Thanks to significant improvements in LC-MS technology, metabolomics is increasingly used as a tool to discriminate the responses of organisms to various stimuli or drugs. In this minireview we discuss all aspects of the LC-MS metabolomics pipeline, using a complex…

Metabolomics experiments have become commonplace in a wide variety of disciplines. By identifying and quantifying metabolites researchers can achieve a systems level understanding of metabolism. These studies produce vast swaths of data which are often only lightly interpreted due to…

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Traditional methods for assessing dietary exposure can be unreliable, with under reporting one of the main problems. In an attempt to overcome such problems there is increasing interest in identifying biomarkers of dietary intake to provide a more accurate measurement.…

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a…

Chemical compounds are usually represented as graph structured data in computers. In this review article, we overview several graph classes relevant to chemical compounds and the computational complexities of several fundamental problems for these graph classes. In particular, we consider…

Natural remedies, such as those based on traditional Chinese medicines, have become more popular also in western countries over the last 10 years. The composition of these herbal products is largely unknown and difficult to determine. Moreover, since plants respond…

Error analysis plays a fundamental role in describing the uncertainty in experimental results.  It has several fundamental uses in metabolomics including experimental design, quality control of experiments, the selection of appropriate statistical methods, and the determination of uncertainty in results. …

Data fusion is the name given to a range of methods for combining multiple sources of evidence.  This mini-review summarizes the use of one such class of methods for combining the rankings obtained when similarity searching is used for ligand-based…