Update citedin in frontmatter .md files

actions-user · actions-user · commit aafd9c632d80 · 2026-02-07T09:00:13.000Z
diff --git a/_pathways/WP1604.md b/_pathways/WP1604.md
@@ -39,6 +39,9 @@ citedin:
 - link: PMC12628759
   title: A computational reference for human genomics analysis in (poly)phenol research
     (2025)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: The principal pathways for the metabolism of codeine occur in the liver,
   although some metabolism occurs in the intestine and brain. Approximately 50-70%
diff --git a/_pathways/WP1992.md b/_pathways/WP1992.md
@@ -23,6 +23,9 @@ citedin:
 - link: 10.1159/000529687
   title: Identification of the Genetic Influence of SARS-CoV-2 Infections on IgA Nephropathy
     Based on Bioinformatics Method (2023)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ExRNA
 description: This catalog pathway was created using the database from [TarBase](http://diana.cslab.ece.ntua.gr/tarbase/)
diff --git a/_pathways/WP2064.md b/_pathways/WP2064.md
@@ -30,6 +30,9 @@ citedin:
     of drugs and chemical compounds for schizophrenia (2023)
 - link: 10.1016/j.tiv.2016.03.009
   title: MicroRNAs as potential biomarkers for doxorubicin-induced cardiotoxicity
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: 'Gene regulatory network model of cranial neural crest cell (CNCC) development,
diff --git a/_pathways/WP2436.md b/_pathways/WP2436.md
@@ -40,6 +40,9 @@ citedin:
 - link: PMC12448840
   title: 'GNNenrich: a novel method for pathway enrichment analysis based on graph
     neural network (2025)'
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: 'Dopamine is an organic chemical of the catecholamine and phenethylamine
diff --git a/_pathways/WP2491.md b/_pathways/WP2491.md
@@ -19,7 +19,10 @@ authors:
 - Fehrhart
 - Eweitz
 - Duan
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: CYP metabolism of the diclofenac drug (a NSAID), commonly used to treat
diff --git a/_pathways/WP2640.md b/_pathways/WP2640.md
@@ -12,7 +12,10 @@ authors:
 - Egonw
 - MaintBot
 - Eweitz
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: 'The CYP P450 metabolism of aripiprazole has been studied and described
   in several papers (like the one in the bibliography), except for the original primary
diff --git a/_pathways/WP2795.md b/_pathways/WP2795.md
@@ -28,6 +28,9 @@ citedin:
 - link: PMC4168754
   title: 'WikiPathways App for Cytoscape: Making biological pathways amenable to network
     analysis and visualization (2014)'
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: Integrated schematic of the more extensively characterized intracellular
   signal-transduction pathways that coordinate the cardiac hypertrophic response.
diff --git a/_pathways/WP2873.md b/_pathways/WP2873.md
@@ -39,6 +39,9 @@ citedin:
 - link: 10.2174/1389200214666131118234138
   title: Pathways for Ligand Activated Nuclear Receptors to Unravel the Genomic Responses
     Induced by Hepatotoxicants (2013)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: The aryl hydrocarbon receptor (AhR) is a transcription factor (part of
diff --git a/_pathways/WP2880.md b/_pathways/WP2880.md
@@ -36,6 +36,9 @@ citedin:
 - link: PMC12519639
   title: Lysosome dysfunction alters intestinal morphology and lipid metabolism in
     early neonatal piglets (2025)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: The glucocorticoid receptor (GR, a.k.a. NR3C1) is a nuclear receptor
   that is activated upon binding of cortisol or glucocorticoids. It mainly regulates
diff --git a/_pathways/WP2884.md b/_pathways/WP2884.md
@@ -66,6 +66,9 @@ citedin:
 - link: PMC11900854
   title: 'Seabirds in crisis: Plastic ingestion induces proteomic signatures of multiorgan
     failure and neurodegeneration (2025)'
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - MetaKids
 - ONTOX
diff --git a/_pathways/WP3298.md b/_pathways/WP3298.md
@@ -40,6 +40,9 @@ citedin:
 - link: 10.1186/s13148-023-01612-8
   title: 'Methylation analysis by targeted bisulfite sequencing in large for gestational
     age (LGA) newborns: the LARGAN cohort (2024)'
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: Melatonin is an important regulator of circadian rythmus and influences
   also insulin secretion, immune function, retinal function and neuroprotection. The
diff --git a/_pathways/WP3664.md b/_pathways/WP3664.md
@@ -25,6 +25,9 @@ citedin:
 - link: PMC9293528
   title: Circulating miRNAs as Epigenetic Mediators of Periodontitis and Preeclampsia
     Association (2022)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - CPTAC
 - ONTOX
diff --git a/_pathways/WP3851.md b/_pathways/WP3851.md
@@ -21,6 +21,9 @@ citedin:
 - link: 10.1155/2022/3515001
   title: Combination of Enrichment Using Gene Ontology and Transcriptomic Analysis
     Revealed Contribution of Interferon Signaling to Severity of COVID-19 (2022)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: 'Toll-like receptors (TLRs) are used by mammals to recognize pathogen-associated
   molecules such as cell wall components. TLR4 activation inhibits a cell''s ability
diff --git a/_pathways/WP3893.md b/_pathways/WP3893.md
@@ -39,6 +39,9 @@ citedin:
 - link: PMC12230134
   title: Central nervous system and systemic inflammatory networks associated with
     acute neurological outcomes in COVID-19 (2025)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: Development and heterogeneity of the innate lymphoid cell (ILC) family.
   ILCs develop from distinct progenitors in the fetal liver or bone marrow and then
diff --git a/_pathways/WP3915.md b/_pathways/WP3915.md
@@ -40,6 +40,9 @@ citedin:
 - link: PMC11980838
   title: EIF3D safeguards the homeostasis of key signaling pathways in human primed
     pluripotency (2025)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: The hepatic ANGPTL8 (Angiopoietin Like Protein 8) regulatory pathway
diff --git a/_pathways/WP4249.md b/_pathways/WP4249.md
@@ -19,6 +19,9 @@ authors:
 citedin:
 - link: PMC9099719
   title: Tumour Stem Cells in Breast Cancer (2022)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - CPTAC
 - ONTOX
diff --git a/_pathways/WP4545.md b/_pathways/WP4545.md
@@ -79,6 +79,9 @@ citedin:
 - link: PMC11346867
   title: Mechanism of inhibition of TLR4/NFκB/NLRP3 inflammatory pathway against AD
     based on the network pharmacology of Erjing Pills (2024)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - IEM
 - Lipids
diff --git a/_pathways/WP4549.md b/_pathways/WP4549.md
@@ -39,6 +39,9 @@ citedin:
 - link: PMC12470172
   title: Altered Neuroinflammatory Transcriptomic Profile in the Hippocampal Dentate
     Gyrus Three Weeks After Lateral Fluid Percussion Injury in Rats (2025)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 - RareDiseases
diff --git a/_pathways/WP4659.md b/_pathways/WP4659.md
@@ -39,6 +39,9 @@ citedin:
 - link: PMC11980838
   title: EIF3D safeguards the homeostasis of key signaling pathways in human primed
     pluripotency (2025)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: 'Gastrin is a peptide hormone which is involved in the process of gastric
   acid secretion. Gastrin release is induced by the gastrin-releasing peptide, a neurotransmitter
diff --git a/_pathways/WP4707.md b/_pathways/WP4707.md
@@ -15,7 +15,10 @@ authors:
 - Egonw
 - Khanspers
 - Eweitz
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: Aspirin effects on miRNAs.
diff --git a/_pathways/WP4725.md b/_pathways/WP4725.md
@@ -29,6 +29,9 @@ citedin:
 - link: 10.1007/s13770-023-00621-1
   title: Reconstructed Human Skin with Hypodermis Shows Essential Role of Adipose
     Tissue in Skin Metabolism (2024)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - IEM
 - Lipids
diff --git a/_pathways/WP4747.md b/_pathways/WP4747.md
@@ -24,6 +24,9 @@ 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: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: UNC-5 Homolog B (UNC5B) is a member of the dependence receptor family.
   It can induce two opposite intracellular signaling cascades depending on the presence
diff --git a/_pathways/WP4880.md b/_pathways/WP4880.md
@@ -60,6 +60,9 @@ 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: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - COVID19
 description: Figure 8 of review. The induction of Type I interferons and signaling
diff --git a/_pathways/WP5044.md b/_pathways/WP5044.md
@@ -17,7 +17,10 @@ authors:
 - Finterly
 - Larsgw
 - Nikita Krstevska
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: The kynurenine pathway is the major path for Tryptophan (Trp) breakdown
diff --git a/_pathways/WP5050.md b/_pathways/WP5050.md
@@ -19,6 +19,10 @@ authors:
 - Fehrhart
 - Eweitz
 - Mkutmon
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: Pyruvate dehydrogenase (PDH) is a central enzyme in relation to the TCA
diff --git a/_pathways/WP5095.md b/_pathways/WP5095.md
@@ -27,6 +27,9 @@ citedin:
 - link: PMC12106470
   title: 'Glypican-3 regulated epithelial mesenchymal transformation-related genes
     in osteosarcoma: based on comprehensive tumor microenvironment profiling (2025)'
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: Inflammatory cytokines leading to cytokine storm after NF-kappa-B and
   prostaglandin activation. KEGG pathway 05171 and a paper by Robb et al. was referenced
diff --git a/_pathways/WP5117.md b/_pathways/WP5117.md
@@ -17,6 +17,9 @@ citedin:
 - link: 10.1097/md.0000000000039057
   title: Investigation of the relationship between COVID-19 and pancreatic cancer
     using bioinformatics and systems biology approaches (2024)
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 description: 'Cohesin complex workings during mitotic and meiotic cell cycles. '
diff --git a/_pathways/WP5202.md b/_pathways/WP5202.md
@@ -14,7 +14,10 @@ authors:
 - Fehrhart
 - Eweitz
 - Egonw
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - RareDiseases
 description: Alström syndrome is a rare autosomal recessive genetic disorder. This
diff --git a/_pathways/WP5222.md b/_pathways/WP5222.md
@@ -20,6 +20,9 @@ authors:
 citedin:
 - link: PMC11761428
   title: 'RIOK1: A Novel Oncogenic Driver in Hepatocellular Carcinoma (2025)'
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - ONTOX
 - RareDiseases
diff --git a/_pathways/WP5269.md b/_pathways/WP5269.md
@@ -23,7 +23,10 @@ authors:
 - Egonw
 - Eweitz
 - Larsgw
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities:
 - RareDiseases
 description: 'Porto sinusoidal vascular disease (PSVD), or formerly known as idiopathic
diff --git a/_pathways/WP5273.md b/_pathways/WP5273.md
@@ -23,7 +23,10 @@ annotations:
 authors:
 - DeSl
 - Eweitz
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: A hypothetical pathway showing the interactions of metabolites produced
   by the intestinal microbiome, which can affects the anticoagulant response of vitamin
diff --git a/_pathways/WP5394.md b/_pathways/WP5394.md
@@ -16,7 +16,10 @@ authors:
 - Juliablad
 - Ddigles
 - Eweitz
-citedin: ''
+citedin:
+- link: PMC12854766
+  title: Hierarchical Mechanistic Modeling of Complex Toxicity Endpoints from Public
+    Concentration-Response Data (2026)
 communities: []
 description: 'One of the main roles of fibroblasts is the secretion of the extracellular
   matrix components such as glycosaminoglycans (GAGs). This pathway describes the
