John Zobolas

Oslo University Hospital

Identification of genomic, molecular and clinical markers predictive of patient survival is important for developing personalized disease prevention, diagnostic and treatment approaches. Modern omics technologies have made it possible to investigate the prognostic impact of markers at multiple molecular levels, including genotype, DNA methylation,...

The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted c...

Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and interpretation of those systems. Defining rules that determine how the output activity of biological entities is regulated...

Treatment with drug combinations carries great promise for personalized therapy. We have previously shown that drug synergies targeting cancer can manually be identified based on a logical framework. We now demonstrate how automated adjustments of model topology and logic equations can greatly reduce the workload traditionally associated with logic...

Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and interpretation of those systems. Defining rules that determine how the output activity of biological entities is regulated...

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 enable the building of regulatory computational models that represent biological systems. However, including a molecular causal int...

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 or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a s...

One of the many challenges that biocurators face, is the continuous evolution of ontologies and controlled vocabularies and their lack of coverage of biological concepts. To help biocurators annotate new information that cannot yet be covered with terms from authoritative resources, we produced an update of PubDictionaries: a resource of publicly e...

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 into regulatory computational models that represent biological systems. However, including a molecular causal interaction into a model require...

VSM is a recently introduced method for entering and displaying any type of knowledge, in a form that is both semantically precise for computation and intuitive for human understanding. VSM is the combination of a new semantic model, and the design for a dedicated user interface to support it. Here we present the implementation of this user interfa...

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 or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a s...

Motivation: Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalisation of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signal...