582 citations · 1.2k across the 19 of their papers we have counts for
4 papers · 1 filter
Molecular causality in the advent of foundation models
Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer +1
Correlation is not causation. As simple as this widely agreed-upon statement may seem, scientifically defining causality and using it to drive our modern biomedical research is imm…
Democratising Knowledge Representation with BioCypher
Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach +26
Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate h…
SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Claudine Chaouiya, Duncan Berenguier, Sarah M Keating +21
Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage o…
Large-scale generation of computational models from biochemical pathway maps
Finja Büchel, Nicolas Rodriguez, Neil Swainston +23
Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often c…