Publications

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75 Publications visible to you, out of a total of 75
A Multiscale Simulation Approach to Compute Protein–Ligand Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics

Abstract

Not specified

Authors: Abraham Muñiz-Chicharro, Gaurav K. Ganotra, Rebecca C. Wade

Date Published: 27th Oct 2025

Publication Type: Journal

Modeling and Predicting Spatio-Temporal Dynamics of PM$_{2.5}$ Concentrations Through Time-Evolving Covariance Models

Abstract

Not specified

Authors: Ghulam A. Qadir, Ying Sun

Date Published: 2025

Publication Type: Journal

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Flexible Metadata Structuring for Research Data Management Through the FAIRDOM-SEEK Platform - Implementing Tailored and Complex Metadata Schemes in SEEK

Abstract (Expand)

Modern research projects increasingly require hybrid metadata approaches that balance adherence to domain-overarching, as well as domain-specific community standards with flexibility for project- or … resource-specific metadata. The FAIRDOM-SEEK platform [1] is a widely used research data management system designed to support diverse domains, from systems biology to health research data, by integrating standardized metadata models (e.g., the ISA framework [2]) with customizable extensions. To address this need, we introduce the Extended Metadata feature in SEEK, which allows researchers to extend core metadata schemas with user-defined fields, hierarchies, and semantic annotations while ensuring interoperability with domain-specific standards. We demonstrate this capability through two use cases: 1. NFDI4Health Local Data Hubs (LDH) [3],[4]: In the context of the German National Research Data Infrastructure for Personal Health Data (NFDI4Health [5]), we have developed Local Data Hubs (LDH) based on the SEEK platform. These hubs support federated data structuring and sharing for sensitive health data from clinical trials, epidemiological studies, and public health research and allow to connect local platforms to the central metadata repository of NFDI4Health, the German Health Study Hub. Given the complexity of the NFDI4Health metadata schema (MDS) [6], the SEEK-based LDH software utilizes the Extended Metadata feature to fully represent the schema, allowing for flexible project-defined metadata extensions. 2. FAIR Data Station (FAIR-DS) [7]: Based on the ISA-framework, with the addition of Observation units from MIAPPE [8], the FAIR-DS is a web application that enables users to create and manage metadata according to FAIR principles. Using packages and terms configured through the UI, it generates Excel spreadsheets which are then populated to gather the metadata. FAIR-DS is then used to validate the metadata and generates RDF datasets representing the content. SEEK has been updated to allow Extended Metadata and Sample Types to be configured automatically via these RDF datasets, and also the content can be imported, and updated, in a single action. The Extended Metadata feature allows users to define additional metadata attributes to be tailored to specific data types, ensuring compliance with standards. When creating a resource, users can select an Extended Metadata type from a dropdown menu, dynamically triggering the rendering of associated metadata input forms within the web interface. This enables seamless integration of resource-specific metadata (e.g., clinical trial study metadata) alongside core descriptive fields. Currently, only instance administrators can create, manage (enable/disable), and delete additional attributes for specific resource types (e.g., ISA items such as Investigation, Study, Assay, as well as Projects and Models) based on specific schemas (e.g., the NFDI4Health MDS). Attribute types range from simple (e.g., string, text, date, integer, Boolean) to complex (e.g., controlled vocabularies linked to ontologies, nested hierarchical structures), with validation rules for mandatory or optional fields. Regular expressions are introduced to ensure correct input formatting. Metadata schemas can be created through backend seed files, JSON uploads, or FAIR-DS RDF imports. These schemas are programmatically accessible via the SEEK REST API, enabling automated metadata creation and retrieval. This ensures interoperability with external tools while adhering to FAIR data principles.

Authors: Xiaoming Hu, Stuart Owen, Frank Meineke, Finn Bacall, Carole Goble, Wolfgang Müller, Martin Golebiewski

Date Published: 2025

Publication Type: InProceedings

The TGF-β1 target WISP1 is highly expressed in liver cirrhosis and cirrhotic HCC microenvironment and involved in pro- and anti-tumorigenic effects

Abstract

Not specified

Authors: Anne Dropmann, Sophie Alex, Katharina Schorn, Chenhao Tong, Tiziana Caccamo, Patricio Godoy, Iryna Ilkavets, Roman Liebe, Daniela Gonzalez, Jan G. Hengstler, Albrecht Piiper, Luca Quagliata, Matthias S. Matter, Oliver Waidmann, Fabian Finkelmeier, Teng Feng, Thomas S. Weiss, Nuh Rahbari, Emrullah Birgin, Erik Rasbach, Stephanie Roessler, Kai Breuhahn, Marcell Tóth, Matthias P. Ebert, Steven Dooley, Seddik Hammad, Nadja M. Meindl-Beinker

Date Published: 1st Nov 2024

Publication Type: Journal

Tumour-specific activation of a tumour-blood transport improves the diagnostic accuracy of blood tumour markers in mice

Abstract

Not specified

Authors: Christian Schmithals, Bianca Kakoschky, Dominic Denk, Maike von Harten, Jan Henrik Klug, Edith Hintermann, Anne Dropmann, Eman Hamza, Anne Claire Jacomin, Jens U. Marquardt, Stefan Zeuzem, Peter Schirmacher, Eva Herrmann, Urs Christen, Thomas J. Vogl, Oliver Waidmann, Steven Dooley, Fabian Finkelmeier, Albrecht Piiper

Date Published: 1st Jul 2024

Publication Type: Journal

Retinoic acid generates a beneficial microenvironment for liver progenitor cell activation in acute liver failure

Abstract (Expand)

Background: When massive necrosis occurs in acute liver failure (ALF), rapid expansion of HSCs called liver progenitor cells (LPCs) in a process called ductular reaction is required for survival. The …tular reaction is required for survival. The underlying mechanisms governing this process are not entirely known to date. In ALF, high levels of retinoic acid (RA), a molecule known for its pleiotropic roles in embryonic development, are secreted by activated HSCs. We hypothesized that RA plays a key role in ductular reaction during ALF. Methods: RNAseq was performed to identify molecular signaling pathways affected by all- trans retinoid acid (atRA) treatment in HepaRG LPCs. Functional assays were performed in HepaRG cells treated with atRA or cocultured with LX-2 cells and in the liver tissue of patients suffering from ALF. Results: Under ALF conditions, activated HSCs secreted RA, inducing RARα nuclear translocation in LPCs. RNAseq data and investigations in HepaRG cells revealed that atRA treatment activated the WNT-β-Catenin pathway, enhanced stemness genes (SOX9, AFP, and others), increased energy storage, and elevated the expression of ATP-binding cassette transporters in a RARα nuclear translocation-dependent manner. Further, atRA treatment–induced pathways were confirmed in a coculture system of HepaRG with LX-2 cells. Patients suffering from ALF who displayed RARα nuclear translocation in the LPCs had significantly better MELD scores than those without. Conclusions: During ALF, RA secreted by activated HSCs promotes LPC activation, a prerequisite for subsequent LPC-mediated liver regeneration.

Authors: Sai Wang, Frederik Link, Stefan Munker, Wenjing Wang, Rilu Feng, Roman Liebe, Yujia Li, Ye Yao, Hui Liu, Chen Shao, Matthias P.A. Ebert, Huiguo Ding, Steven Dooley, Hong-Lei Weng, Shan-Shan Wang

Date Published: 2024

Publication Type: Journal

EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows

Abstract (Expand)

This EuroScienceGateway report gives an overview of FAIR Digital Objects (FDO), considering their use for computational workflows as scholarly objects. EuroScienceGateway has progressed the technologies … Signposting and RO-Crate for implementing Workflow FDOs with the registry WorkflowHub and the workflow system Galaxy, and initiated work with academic publishers to encourage workflow citation practices. Here we document how WorkflowHub supports research software best practices for workflows, and assist building FAIR Computational Workflows. Provenance of workflow executions has been made possible in an interoperable way across many workflow systems using Workflow Run Crate profiles, including from Galaxy.  Finally this report explores how Workflow FDOs are exposed and can be utilised, e.g. gathered in knowledge graphs and having tighter workflow system integration.

Authors: Stian Soiland-Reyes, Eli Chadwick, Finn Bacall, José M. Fernández, Björn Grüning, Hakan Bayındır

Date Published: 2024

Publication Type: Tech report

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