Merge pull request #1572 from unipept/feature/update-about-page

Update all publications and the about page
unipept · Dec 11, 2024 · 512301b · 512301b
2 parents 56234b2 + a026464
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diff --git a/src/components/pages/AboutPage.vue b/src/components/pages/AboutPage.vue
@@ -30,6 +30,18 @@
                             If you use Unipept for your research, please cite:
                         </span>
                         <ul class="pl-6">
+                            <li>
+                                Unipept in 2024: Vande Moortele et al. (2024)
+                                <RLink to="https://doi.org/10.1101/2024.09.26.615136">
+                                    doi.org/10.1101/2024.09.26.615136
+                                </RLink>
+                            </li>
+                            <li>
+                              Unipept Desktop 2.0: Verschaffelt et al. (2023)
+                              <RLink to="https://doi.org/10.1021/acs.jproteome.3c00091">
+                                  doi.org/10.1021/acs.jproteome.3c00091
+                              </RLink>
+                            </li>
                             <li>
                                 Unipept Desktop: Verschaffelt et al. (2021)
                                 <RLink to="https://doi.org/10.1021/acs.jproteome.0c00855">
@@ -162,9 +174,11 @@ import ugentLogoImage from "@/assets/about/ugent-logo.png";
 const members = [
     { name: "Bart Mesuere", title: "Project lead", imgUrl: "https://avatars.githubusercontent.com/u/481872?v=4" },
     { name: "Pieter Verschaffelt", title: "PostDoc", imgUrl: "https://avatars.githubusercontent.com/u/9608686?v=4" },
+    { name: "Tim Van Den Bossche", title: "PostDoc", imgUrl: "" },
     { name: "Tibo Vande Moortele", title: "PhD student", imgUrl: "https://avatars.githubusercontent.com/u/34175340?v=4" },
-    { name: "Stijn De Clercq", title: "Master student 2023 - 2024", imgUrl: "" },
-    { name: "Bram Devlaminck", title: "Master student 2023 - 2024", imgUrl: "" },
+    { name: "Simon Van de Vyver", title: "PhD student", imgUrl: "" },
+    { name: "Tanja Holstein", title: "PhD student", imgUrl: "" },
+    { name: "Jasper Janin", title: "Master student 2024 - 2025", imgUrl: "" },
     { name: "Peter Dawyndt", title: "P.I.", imgUrl: "https://avatars.githubusercontent.com/u/5736113?v=4" },
     { name: "Lennart Martens", title: "P.I.", imgUrl: "" }
 ];
@@ -178,6 +192,8 @@ const former_members = [
     { name: "Kevin Velghe", title: "Master's student 2015-2016", imgUrl: "" },
     { name: "Aranka Steyaert", title: "Master's student 2016-2017", imgUrl: "" },
     { name: "Niels De Graef", title: "Master's student 2016-2018", imgUrl: "https://avatars.githubusercontent.com/u/1382976?v=4" },
+    { name: "Stijn De Clercq", title: "Master student 2023 - 2024", imgUrl: "" },
+    { name: "Bram Devlaminck", title: "Master student 2023 - 2024", imgUrl: "" },
     { name: "Peter Vandamme", title: "Advisor", imgUrl: "" },
     { name: "Bart Devreese", title: "Advisor", imgUrl: "" },
 ];

diff --git a/src/components/pages/PublicationsPage.vue b/src/components/pages/PublicationsPage.vue
@@ -7,6 +7,27 @@
             This page lists all Unipept peer-reviewed journal articles in reverse-chronological order.
         </h3>
 
+        <publication-card
+            class="mt-5"
+            title="Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages, Semi-Tryptic and Non-Tryptic Peptides"
+            :authors='["Tibo Vande Moortele", "Bram Devlaminck", "Simon Van de Vyver", "Tim Van Den Bossche", "Lennart Martens", "Peter Dawyndt", "Bart Mesuere", "Pieter Verschaffelt"]'
+            journal="BioRXiv"
+            year="2024"
+            doi="doi.org/10.1101/2024.09.26.615136"
+            google-scholar="https://scholar.google.com/scholar?hl=nl&as_sdt=0%2C5&q=unipept+in+2024&btnG=&oq=unipe"
+            :image="Publication2023Image"
+        >
+            <template #abstract>
+                Unipept, a pioneering software tool in metaproteomics, has significantly advanced the analysis of complex ecosystems by facilitating both taxonomic and functional insights from environmental samples.
+                From the onset, Unipept’s capabilities focused on tryptic peptides, utilizing the predictability and consistency of trypsin digestion to efficiently construct a protein reference database.
+                However, the evolving landscape of proteomics and emerging fields like immunopeptidomics necessitate a more versatile approach that extends beyond the analysis of tryptic peptides.
+                In this article, we present a significant update to the underlying index structure of Unipept, which is now powered by a Sparse Suffix Array index.
+                This advancement enables the analysis of semi-tryptic peptides, peptides with missed cleavages, and non-tryptic peptides such as those encountered in other research fields such as immunopeptidomics (e.g. MHC- and HLA-peptides).
+                This new index benefits all tools in the Unipept ecosystem such as the web application, desktop tool, API and command line interface.
+                A benchmark study highlights significantly improved performance in handling missed cleavages, preserving the same level of accuracy.
+            </template>
+        </publication-card>
+
         <publication-card
             class="mt-5"
             title="Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses"

diff --git a/src/router/index.ts b/src/router/index.ts
@@ -2,8 +2,8 @@
 import { createRouter, createWebHistory } from 'vue-router'
 
 const tpaMeta = {
-    publication: "Gurdeep Singh et al. (2019) Journal of Proteome Research",
-    publicationLink: "doi:10.1021/acs.jproteome.8b00716",
+    publication: "Vande Moortele et al. (2024) BioRXiv",
+    publicationLink: "doi.org/10.1101/2024.09.26.615136",
 };
 
 const apidocsMeta = {
@@ -27,17 +27,17 @@ const newsMeta = {
 };
 
 const desktopMeta = {
-    publication: "Verschaffelt et al. (2021) Journal of Proteome Research",
-    publicationLink: "doi.org/10.1021/acs.jproteome.0c00855"
+    publication: "Verschaffelt et al. (2023) Journal of Proteome Research",
+    publicationLink: "doi.org/10.1021/acs.jproteome.3c00091"
 }
 
 const routes = [
     {
         path: "/",
         component: () => import("@/components/pages/HomePage.vue"),
         meta: {
-            publication: "Gurdeep Singh et al. (2019) Journal of Proteome Research",
-            publicationLink: "doi:10.1021/acs.jproteome.8b00716"
+            publication: "Vande Moortele et al. (2024) BioRXiv",
+            publicationLink: "doi.org/10.1101/2024.09.26.615136"
         }
     },
     {
@@ -55,8 +55,8 @@ const routes = [
         path: "/mpa",
         component: () => import("@/components/pages/features/MetaproteomeAnalysisPage.vue"),
         meta: {
-            publication: "Gurdeep Singh et al. (2019) Journal of Proteome Research",
-            publicationLink: "doi:10.1021/acs.jproteome.8b00716"
+            publication: "Vande Moortele et al. (2024) BioRXiv",
+            publicationLink: "doi.org/10.1101/2024.09.26.615136"
         }
     },
     {