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It is basic question in biology and other fields to identify the char- acteristic properties that on one hand are shared by structures from a particular realm, like gene regulation, protein-protein interaction or neu- ral networks or foodwebs, and that on the other hand distinguish them from other structures. We introduce and apply a general method, based on the spectrum of the normalized graph Laplacian, that yields repre- sentations, the spectral plots, that allow us to find and visualize such properties systematically. We present such visualizations for a wide range of biological networks and compare them with those for networks derived from theoretical schemes. The differences that we find are quite striking and suggest that the search for universal properties of biological networks should be complemented by an understanding of more specific features of biological organization principles at different scales.
In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations. To help modelers perform these steps, we developed the software PyBioNetFit. PyBioNet
Modeling biological rhythms helps understand the complex principles behind the physical and psychological abnormalities of human bodies, to plan life schedules, and avoid persisting fatigue and mood and sleep alterations due to the desynchronization
Equation learning methods present a promising tool to aid scientists in the modeling process for biological data. Previous equation learning studies have demonstrated that these methods can infer models from rich datasets, however, the performance of
The origins of herbal medicines are important for their treatment effect, which could be potentially distinguished by electronic nose system. As the odor fingerprint of herbal medicines from different origins can be tiny, the discrimination of origin
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in such a way to