Related papers: Accurate, fully-automated NMR spectral profiling f…
Nuclear Magnetic Resonance (NMR) spectra are widely used in metabolomics to obtain profiles of metabolites dissolved in biofluids such as cell supernatants. Methods for estimating metabolite concentrations from these spectra are presently…
Motivation: NMR spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or…
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…
Liquid state NMR is a powerful tool for the analysis of complex mixtures of unknown molecules. This capacity has been used in many analytical approaches: metabolomics, identification of active compounds in natural extracts, characterization…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
The success of metabolomics studies depends upon the "fitness" of each biological sample used for analysis: it is critical that metabolite levels reported for a biological sample represent an accurate snapshot of the studied organism's…
Purpose: Proton magnetic resonance spectroscopic imaging ($^1$H MRSI) enables the mapping of whole-brain metabolites concentrations in-vivo. However, a long-standing problem for its clinical applicability is the metabolic quantification,…
With the maturation of metabolomics science and proliferation of biobanks, clinical metabolic profiling is an increasingly opportunistic frontier for advancing translational clinical research. Automated Machine Learning (AutoML) approaches…
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…
Magnetic resonance spectroscopy (MRS) is a non-invasive technique to measure the metabolic composition of tissues, offering valuable insights into neurological disorders, tumor detection, and other metabolic dysfunctions. However, accurate…
Background. Emerging technologies now allow for mass spectrometry based profiling of up to thousands of small molecule metabolites (metabolomics) in an increasing number of biosamples. While offering great promise for revealing insight into…
Untargeted metabolomics based on liquid chromatography-mass spectrometry technology is quickly gaining widespread application given its ability to depict the global metabolic pattern in biological samples. However, the data is noisy and…
Untargeted metabolomic studies are revealing large numbers of naturally occurring metabolites that cannot be characterized because their chemical structures and MS/MS spectra are not available in databases. Here we present iMet, a…
Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a…
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…
Metabolite analysis of peritoneal dialysis (PD) effluent may provide information regarding onset and progression of complications associated with prolonged PD therapy. In this context, the NMR detectable small metabolites of PD effluent…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
Mutational signatures are patterns of somatic mutations in tumor genomes that provide insights into underlying mutagenic processes and cancer origin. Developing reliable methods for their estimation is of growing importance in cancer…
The metabolism of an organism is regulated at the cellular level, yet is strongly influenced by its environment. The precise metabolomic study of living organisms is currently hampered by measurement sensitivity: most metabolomic…
Metabolic fluxes are the rates of life-sustaining chemical reactions within a cell and metabolites are the components. Determining the changes in these fluxes is crucial to understanding diseases with metabolic causes and consequences.…