Now showing items 1-12 of 12

    • Age-dependent effects of UCP2 deficiency on experimental acute pancreatitis in mice 

      Muller, Sarah; Kaiser, Hannah; Kruger, Burkhard; Fitzner, Brit; Lange, Falko; Bock, Cristin N.; Nizze, Horst; Ibrahim, Saleh M.; Fuellen, Georg; Wolkenhauer, Olaf; Jaster, Robert (PLoS, 2014-04-10)
      Reactive oxygen species (ROS) have been implicated in the pathogenesis of acute pancreatitis (AP) for many years but experimental evidence is still limited. Uncoupling protein 2 (UCP2)-deficient mice are an accepted model ...

    • Annotation-based feature extraction from sets of SBML models 

      Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron (BioMed Central, 2015-04-15)
      Background: Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concepts ...

    • Anti-inflammatory effects of reactive oxygen species : a multi-valued logical model validated by formal concept analysis 

      Wollbold, Johannes; Jaster, Robert; Muller, Sarah; Rateitschak, Katja; Wolkenhauer, Olaf (BioMed Central, 2014-09)
      Background: Recent findings suggest that in pancreatic acinar cells stimulated with bile acid, a pro-apoptotic effect of reactive oxygen species (ROS) dominates their effect on necrosis and spreading of inflammation. The ...

    • COMODI : an ontology to characterise differences in versions of computational models in biology 

      Scharm, Martin; Waltemath, Dagmar; Mendes, Pedro; Wolkenhauer, Olaf (BioMed Central, 2016-07-11)
      Background: Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying ...

    • Dissecting long-term glucose metabolism identifies new susceptibility period for metabolic dysfunction in aged mice 

      Chauhan, Anuradha; Weiss, Heike; Koch, Franziska; Ibrahim, Saleh M.; Vera, Julio; Wolkenhauer, Olaf; Tiedge, Markus (Public Library of Science, 2015)
      Metabolic disorders, like diabetes and obesity, are pathogenic outcomes of imbalance in glucose metabolism. Nutrient excess and mitochondrial imbalance are implicated in dysfunctional glucose metabolism with age. We used ...

    • Enabling multiscale modeling in systems medicine 

      Wolkenhauer, Olaf; Auffray, Charles; Brass, Olivier; Clairambault, Jean; Deutsch, Andreas; Drasdo, Dirk; Gervasio, Francesco; Preziosi, Luigi; Maini, Philip; Marciniak-Czochra, Anna; Kossow, Christina; Kuepfer, Lars; Rateitschak, Katja; Ramis-Conde, Ignacio; Ribba, Benjamin; Schuppert, Andreas; Smallwood, Rod; Stamatakos, Georgios; Winter, Felix; Byrne, Helen (BioMed Central, 2014-03)
      [See article for abstract].

    • Evolution of computational models in BioModels Database and the Physiome Model Repository 

      Scharm, Martin; Gebhardt, Tom; Toure, Vasundra; Bagnacani, Andrea; Salehzadeh-Yazdi, Ali; Wolkenhauer, Olaf; Waltemath, Dagmar (BioMed Central, 2018-04-12)
      ENGLISH SUMMARY : Background: A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and ...

    • Parameter identifiability and sensitivity analysis predict targets for enhancement of STAT1 activity in pancreatic cancer and stellate cells 

      Rateitschak, Katja; Winter, Felix; Lange, Falko; Jaster, Robert; Wolkenhauer, Olaf (Public Library of Science, 2012-12)
      The present work exemplifies how parameter identifiability analysis can be used to gain insights into differences in experimental systems and how uncertainty in parameter estimates can be handled. The case study, presented ...

    • The role of theory and modeling in medical research 

      Wolkenhauer, Olaf (Frontiers Media, 2013-12-19)
      No abstract available.

    • Systems approach to the study of brain damage in the very preterm newborn 

      Leviton, Alan; Gressens, Pierre; Wolkenhauer, Olaf; Dammann, Olaf (Frontiers Media, 2016)
      Background: A systems approach to the study of brain damage in very preterm newborns has been lacking. Methods: In this perspective piece, we offer encephalopathy of prematurity as an example of the complexity and ...

    • TRAPLINE : a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation 

      Wolfien, Markus; Rimmbach, Christian; Schmitz, Ulf; Jung, Julia Jeannine; Krebs, Stefan; Steinhoff, Gustav; David, Robert; Wolkenhauer, Olaf (BioMed Central, 2016)
      Background: Technical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysis ...

    • Why model? 

      Wolkenhauer, Olaf (Frontiers Media, 2014-01-28)
      Next generation sequencing technologies are bringing about a renaissance of mining approaches. A comprehensive picture of the genetic landscape of an individual patient will be useful, for example, to identify groups of ...