Stellenbosch Institute for Advanced Studies (STIAS)

Recent Submissions

  • 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 ...

  • Death domain signaling by disulfide-linked dimers of the p75 neurotrophin receptor mediates neuronal death in the CNS 

    Tanaka, Kazuhiro; Kelly, Claire E.; Goh, Ket Yin; Lim, Kim Buay; Ibanez, Carlos F. (Society for Neuroscience, 2016-05-18)
    The p75 neurotrophin receptor (p75NTR) mediates neuronal death in response to neural insults by activating a caspase apoptotic pathway. The oligomeric state and activation mechanism that enable p75NTR to mediate these ...

  • 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 ...

  • Strategies for managing complex social-ecological systems in the face of uncertainty : examples from South Africa and beyond 

    Biggs, Reinette Oonsie; Rhode, Clint; Archibald, Sally; Kunene, Lucky Makhosini; Mutanga, Shingirirai S.; Nkuna, Nghamula; Ocholla, Peter Omondi; Phadima, Lehlohonolo Joe (Resilience Alliance, 2015)
    Improving our ability to manage complex, rapidly changing social-ecological systems is one of the defining challenges of the 21st century. This is particularly crucial if large-scale poverty alleviation is to be secured ...

  • On the physiology of jouissance : interpreting the mesolimbic dopaminergic reward functions from a psychoanalytic perspective 

    Bazan, Ariane; Detandt, Sandrine (Frontiers, 2013-11-06)
    Jouissance is a Lacanian concept, infamous for being impervious to understanding and which expresses the paradoxical satisfaction that a subject may derive from his symptom. On the basis of Freud’s “experience of satisfaction” ...

  • After Fukushima : the precautionary principle revisited 

    Huber, Wolfgang (AOSIS Publishing, 2012-12-06)
    Etienne de Villiers, more than other theologians, elaborates on basic elements of a Christian ethics of responsibility. He distinguishes between retrospective and prospective responsibility. The prospective aspect attracted ...

  • 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 ...

  • 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 ...

  • Progress in human embryonic stem cell research in the United States between 2001 and 2010 

    Vakili, Keyvan; McGahan, Anita M.; Rezaie, Rahim; Mitchell, Will; Daar, Abdallah S. (Public Library of Science, 2015)
    On August 9th, 2001, the federal government of the United States announced a policy restricting federal funds available for research on human embryonic stem cell (hESCs) out of concern for the “vast ethical mine fields” ...

  • 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 ...

  • On the modularity of the intrinsic flexibility of the µ opioid receptor : a computational study 

    Fossepre, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P. (Public Library of Science, 2015)
    The µ opioid receptor (µOR), the principal target to control pain, belongs to the G protein-coupled receptors (GPCRs) family, one of the most highlighted protein families due to their importance as therapeutic targets. The ...

  • 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].

  • The role of theory and modeling in medical research 

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

  • 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 ...

  • “Deeper into a hole?” : borrowing and lending in South Africa 

    James, Deborah (University of Chicago Press Journals, 2014-08)
    In South Africa, with upward mobility much aspired to but seldom attained, householders must spend money they have not yet earned. Borrowing both from formal institutions and smaller moneylenders (legal and illegal) positions ...

  • Observed full blood count and lymphocyte subset values in a cohort of clinically healthy South African children from a semi-informal settlement in Cape Town 

    Lawrie, Denise; Payne, Helen; Nieuwoudt, Martin; Glencross, Deborah Kim (Health & Medical Publishing Group, 2015-09)
    Background. The paediatric full blood count and lymphocyte subset reference intervals used by the National Health Laboratory Service (NHLS), South Africa (SA), are taken from two international reference interval publications. ...

  • 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 ...

  • Declaration on mental health in Africa : moving to implementation 

    Daar, Abdallah S.; Jacobs, Marian; Wall, Stig; Groenewald, Johann; Eaton, Julian; Patel, Vikram; Dos Santos, Palmira; Kagee, Ashraf; Gevers, Anik; Sunkel, Charlene; Andrews, Gail; Daniels, Ingrid; Ndetei, David (Co-Action Publishing, 2014-06-16)
    Urgent action is needed to address mental health issues globally. In Africa, where mental health disorders account for a huge burden of disease and disability, and where in general less than 1% of the already small health ...

  • 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 ...

  • A view from Silicon Valley 

    Botha, Roelof (Stellenbosch : Stellenbosch University, 2012-04-10)
    As per: http://blogs.sun.ac.za/news/2012/03/26/internet-entrepreneur-roelof-botha-at-su-on-april-10. "Internet entrepreneur and venture capital specialist, Roelof Botha, will visit Stellenbosch University (SU) on 10 April ...

  • Religion and violence in a globalised world 

    Wolfgang, Huber (AOSIS Publishing, 2011-11-18)
    Violent religious extremism is seen as one of the mega-problems of the 21st century. This article – based on a key lecture at the conference on ‘Violence in a democratic South Africa’ at the University of Pretoria and ...

  • Overcoming violence - a basic task of Christian churches 

    Huber, Wolfgang (AOSIS Publishing, 2011-12-12)
    In this article – based on the second of two keynote lectures at a conference on violence – the view is developed that the task of the church with respect to violence consists mainly in overcoming violence. In the first ...