• CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator 

      Touré, Vasundra; Zobolas, John; Kuiper, Martin; Vercruysse, Steven (Journal article; Peer reviewed, 2021)
      Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and can be used for connecting biological molecules together to ...
    • CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination 

      Perfetto, Livia; Acencio, Marcio Luis; Bradley, Glyn; Cesareni, Gianni; del Toro, Noemi; Fazekas, David; Hermjakob, Henning; Korcsmaros, Tamas; Kuiper, Martin; Lægreid, Astrid; Lo Surdo, Prisca; Lovering, Ruth C.; Orchard, Sandra; Porras, Pablo; Thomas, Paul; Touré, Vasundra; Zobolas, John; Licata, Luana (Peer reviewed; Journal article, 2019)
      Motivation Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalization of such information in models ...
    • Evolution of computational models in BioModels Database and the Physiome Model Repository 

      Scharm, Martin; Gebhardt, Tom; Touré, Vasundra; Bagnacani, Andrea; Salehzadeh-Yazdi, Ali; Wolkenhauer, Olaf; Waltemath, Dagmar (Journal article; Peer reviewed, 2018)
      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 refined. Even ...
    • Improving the FAIRness of causal interactions in systems biology 

      Touré, Vasundra (Doctoral theses at NTNU;2020:293, Doctoral thesis, 2020)
      In molecular systems biology, regulatory process models are built and computationally simulated to represent and analyse the behaviour of cellular systems and how they respond to perturbations. A considerable amount of ...
    • A middle-out modeling strategy to extend a colon cancer logical model improves drug synergy predictions in epithelial-derived cancer cell lines 

      Tsirvouli, Eirini; Touré, Vasundra; Niederdorfer, Barbara; Vazquez Garcia, Miguel; Flobak, Åsmund; Kuiper, Martin (Peer reviewed; Journal article, 2020)
      Cancer is a heterogeneous and complex disease and one of the leading causes of death worldwide. The high tumor heterogeneity between individuals affected by the same cancer type is accompanied by distinct molecular and ...
    • The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST) 

      Touré, Vasundra; Vercruysse, Steven; Acencio, Marcio Luis; Lovering, Ruth C.; Orchard, Sandra; Bradley, Glyn; Casals-Casas, Cristina; Chaouiya, Claudine; del-Toro, Noemi; Flobak, Åsmund; Gaudet, Pascale; Hermjakob, Henning; Hoyt, Charles Tapley; Licata, Luana; Lægreid, Astrid; Mungall, Christopher; Niknejad, Anne; Panni, Simona; Perfetto, Livia; Porras, Pablo; Pratt, Dexter; Saez-Rodriguez, Julio; Thieffry, Denis; Thomas, Paul; Türei, Dénes; Kuiper, Martin (Peer reviewed; Journal article, 2020)
      Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a ...
    • Signaling Pathway Modules: network organization elements for understanding cancer and designing therapies. 

      Tsirvouli, Eirini (Master thesis, 2019)
      Cancer is a heterogeneous, complex disease and one of the leading causes of death worldwide. The high heterogeneity between individuals, even those affected by the same cancer type, can lead to distinct molecular and ...
    • Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction 

      Niederdorfer, Barbara; Touré, Vasundra; Vazques, Miguel; Thommesen, Liv; Kuiper, Martin Tremen R.; Lægreid, Astrid; Flobak, Åsmund (Journal article; Peer reviewed, 2020)
      Discrete dynamical modeling shows promise in prioritizing drug combinations for screening efforts by reducing the experimental workload inherent to the vast numbers of possible drug combinations. We have investigated ...
    • Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 

      Rougny, Adrien; Touré, Vasundra; Moodie, Stuart; Balaur, Irina; Czauderna, Tobias; Borlinghaus, Hanna; Dogrusoz, Ugur; Mazein, Alexander; Dräger, Andreas; Blinov, Michael L.; Villéger, Alice; Haw, Robin; Demir, Emek; Mi, Huaiyu; Sorokin, Anatoly; Schreiber, Falk; Luna, Augustin (Journal article; Peer reviewed, 2019)
      The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support ...
    • UniBioDicts: Unified access to biological dictionaries 

      Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven (Peer reviewed; Journal article, 2020)
      We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts ...