Sunday, March 30, 2008

Job: Postdoctoral Researcher at EBI, Hinxton/UK

NatureJobs reports:
    Research into and development of methods for computer-assisted structure elucidation of biological metabolites based on mass spectrometry and NMR data. For this position in the Steinbeck group, the postdoctoral researchers need to hold a PhD degree in chemistry, biology, bioinformatics, computer science or a related field. They have good knowledge of standard software development and the ability to use, modify and adapt others code if necessary. Applicants should have proven experience with programming in Java as well as chemoinformatics and bioinformatics software development. The successful applicant must work on their own initiative, but work as part of a wider team and collaborate with colleagues, internally and externally where required. The position is based in the Chemoinformatics and Metabolism (Steinbeck Research Group). It is initially termed for 12 months, extension may be possible.

Paper: Genetic algorithm based two-mode clustering of metabolomics data

Jos Hageman (UvA, now Biometris in Wageningen) published the paper Genetic algorithm based two-mode clustering of metabolomics data (DOI:10.1007/s11306-008-0105-7):
    In this paper we introduce a two-mode clustering method based on a genetic algorithm that uses a criterion that searches for homogeneous clusters. Furthermore we introduce a cluster stability criterion to validate the clusters and we provide an extended knee plot to select the optimal number of clusters in both experimental and metabolite modes. The genetic algorithm-based two-mode clustering gave biological relevant results when it was applied to two real life metabolomics data sets.
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Saturday, March 1, 2008

Paper: Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics

Velitchka Mihaleva et al. (Plant Research International/Wageningen University) just published a paper in Metabolomics: Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics (doi:10.1007/s11306-008-0108-4):
    Experimental LC/TOF-MS platforms equipped with a time-to-digital converter (TDC) give the best mass estimate for those mass signals with an intensity similar to that of the lock-mass used for internal calibration. However, they systematically underestimate the mass obtained at higher signal intensity and overestimate it at low signal intensities compared to that of the lock-mass. To compensate for these effects, specific tools are required for correction and automation of accurate mass calculations from LC/MS signals. Here, we present a computational procedure for the derivation of an intensity-dependent mass correction function.

If you are working in NL and you would like to see you paper listed in this blog too, please send me an email.