175 citations · 254 across the 10 of their papers we have counts for
10 papers
On the effects of alternative optima in context-specific metabolic model predictions
Semidán Robaina-Estévez, Zoran Nikoloski
Recent methodological developments have facilitated the integration of high-throughput data into genome-scale models to obtain context-specific metabolic reconstructions. A unique…
DeFiNe: an optimisation-based method for robust disentangling of filamentous networks
David Breuer, Zoran Nikoloski
Thread-like structures are pervasive across scales, from polymeric proteins to root systems to galaxy filaments, and their characteristics can be readily investigated in the networ…
Control principles of metabolic networks
Georg Basler, Zoran Nikoloski, Abdelhalim Larhlimi +2
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient con…
Quantitative analyses of the plant cytoskeleton reveal underlying organizational principles
David Breuer, Alexander Ivakov, Arun Sampathkumar +3
The actin and microtubule cytoskeletons are vital structures for cell growth and development across all species. While individual molecular mechanisms underpinning actin and microt…
img2net: Automated network-based analysis of imaged phenotypes
David Breuer, Zoran Nikoloski
Automated analysis of imaged phenotypes enables fast and reproducible quantification of biologically relevant features. Despite recent developments, recordings of complex, networke…
Assessing the significance of knockout cascades in metabolic networks
Oriol Güell, Francesc Sagués, Georg Basler +2
Complex networks have been shown to be robust against random structural perturbations, but vulnerable against targeted attacks. Robustness analysis usually simulates the removal of…
On the relation between reactions and complexes of (bio)chemical reaction networks
Jost Neigenfind, Sergio Grimbs, Zoran Nikoloski
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maint…
Biochemical network decomposition reveals absolute concentration robustness
Jost Neigenfind, Sergio Grimbs, Zoran Nikoloski
Robustness of biochemical systems has become one of the central questions in Systems Biology, although it is notoriously difficult to formally capture its multifaceted nature. Main…
Probabilistic Inductive Classes of Graphs
Nataša Kejžar, Zoran Nikoloski, Vladimir Batagelj
Models of complex networks are generally defined as graph stochastic processes in which edges and vertices are added or deleted over time to simulate the evolution of networks. Her…
Maximizing Modularity is hard
U. Brandes, D. Delling, M. Gaertler +4
Several algorithms have been proposed to compute partitions of networks into communities that score high on a graph clustering index called modularity. While publications on these…