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Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
The exposome recognizes that individuals are exposed simultaneously to a multitude of different environmental factors and takes a holistic approach to the discovery of etiological factors for disease. However, challenges arise when trying…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Systems Biology is a fundamental field and paradigm that introduces a new era in Biology. The crux of its functionality and usefulness relies on metabolic networks that model the reactions occurring inside an organism and provide the means…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
This volume contains the accepted papers at the third Workshop on Membrane Computing and Biologically Inspired Process Calculi, held in Bologna on 5th September 2009. The papers are devoted to both membrane computing and biologically…
Magnetic Resonance Spectroscopic Imaging (MRSI) is a valuable tool for studying metabolic activities in the human body, but the current applications are limited to low spatial resolutions. The existing deep learning-based MRSI…
Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees.…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
High-throughput metabolomics investigations, when conducted in large human cohorts, represent a potentially powerful tool for elucidating the biochemical diversity and mechanisms underlying human health and disease. Large-scale metabolomics…
This volume contains the proceedings of the Ninth Workshop on Model-Based Testing (MBT 2014), which was held in Grenoble, France on April 6, 2014 as a satellite workshop of the European Joint Conferences on Theory and Practice of Software…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
In recent years, we have witnessed a dramatic data explosion in genomics, thanks to the improvement in sequencing technologies and the drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…
One of the major research questions regarding human microbiome studies is the feasibility of designing interventions that modulate the composition of the microbiome to promote health and cure disease. This requires extensive understanding…
Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…
While developing an information system for the University of Bern, we were faced with two major issues: managing software changes and adapting Business Information Models. Software techniques well-suited to software development teams exist,…