Gutenberg Open Science

The Open Science Repository of Johannes Gutenberg University Mainz.

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ZeitschriftenaufsatzAccess status: Open Access ,
Xsurvey : web tool to query the set of homorepeats of all reference proteomes
(2025) Andrade-Navarro, Miguel A.; Mier, Pablo
Homorepeats are low complexity regions in protein sequences composed of repetitions of one specific amino acid residue. There is currently no automatic way to compare the set of homorepeats between two or more species. Here we present Xsurvey, a web tool to query the set of homorepeats of 23,150 completely-sequenced proteomes. The polyX usage values can be easily compared visually, which simplifies the interpretation of the results.
ZeitschriftenaufsatzAccess status: Open Access ,
A map of the lipid–metabolite–protein network to aid multi-omics integration
(2025) Anyaegbunam, Uchenna Alex; Vagiona, Aimilia-Christina; ten Cate, Vincent; Bauer, Katrin; Schmidlin, Thierry; Distler, Ute; Tenzer, Stefan; Araldi, Elisa; Bindila, Laura; Wild, Philipp; Andrade-Navarro, Miguel A.
The integration of multi-omics data offers transformative potential for elucidating complex molecular mechanisms underlying biological processes and diseases. In this study, we developed a lipid–metabolite–protein network that combines a protein–protein interaction network and enzymatic and genetic interactions of proteins with metabolites and lipids to provide a unified framework for multi-omics integration. Using hyperbolic embedding, the network visualizes connections across omics layers, accessible through a user-friendly Shiny R (version 1.10.0) software package. This framework ranks molecules across omics layers based on functional proximity, enabling intuitive exploration. Application in a cardiovascular disease (CVD) case study identified lipids and metabolites associated with CVD-related proteins. The analysis confirmed known associations, like cholesterol esters and sphingomyelin, and highlighted potential novel biomarkers, such as 4-imidazoleacetate and indoleacetaldehyde. Furthermore, we used the network to analyze empagliflozin’s temporal effects on lipid metabolism. Functional enrichment analysis of proteins associated with lipid signatures revealed dynamic shifts in biological processes, with early effects impacting phospholipid metabolism and long-term effects affecting sphingolipid biosynthesis. Our framework offers a versatile tool for hypothesis generation, functional analysis, and biomarker discovery. By bridging molecular layers, this approach advances our understanding of disease mechanisms and therapeutic effects, with broad applications in computational biology and precision medicine.
ZeitschriftenaufsatzAccess status: Open Access ,
Creating somatic symptoms in the lab : stability and predictive validity of symptoms in the affect and symptom paradigm in a sample from the general population over 18 months
(2025) Petzke, Tara M.; Köteles, Ferenc; Van den Bergh, Omer; Witthöft, Michael
Objective: The Affect and Symptom Paradigm (ASP) is an experimental setup that can reliably provoke somatic symptoms in a laboratory setting through the mere presentation of negative pictures. People with persistent somatic symptoms show characteristic effects in this paradigm, including elevated symptom reports and differential brain pattern activation, which suggests that the ASP might be a valuable diagnostic tool. In this cohort study, we tested the temporal stability and ability of the ASP to predict somatic symptom distress over a longer period of time. Methods: We assessed N=91 participants from the general population (69% female) over 2 time points, which were 18 months apart. Participants completed the ASP as well as a questionnaire on somatic symptom distress [Patient Health Questionnaire-15 (PHQ-15)]. Correlation analyses (Bayesian and frequentist) as well as cross-lagged-panel models were used to test the temporal stability and cross-lagged associations. Results: In the cross-lagged-panel models, somatic symptom distress (PHQ-15) at T1 significantly predicted ASP symptom provocation at T2 (β=0.22, p=.029) while controlling for the ASP at T1. Moreover, ASP symptom provocation at T1 significantly predicted cardiorespiratory symptoms (but not overall symptoms) in the PHQ-15 at T2 (β=0.275, p=.019). The autoregressive paths indicated moderate-to-high temporal stability (all β>0.27, all p<.050). Conclusions: The outcome of experimental somatic symptom provocation using the ASP appears stable over time and can significantly predict variability in the experience of cardiorespiratory symptoms (in the PHQ-15) 1.5 years later. Large cohort and intervention studies on chronic somatic symptoms and functional disorders may benefit from including experimental measures such as the ASP.