Related papers: NMR microscopy for in vivo metabolomics, digitally…
One of the great challenges in biology is to observe, at sufficient detail, the real-time workings of the cell. Many methods exist to do cell measurements invasively. For example, mass spectrometry has tremendous mass sensitivity but…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
Animal behavior reflects interactions between the nervous system, body, and environment. Therefore, biomechanics and environmental context must be considered to understand algorithms for behavioral control. Neuromechanical digital twins,…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
In vivo H nuclear magnetic resonance (NMR) spectroscopy is an important tool for performing non-invasive quantitative assessments of brain tumour glucose metabolism. Brain tumours are considered fast-growth tumours because of their high…
Hyperpolarized nuclear magnetic resonance and lab-on-a-chip microfluidics are two dynamic, but until recently quite distinct, fields of research. Recent developments in both areas increased their synergistic overlap. By microfluidic…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks, and so far the best way is to proceed interactively with a spectra viewer. NMRProcFlow is a graphical and…
Cellular metabolic rate is a good indicator of the physiological state of cells and its changes, which can be measured by total heat flux accompanying metabolism. Chip calorimeters can provide label-free and high throughput measurements of…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Magnetic resonance spectroscopy (MRS) is an important technique in biomedical research and it has the unique capability to give a non-invasive access to the biochemical content (metabolites) of scanned organs. In the literature, the…
Real-time temperature monitoring inside living organisms provides a direct measure of their biological activities, such as homeostatic thermoregulation and energy metabolism. However, it is challenging to reduce the size of bio-compatible…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Many diseases cause significant changes to the concentrations of small molecules (aka metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile". This…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
The turn of the millennium has seen a growing interest in the study of live cells by infrared (IR) spectroscopy, driven by the versatility, wealth of molecular information, and potential for high-throughput screening of the technique.…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…