update CHARM app and SG paper

Author: ritamtbsilva

publications.html

@@ -245,6 +245,15 @@ <h1 class="pubs-page-h1">Lab Publications</h1>
       <!-- Preprints -->
       <div class="pubs-year">Preprints</div>
       <ul class="pubs-list">
+        <li class="pubs-item pubs-selected"
+            data-selected="true"
+            data-year="preprint"
+            data-authors="Kaizeler A, Coutinho D, Vieira DV, Morais VA, Barbosa-Morais NL"
+            data-journal="bioRxiv, 2026.09.08.749846">
+          <strong>Kaizeler A</strong>, Coutinho D, <strong>Vieira DV</strong>, Morais VA, <strong>Barbosa-Morais NL</strong>.
+          "<a href="https://doi.org/10.64898/2026.09.08.749846" target="_blank" rel="noopener">Revisiting Stress Granule Transcriptomes Suggests Mitochondrial RNA Enrichment Despite Methodological Bias.</a>"
+          <em>bioRxiv</em>, 2026.09.08.749846.
+        </li>
         <li class="pubs-item pubs-selected"
             data-selected="true"
             data-year="preprint"

sections/nuno.html

@@ -492,6 +492,11 @@ <h1 class="nuno-hero-name">Nuno L. Barbosa-Morais</h1>
         <div class="nuno-pub-section-title">Preprints</div>
 
         <ul class="nuno-pub-list">
+          <li class="nuno-pub-item key-paper">
+            Kaizeler A, Coutinho D, Vieira DV, Morais VA, <strong>Barbosa-Morais NL</strong>.
+            "<a href="https://doi.org/10.64898/2026.09.08.749846" target="_blank" rel="noopener">Revisiting Stress Granule Transcriptomes Suggests Mitochondrial RNA Enrichment Despite Methodological Bias.</a>"
+            <em>bioRxiv</em>, 2026.09.08.749846.
+          </li>
           <li class="nuno-pub-item key-paper">
             Marques D<sup>+</sup>, Fernandes C, <strong>Barbosa-Morais NL</strong><sup>+</sup>, Reis C<sup>+</sup>.
             "<a href="https://doi.org/10.1101/2025.06.16.659930" target="_blank" rel="noopener">Circadian disruption beneath the surface: a screening approach to identify actigraphy-based markers of split shift work in submariners.</a>"

sections/research.html

@@ -154,6 +154,9 @@ <h2 class="section-title fade-up">Research</h2>
           <p class="research-card-desc">
             Stress granules (SGs) are membraneless cytoplasmic condensates that form rapidly in response to a wide range of cellular stressors, including hypoxia, nutrient deprivation, oxidative stress, viral infection, and chemotherapy, and dissolve upon stress resolution. Composed of stalled preinitiation complexes, mRNAs, and a rich complement of RNA-binding proteins, they are thought to selectively sequester specific transcripts and proteins, including regulators of apoptosis, senescence, and immune signalling, thereby fine-tuning the cellular response to environmental challenge. Beyond their physiological roles, SGs have been implicated in cancer, where they may promote survival and confer resistance to therapy, as well as in neurodegeneration and antiviral defence. Nevertheless, the precise composition of SGs and the functional significance of their molecular cargo remain contested, partly due to methodological inconsistencies between purification approaches. This project performs an unbiased integration of publicly available human SG transcriptomic datasets, spanning multiple cell lines, stressors, and purification methods, to resolve these discrepancies, identify reproducible features of SG-enriched transcriptomes, and probe the implications of SG biology for cancer and other pathological contexts.
           </p>
+          <p class="research-card-preprint">
+              <a href="https://www.biorxiv.org/content/10.64898/2026.09.08.749846v1" target="_blank" rel="noopener"><svg width="11" height="11" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" aria-hidden="true"><path d="M14 2H6a2 2 0 0 0-2 2v16a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V8z"/><polyline points="14 2 14 8 20 8"/></svg> Preprint (bioRxiv)</a>
+            </p>
         </div>
       </div>
 

sections/software.html

@@ -59,6 +59,8 @@ <h2 class="section-title fade-up">Bioinformatics tools</h2>
                target="_blank" rel="noopener">Paper</a>
             <a class="tool-link" href="https://github.com/DiseaseTranscriptomicsLab/voyAGEr"
                target="_blank" rel="noopener">GitHub</a>
+            <a class="tool-link" href="https://diseasetranscriptomicslab.github.io/voyAGEr/www/voyAGEr-WebAppTutorial.html"
+               target="_blank" rel="noopener">Documentation</a>
           </div>
           <a class="tool-link launch"
              href="https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr"
@@ -97,6 +99,8 @@ <h2 class="section-title fade-up">Bioinformatics tools</h2>
                target="_blank" rel="noopener">Paper</a>
             <a class="tool-link" href="https://github.com/DiseaseTranscriptomicsLab/betAS"
                target="_blank" rel="noopener">GitHub</a>
+            <a class="tool-link" href="https://diseasetranscriptomicslab.github.io/betAS/inst/betAS_tutorial.html"
+               target="_blank" rel="noopener">Documentation</a>
           </div>
           <a class="tool-link launch"
              href="https://compbio.imm.medicina.ulisboa.pt/app/betAS"
@@ -208,7 +212,7 @@ <h2 class="section-title fade-up">Bioinformatics tools</h2>
             <circle cx="12" cy="12" r="10"/>
             <path d="M2 12h20M12 2a15.3 15.3 0 0 1 4 10 15.3 15.3 0 0 1-4 10 15.3 15.3 0 0 1-4-10 15.3 15.3 0 0 1 4-10z"/>
           </svg>
-          Web App (in development)
+          Online Web App
         </span>
         <div class="tool-name">CHARM</div>
         <p class="tool-desc">
@@ -219,7 +223,12 @@ <h2 class="section-title fade-up">Bioinformatics tools</h2>
           <div class="tool-link-row">
             <a class="tool-link" href="https://github.com/DiseaseTranscriptomicsLab/CHARM/"
                target="_blank" rel="noopener">GitHub</a>
+            <a class="tool-link" href="https://diseasetranscriptomicslab.github.io/CHARM/tutorial.html"
+               target="_blank" rel="noopener">Documentation</a>
           </div>
+          <a class="tool-link launch"
+             href="https://compbio.imm.medicina.ulisboa.pt/app/CHARM"
+             target="_blank" rel="noopener">Launch app ↗</a>
         </div>
       </div>
 
@@ -255,6 +264,8 @@ <h2 class="section-title fade-up">Bioinformatics tools</h2>
                target="_blank" rel="noopener">Bioconductor</a>
             <a class="tool-link" href="https://github.com/DiseaseTranscriptomicsLab/markeR/"
                target="_blank" rel="noopener">GitHub</a>
+            <a class="tool-link" href="https://diseasetranscriptomicslab.github.io/markeR/articles/markeR.html"
+               target="_blank" rel="noopener">Documentation</a>
           </div>
           <a class="tool-link launch"
              href="https://compbio.imm.medicina.ulisboa.pt/app/markeR"

sections/team.html

@@ -285,7 +285,7 @@ <h2 class="section-title fade-up">Meet the team</h2>
       <div class="member-card fade-up" style="transition-delay:.3s;">
         <div class="member-photo"><img src="assets/photos/Alessandro.jpg" alt="Alessandro Minguzzi" /></div>
         <div class="member-info">
-          <span class="member-role-badge">PhD Student (starts Sep 2026)</span>
+          <span class="member-role-badge">PhD Student</span>
           <div class="member-name-row">
             <div class="member-name">Alessandro Minguzzi</div>
             <span class="member-flag">🇮🇹</span>