigen acquisition and
- retention by LNSCs to modulate cellular and humoral immunity
- short: "Project 3 will use stabilized DNA conjugates to track antibody:antigen
- complexes to determine the spatial and cellular localization of immune
- complexes"
- hypothesis: We hypothesize that antibody isotype in an IC regulates protective
- immunity by determining which LNSC populations acquire and retain antigen
- via isotype-specific interactions with complement and Fc receptors (FcRs)
- image: /images/project-3.png
- abstract: "Project 3 will engineer monoclonal antibodies (mAbs) with fixed
- antigen specificity on discrete antibody isotypes and subclasses. Using
- stabilized DNA conjugates, Projects 2 and 3 will track antibody:antigen
- complexes to determine the spatial and cellular localization of ICs in
- comparison with free antigen. Project 3 also investigates how FcR expression
- by LNSCs impacts IC acquisition and will work with Project 1 to determine
- viral antigen retention and define consequences to protective humoral and
- cellular immunity. This project will use mouse models engineered to
- manipulate complement receptor and FcR expression by discrete LNSC
- populations and will define how different LNSC populations use antibody to
- determine antigen uptake and localization."
+ title: TBD
+ short: "Project 3 will..."
+ hypothesis: We hypothesize...
+ image:
+ abstract: "Project 3 will..."
core-b:
title: Mouse transgenics and tissue characterization
@@ -77,29 +62,16 @@ core-b:
mouse LNSCs and lymphoid tissues"
core-c:
- title: Molecular technologies
- short: "Core C will apply new molecular tools to
- understand the contributions of lymph node stromal cells to immune responses"
- abstract: "Core C will apply new molecular tools to
- understand the contributions of lymph node stromal cells to immune
+ title: Molecular technologies and informatics
+ short: "Core C will develop and apply new molecular tools and bioinformatic
+ approaches to probe LNSC and immune cell biology"
+ abstract: "Core C will apply new molecular tools and bioinformatic approaches
+ to understand the contributions of lymph node stromal cells to immune
responses, this includes the following tasks.\n\n
- **Task 1.** Generate validated reagents for and execute single-cell and
- spatial transcriptomic experiments to probe LNSC biology\n\n
- **Task 2.** Production of customized lipid nanoparticles with mRNA and siRNA
- cargo\n\n
- **Task 3.** Expression and purification of antibodies, antigens, and immune
- complexes"
-
-core-d:
- title: Bioinformatics
- short: "Core D will apply new informatics approaches to
- understand the contributions of LNSCs to immune responses"
- abstract: "Core D will apply new informatics approaches to
- understand the contributions of LNSCs to immune responses, this includes the
- following tasks.\n\n
- **Task 1.** Provide a bioinformatics resource for rigorous and reproducible
+ **Task 1.** Generate and supply validated reagents for single-cell and
+ spatial transcriptomic experiments to evaluate LNSC contributions to
+ immunity and infection\n\n
+ **Task 2.** Provide a bioinformatics resource for rigorous and reproducible
analysis of sequencing experiments\n\n
- **Task 2.** Develop pipelines for large scale meta-analysis of single-cell
- and spatial transcriptomic data\n\n
- **Task 3.** Curate a public-facing LNSC atlas to allow for interactive
- exploration of published datasets"
+ **Task 3.** Develop pipelines for large scale meta-analysis of single-cell
+ and spatial transcriptomic data"
diff --git a/pubs.yml b/pubs.yml
index c0f657b..5e6ed21 100644
--- a/pubs.yml
+++ b/pubs.yml
@@ -1,3 +1,42 @@
+- pubmed: https://pubmed.ncbi.nlm.nih.gov/38617225/
+ key: 2024-sheridan-38617225
+ title: A specific and portable gene expression program underlies antigen archiving
+ by lymphatic endothelial cells
+ pmid: PMID 38617225
+ date: April 02, 2024
+ year: '2024'
+ authors:
+ - Ryan Sheridan
+ - Thu Doan
+ - Cormac Lucas
+ - Tadg Forward
+ - Aspen Uecker-Martin
+ - Thomas Morrison
+ - Jay Hesselberth
+ - Beth Tamburini
+ abstract: Antigens from protein subunit vaccination traffic from the tissue to the
+ draining lymph node, either passively via the lymph or carried by dendritic cells
+ at the local injection site. Lymph node (LN) lymphatic endothelial cells (LEC)
+ actively acquire and archive foreign antigens, and archived antigen can be released
+ during subsequent inflammatory stimulus to improve immune responses. Here, we
+ answer questions about how LECs achieve durable antigen archiving and whether
+ there are transcriptional signatures associated with LECs containing high levels
+ of antigen. We used single cell sequencing in dissociated LN tissue to quantify
+ antigen levels in LEC and dendritic cell populations at multiple timepoints after
+ immunization, and used machine learning to define a unique transcriptional program
+ within archiving LECs that can predict LEC archiving capacity in independent data
+ sets. Finally, we validated this modeling, showing we could predict antigen archiving
+ from a transcriptional dataset of CHIKV infected mice and demonstrated in vivo
+ the accuracy of our prediction. Collectively, our findings establish a unique
+ transcriptional program in LECs that promotes antigen archiving that can be translated
+ to other systems.
+ pdf: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11014631/pdf/nihpp-2024.04.01.587647v1.pdf
+ image: /images/2024-sheridan-38617225.jpg
+ project:
+ - project-1
+ - project-2
+ - project-3
+ - core-c
- pubmed: https://pubmed.ncbi.nlm.nih.gov/33843587/
links:
github: https://github.com/rnabioco/antigen-tracking
@@ -5,8 +44,8 @@
geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150719
project:
- project-2
+ - project-3
- core-c
- - core-d
fig_number: 7
key: 2021-walsh-33843587
title: Molecular tracking devices quantify antigen distribution and archiving in
@@ -75,13 +114,13 @@
links:
github: https://github.com/rnabioco/morrison-chikv
geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174667
- atlas: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+ atlas: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
fig_number: 11
project:
- project-1
- project-2
+ - project-3
- core-c
- - core-d
key: 2021-carpentier-34618370
title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to
limit viremia and viral dissemination
@@ -153,12 +192,12 @@
links:
github: https://github.com/rnabioco/morrison-lnsc
geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243638
- atlas: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+ atlas: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
project:
- project-1
- project-2
+ - project-3
- core-c
- - core-d
key: 2024-lucas-38194268
title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell
composition and function via MARCO
@@ -269,8 +308,8 @@
- pubmed: https://pubmed.ncbi.nlm.nih.gov/31156626/
project:
- project-2
+ - project-3
- core-c
- - core-d
links:
geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129933
key: 2019-tamburini-31156626
@@ -347,8 +386,8 @@
project:
- project-1
- project-2
+ - project-3
- core-c
- - core-d
key: 2023-tamburini-37841845
title: Vaccine-induced antigen archiving enhances local memory CD8+ T cell responses
following an unrelated viral infection
diff --git a/pubs/2019-tamburini-31156626/index.qmd b/pubs/2019-tamburini-31156626/index.qmd
index 3d86649..0c1422d 100644
--- a/pubs/2019-tamburini-31156626/index.qmd
+++ b/pubs/2019-tamburini-31156626/index.qmd
@@ -4,7 +4,7 @@ title: Chronic Liver Disease in Humans Causes Expansion and Differentiation of L
image: /images/2019-tamburini-31156626.jpg
subtitle: 'PMID 31156626'
date: 'May 15, 2019'
-categories: [Project-2, Core-C, Core-D, 2019]
+categories: [Project-2, Project-3, Core-C, 2019]
about:
id: about
template: jolla
diff --git a/pubs/2021-carpentier-34618370/index.qmd b/pubs/2021-carpentier-34618370/index.qmd
index 6397121..06cb5b2 100644
--- a/pubs/2021-carpentier-34618370/index.qmd
+++ b/pubs/2021-carpentier-34618370/index.qmd
@@ -4,7 +4,7 @@ title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses t
image: /images/2021-carpentier-34618370.jpg
subtitle: 'PMID 34618370'
date: 'November 15, 2021'
-categories: [Project-1, Project-2, Core-C, Core-D, 2021]
+categories: [Project-1, Project-2, Project-3, Core-C, 2021]
about:
id: about
template: jolla
@@ -22,7 +22,7 @@ about:
href: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174667
- text: Atlas
icon: compass
- href: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+ href: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
---
Kathryn Carpentier, [Ryan Sheridan](https://orcid.org/0000-0003-4012-3147), Cormac Lucas, Bennett Davenport, [Frances Li](https://orcid.org/0000-0001-8798-8290), [Erin Lucas](http://orcid.org/0000-0001-7705-2069), Mary McCarthy, Glennys Reynoso, Nicholas May, [Beth Tamburini](https://orcid.org/0000-0003-1991-231X), [Jay Hesselberth](https://scholar.google.com/citations?user=EnOmNEYAAAAJ), Heather Hickman, [Thomas Morrison](https://scholar.google.com/citations?user=ljkm0eMAAAAJ&hl=en&oi=ao)
diff --git a/pubs/2021-walsh-33843587/index.qmd b/pubs/2021-walsh-33843587/index.qmd
index 157c411..2bfb89d 100644
--- a/pubs/2021-walsh-33843587/index.qmd
+++ b/pubs/2021-walsh-33843587/index.qmd
@@ -4,7 +4,7 @@ title: Molecular tracking devices quantify antigen distribution and archiving in
image: /images/2021-walsh-33843587.jpg
subtitle: 'PMID 33843587'
date: 'April 12, 2021'
-categories: [Project-2, Core-C, Core-D, 2021]
+categories: [Project-2, Project-3, Core-C, 2021]
about:
id: about
template: jolla
diff --git a/pubs/2023-tamburini-37841845/index.qmd b/pubs/2023-tamburini-37841845/index.qmd
index ac493c3..90b49be 100644
--- a/pubs/2023-tamburini-37841845/index.qmd
+++ b/pubs/2023-tamburini-37841845/index.qmd
@@ -4,7 +4,7 @@ title: Vaccine-induced antigen archiving enhances local memory CD8+ T cell respo
image: /images/2023-tamburini-37841845.jpg
subtitle: 'PMID 37841845'
date: 'September 25, 2023'
-categories: [Project-1, Project-2, Core-C, Core-D, 2023]
+categories: [Project-1, Project-2, Project-3, Core-C, 2023]
about:
id: about
template: jolla
diff --git a/pubs/2024-lucas-38194268/index.qmd b/pubs/2024-lucas-38194268/index.qmd
index 7316ddd..1ec2259 100644
--- a/pubs/2024-lucas-38194268/index.qmd
+++ b/pubs/2024-lucas-38194268/index.qmd
@@ -4,7 +4,7 @@ title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cel
image: /images/2024-lucas-38194268.jpg
subtitle: 'PMID 38194268'
date: 'January 09, 2024'
-categories: [Project-1, Project-2, Core-C, Core-D, 2024]
+categories: [Project-1, Project-2, Project-3, Core-C, 2024]
about:
id: about
template: jolla
@@ -22,7 +22,7 @@ about:
href: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243638
- text: Atlas
icon: compass
- href: https://morrison-lnsc-browser.s3.amazonaws.com/index.html
+ href: http://morrison-lnsc-browser.s3-website-us-east-1.amazonaws.com
---
Cormac Lucas, [Ryan Sheridan](https://orcid.org/0000-0003-4012-3147), Glennys Reynoso, Bennett Davenport, Mary McCarthy, Aspen Martin, [Jay Hesselberth](https://scholar.google.com/citations?user=EnOmNEYAAAAJ), Heather Hickman, [Beth Tamburini](https://orcid.org/0000-0003-1991-231X), [Thomas Morrison](https://scholar.google.com/citations?user=ljkm0eMAAAAJ&hl=en&oi=ao)
diff --git a/pubs/2024-sheridan-38617225/index.qmd b/pubs/2024-sheridan-38617225/index.qmd
new file mode 100644
index 0000000..a4d47e2
--- /dev/null
+++ b/pubs/2024-sheridan-38617225/index.qmd
@@ -0,0 +1,22 @@
+---
+title: A specific and portable gene expression program underlies antigen archiving by lymphatic endothelial cells
+
+image: /images/2024-sheridan-38617225.jpg
+subtitle: 'PMID 38617225'
+date: 'April 02, 2024'
+categories: [Project-1, Project-2, Project-3, Core-C, 2024]
+about:
+ id: about
+ template: jolla
+ links:
+ - text: Pubmed
+ icon: file-earmark
+ href: https://pubmed.ncbi.nlm.nih.gov/38617225/
+ - text: PDF
+ icon: filetype-pdf
+ href: /docs/2024-sheridan-38617225.pdf
+---
+
+[Ryan Sheridan](https://orcid.org/0000-0003-4012-3147), Thu Doan, Cormac Lucas, Tadg Forward, Aspen Uecker-Martin, [Thomas Morrison](https://scholar.google.com/citations?user=ljkm0eMAAAAJ&hl=en&oi=ao), [Jay Hesselberth](https://scholar.google.com/citations?user=EnOmNEYAAAAJ), [Beth Tamburini](https://orcid.org/0000-0003-1991-231X)
+
+Antigens from protein subunit vaccination traffic from the tissue to the draining lymph node, either passively via the lymph or carried by dendritic cells at the local injection site. Lymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens, and archived antigen can be released during subsequent inflammatory stimulus to improve immune responses. Here, we answer questions about how LECs achieve durable antigen archiving and whether there are transcriptional signatures associated with LECs containing high levels of antigen. We used single cell sequencing in dissociated LN tissue to quantify antigen levels in LEC and dendritic cell populations at multiple timepoints after immunization, and used machine learning to define a unique transcriptional program within archiving LECs that can predict LEC archiving capacity in independent data sets. Finally, we validated this modeling, showing we could predict antigen archiving from a transcriptional dataset of CHIKV infected mice and demonstrated in vivo the accuracy of our prediction. Collectively, our findings establish a unique transcriptional program in LECs that promotes antigen archiving that can be translated to other systems.
diff --git a/timeline.json b/timeline.json
index a3036e5..26b8e4a 100644
--- a/timeline.json
+++ b/timeline.json
@@ -1 +1 @@
-[{"key":"2021-walsh-33843587","date":"2021-01-01","authors":"Sheridan, Hesselberth, Tamburini","year":"2021","url":"pubs/2021-walsh-33843587","name":"proj","lab":"Project-2, Core-C, Core-D","style":{"font-weight":["normal"]}},{"key":"2021-walsh-33843587","date":"2021-01-01","authors":"Sheridan, Hesselberth, Tamburini","year":"2021","url":"pubs/2021-walsh-33843587","name":"pmid","lab":"PMID33843587","style":{"font-weight":["bold"]}},{"key":"2017-kedl-29229919","date":"2017-01-01","authors":"Tamburini","year":"2017","url":"pubs/2017-kedl-29229919","name":"proj","lab":"Project-2","style":{"font-weight":["normal"]}},{"key":"2017-kedl-29229919","date":"2017-01-01","authors":"Tamburini","year":"2017","url":"pubs/2017-kedl-29229919","name":"pmid","lab":"PMID29229919","style":{"font-weight":["bold"]}},{"key":"2021-carpentier-34618370","date":"2021-01-01","authors":"Sheridan, Tamburini, Hesselberth, Morrison","year":"2021","url":"pubs/2021-carpentier-34618370","name":"proj","lab":"Project-1, 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