Update citedin in frontmatter .md files

actions-user · actions-user · commit 6571c970f304 · 2026-04-04T09:01:09.000Z
diff --git a/_pathways/WP2328.md b/_pathways/WP2328.md
@@ -67,6 +67,9 @@ citedin:
 - link: PMC12652001
   title: Integrative Bioinformatics Analysis Reveals Key Regulatory Genes and Therapeutic
     Targets in Ulcerative Colitis Pathogenesis (2025)
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities:
 - ONTOX
 description: This pathway illustrates molecular interactions involved in the fundamental
diff --git a/_pathways/WP2380.md b/_pathways/WP2380.md
@@ -26,6 +26,9 @@ citedin:
   title: 'A Practical Strategy for Exploring the Pharmacological Mechanism of Luteolin
     Against COVID-19/Asthma Comorbidity: Findings of System Pharmacology and Bioinformatics
     Analysis (2024)'
+- link: PMC12948272
+  title: 'CLinNET: An Interpretable and Uncertainty-Aware Deep Learning Framework
+    for Multi-Modal Clinical Genomics (2026)'
 communities:
 - ONTOX
 description: Brain-derived neurotrophic factor (BDNF) is a neurotrophin essential
diff --git a/_pathways/WP2431.md b/_pathways/WP2431.md
@@ -91,6 +91,9 @@ citedin:
 - link: PMC12230732
   title: 'L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine
     (2025)'
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities:
 - Diseases
 - ExRNA
diff --git a/_pathways/WP254.md b/_pathways/WP254.md
@@ -104,6 +104,9 @@ citedin:
   title: Serum extracellular vesicle microRNAs as potential biomarkers to predict
     pembrolizumab response and prognosis in metastatic non-small cell lung cancer
     patients (2025)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities:
 - CPTAC
 - Mitochondrion
diff --git a/_pathways/WP2863.md b/_pathways/WP2863.md
@@ -13,7 +13,7 @@ citedin: ''
 communities:
 - Plants
 description: This plant pathway represents the Krebs cycle (mitochondrion). Pyruvate
-  is imported from the glycolysis ([WP2862](/pathways/WP2862.html))
+  is imported from the glycolysis ([WP2862](https://classic.wikipathways.org/instance/WP2862))
   and converted to acetyl-CoA, which enters the Krebs cycle by getting linked with
   oxaloacetic acid to form citric acid. The cycle produces ATP and NADH, releases
   CO2 and finally regenerated oxaloacetic acid.
@@ -34,7 +34,7 @@ schema-jsonld:
     '@type': Organization
     name: WikiPathways
   description: This plant pathway represents the Krebs cycle (mitochondrion). Pyruvate
-    is imported from the glycolysis ([WP2862](/pathways/WP2862.html))
+    is imported from the glycolysis ([WP2862](https://classic.wikipathways.org/instance/WP2862))
     and converted to acetyl-CoA, which enters the Krebs cycle by getting linked with
     oxaloacetic acid to form citric acid. The cycle produces ATP and NADH, releases
     CO2 and finally regenerated oxaloacetic acid.
diff --git a/_pathways/WP3287.md b/_pathways/WP3287.md
@@ -11,6 +11,10 @@ authors:
 - Egonw
 - MaintBot
 - Eweitz
+citedin:
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities:
 - AOP
 - Nanomaterials
diff --git a/_pathways/WP3959.md b/_pathways/WP3959.md
@@ -38,6 +38,9 @@ citedin:
   title: Autistic spectrum disorder (ASD) - Gene, molecular and pathway signatures
     linking systemic inflammation, mitochondrial dysfunction, transsynaptic signalling,
     and neurodevelopmen (2023)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities:
 - CPTAC
 description: 'Wide-ranging correlations are found between the initial physical features
diff --git a/_pathways/WP4172.md b/_pathways/WP4172.md
@@ -88,6 +88,9 @@ citedin:
 - link: PMC12652001
   title: Integrative Bioinformatics Analysis Reveals Key Regulatory Genes and Therapeutic
     Targets in Ulcerative Colitis Pathogenesis (2025)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities:
 - CPTAC
 - ONTOX
diff --git a/_pathways/WP4478.md b/_pathways/WP4478.md
@@ -9,7 +9,10 @@ authors:
 - Khanspers
 - Eweitz
 - Egonw
-citedin: ''
+citedin:
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities: []
 description: Lactoferrin (LTF) activates NF-kB via danger signal receptors TLR2/4
   and CD14. LTF may also activate NF-kB via additional receptors RAGE and TREM1.
diff --git a/_pathways/WP4540.md b/_pathways/WP4540.md
@@ -28,6 +28,9 @@ citedin:
 - link: PMC7709568
   title: β-hydroxybutyrate does not alter the effects of glucose deprivation on breast
     cancer cells (2021)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities:
 - Diseases
 - RareDiseases
diff --git a/_pathways/WP4549.md b/_pathways/WP4549.md
@@ -42,6 +42,9 @@ citedin:
 - link: PMC12854766
   title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
     Concentration-Response Data (2026)
+- link: PMC12948272
+  title: 'CLinNET: An Interpretable and Uncertainty-Aware Deep Learning Framework
+    for Multi-Modal Clinical Genomics (2026)'
 communities:
 - ONTOX
 - RareDiseases
diff --git a/_pathways/WP4657.md b/_pathways/WP4657.md
@@ -28,6 +28,9 @@ citedin:
 - link: 10.1016/j.softx.2024.101701
   title: 'ODAMNet: A Python package to identify molecular relationships between chemicals
     and rare diseases using overlap, active module and random walk approaches (2024)'
+- link: PMC12948272
+  title: 'CLinNET: An Interpretable and Uncertainty-Aware Deep Learning Framework
+    for Multi-Modal Clinical Genomics (2026)'
 communities:
 - ONTOX
 - RareDiseases
diff --git a/_pathways/WP466.md b/_pathways/WP466.md
@@ -43,6 +43,12 @@ citedin:
 - link: PMC4164264
   title: Diarylheptanoids from Alpinia officinarum Cause Distinct but Overlapping
     Effects on the Translatome of B Lymphoblastoid Cells (2014)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities:
 - ONTOX
 description: 'Studies in the past decade have suggested that the basic mechanism of
diff --git a/_pathways/WP4754.md b/_pathways/WP4754.md
@@ -61,6 +61,12 @@ citedin:
 - link: PMC12230134
   title: Central nervous system and systemic inflammatory networks associated with
     acute neurological outcomes in COVID-19 (2025)
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities: []
 description: Interleukin-18 (IL-18) is a member of the IL-1 family of cytokines and
   was initially described as an IFN-γ-inducing factor derived from anti-CD3-stimulated
diff --git a/_pathways/WP4877.md b/_pathways/WP4877.md
@@ -46,6 +46,9 @@ citedin:
 - link: PMC12323659
   title: Decoding the transcriptome from bulk RNA of infection-naïve versus imprinted
     patients with SARS-CoV-2 Omicron B.1.1.529 (2025)
+- link: PMC13018128
+  title: C-terminus-outward orientation of SARS-CoV-2 envelope proteins on viral capsid
+    enables a novel virus-cell interaction pathway (2026)
 communities:
 - COVID19
 description: 'This pathway describes the activation of the human MAPK signaling system
diff --git a/_pathways/WP4891.md b/_pathways/WP4891.md
@@ -78,6 +78,9 @@ citedin:
 - link: PMC12323659
   title: Decoding the transcriptome from bulk RNA of infection-naïve versus imprinted
     patients with SARS-CoV-2 Omicron B.1.1.529 (2025)
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities:
 - AOP
 - COVID19
diff --git a/_pathways/WP4950.md b/_pathways/WP4950.md
@@ -20,6 +20,9 @@ citedin:
 - link: PMC12034122
   title: Characterization and comparative profiling of piRNAs in serum biopsies of
     pediatric Wilms tumor patients (2025)
+- link: PMC12860421
+  title: Convergent Multistage Evidence Implicates the CCR2–Artemin Immune–Inflammation
+    Axis in Acute Myeloid Leukemia
 communities:
 - ONTOX
 - RareDiseases
diff --git a/_pathways/WP4969.md b/_pathways/WP4969.md
@@ -20,7 +20,10 @@ authors:
 - Penny
 - Eweitz
 - DeSl
-citedin: ''
+citedin:
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities:
 - COVID19
 description: This pathway describes imbalances in the Renin Angiotensin System and
diff --git a/_pathways/WP5039.md b/_pathways/WP5039.md
@@ -73,6 +73,9 @@ citedin:
 - link: PMC11821529
   title: Bat genomes illuminate adaptations to viral tolerance and disease resistance
     (2025)
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities:
 - COVID19
 description: SARS-CoV-2 Innate immunity evasion mechanisms and cell-specific immune
diff --git a/_pathways/WP530.md b/_pathways/WP530.md
@@ -102,6 +102,9 @@ citedin:
 - link: PMC11966866
   title: 'Heme-induced lung injury in human precision cut lung slices: a new model
     for acute lung injury (2025)'
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities:
 - ONTOX
 - PancCanNet
diff --git a/_pathways/WP5345.md b/_pathways/WP5345.md
@@ -27,7 +27,10 @@ authors:
 - Ash iyer
 - AlexanderPico
 - Eweitz
-citedin: ''
+citedin:
+- link: PMC12933876
+  title: Comprehensive Clinical, Diagnostic, and In Silico Assessment of a Novel 1p36.33p36.32
+    Copy Number Variant (2026)
 communities:
 - Diseases
 - ONTOX
diff --git a/_pathways/WP615.md b/_pathways/WP615.md
@@ -43,6 +43,9 @@ citedin:
   title: A bioinformatics approach combined with experimental validation analyzes
     the efficacy of azithromycin in treating SARS-CoV-2 infection in patients with
     IPF and COPD (2025)
+- link: PMC13001922
+  title: Gene expression and metadata based identification of key genes for lung cancer,
+    COPD, and IPF using machine learning and statistical models (2026)
 communities: []
 description: Senescense and autophagy pathways in cancer.  Proteins on this pathway
   have targeted assays available via the [CPTAC Assay Portal](https://assays.cancer.gov/available_assays?wp_id=WP615
diff --git a/_pathways/WP673.md b/_pathways/WP673.md
@@ -62,6 +62,9 @@ citedin:
   title: Serum extracellular vesicle microRNAs as potential biomarkers to predict
     pembrolizumab response and prognosis in metastatic non-small cell lung cancer
     patients (2025)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities:
 - CPTAC
 - ExRNA
diff --git a/_pathways/WP707.md b/_pathways/WP707.md
@@ -50,6 +50,9 @@ citedin:
   title: Long Term Culture of the A549 Cancer Cell Line Promotes Multilamellar Body
     Formation and Differentiation towards an Alveolar Type II Pneumocyte Phenotype
     (2016)
+- link: PMC13001926
+  title: Non-invasive host transcriptome and HPV oncogene expression map the molecular
+    landscape of HPV-driven cervical lesions (2026)
 communities:
 - CPTAC
 - ONTOX
