Filters

2015 - 201912020 - 20221

More filters

2022 - 20232
Reset filters

Settings

Publisher: Oxford : Oxford University Press × WGL Institute: IPHT ×

Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry
    (Oxford : Oxford University Press, 2015) Oetjen, Janina; Veselkov, Kirill; Watrous, Jeramie; McKenzie, James S.; Becker, Michael; Hauberg-Lotte, Lena; Kobarg, Jan Hendrik; Strittmatter, Nicole; Mróz, Anna K.; Hoffmann, Franziska; Trede, Dennis; Palmer, Andrew; Schiffler, Stefan; Steinhorst, Klaus; Aichler, Michaela; Goldin, Robert; Guntinas-Lichius, Orlando; von Eggeling, Ferdinand; Thiele, Herbert; Maedler, Kathrin; Walch, Axel; Maass, Peter; Dorrestein, Pieter C.; Takats, Zoltan; Alexandrov, Theodore
    Background: Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. Findings: High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. Conclusions: With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets.
  • Thumbnail Image
    Item
    What the Phage: a scalable workflow for the identification and analysis of phage sequences
    (Oxford : Oxford University Press, 2022) Marquet, Mike; Hölzer, Martin; Pletz, Mathias W; Viehweger, Adrian; Makarewicz, Oliwia; Ehricht, Ralf; Brandt, Christian
    Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed "What the Phage"(WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).