@article{KrausMathewStephenSchapranow2021,
  author    = {Kraus, Sara Milena and Mathew-Stephen, Mariet and Schapranow, Matthieu-Patrick},
  title     = {Eatomics},
  series = {Journal of proteome research},
  volume    = {20},
  journal   = {Journal of proteome research},
  number    = {1},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1535-3893},
  doi       = {10.1021/acs.jproteome.0c00398},
  pages     = {1070 -- 1078},
  year      = {2021},
  abstract  = {Quantitative proteomics data are becoming increasingly more available, and as a consequence are being analyzed and interpreted by a larger group of users. However, many of these users have less programming experience. Furthermore, experimental designs and setups are getting more complicated, especially when tissue biopsies are analyzed. Luckily, the proteomics community has already established some best practices on how to conduct quality control, differential abundance analysis and enrichment analysis. However, an easy-to-use application that wraps together all steps for the exploration and flexible analysis of quantitative proteomics data is not yet available. For Eatomics, we utilize the R Shiny framework to implement carefully chosen parts of established analysis workflows to (i) make them accessible in a user-friendly way, (ii) add a multitude of interactive exploration possibilities, and (iii) develop a unique experimental design setup module, which interactively translates a given research hypothesis into a differential abundance and enrichment analysis formula. In this, we aim to fulfill the needs of a growing group of inexperienced quantitative proteomics data analysts. Eatomics may be tested with demo data directly online via https://we.analyzegenomes.com/now/eatomics/or with the user's own data by installation from the Github repository at https://github.com/Millchmaedchen/Eatomics.},
  language  = {en}
}
@article{NordmeyerKrausZiehmetal.2023,
  author    = {Nordmeyer, Sarah and Kraus, Milena and Ziehm, Matthias and Kirchner, Marieluise and Schafstedde, Marie and Kelm, Marcus and Niquet, Sylvia and Stephen, Mariet Mathew and Baczko, Istvan and Knosalla, Christoph and Schapranow, Matthieu-Patrick and Dittmar, Gunnar and Gotthardt, Michael and Falcke, Martin and Regitz-Zagrosek, Vera and Kuehne, Titus and Mertins, Philipp},
  title     = {Disease- and sex-specific differences in patients with heart valve disease},
  series = {Life Science Alliance},
  volume    = {6},
  journal   = {Life Science Alliance},
  number    = {3},
  publisher = {EMBO Press},
  address   = {Heidelberg},
  issn      = {2575-1077},
  doi       = {10.26508/lsa.202201411},
  pages     = {18},
  year      = {2023},
  abstract  = {Pressure overload in patients with aortic valve stenosis and volume overload in mitral valve regurgitation trigger specific forms of cardiac remodeling; however, little is known about similarities and differences in myocardial proteome regulation. We performed proteome profiling of 75 human left ventricular myocardial biopsies (aortic stenosis = 41, mitral regurgitation = 17, and controls = 17) using high-resolution tandem mass spectrometry next to clinical and hemodynamic parameter acquisition. In patients of both disease groups, proteins related to ECM and cytoskeleton were more abundant, whereas those related to energy metabolism and proteostasis were less abundant compared with controls. In addition, disease group-specific and sex-specific differences have been observed. Male patients with aortic stenosis showed more proteins related to fibrosis and less to energy metabolism, whereas female patients showed strong reduction in proteostasis-related proteins. Clinical imaging was in line with proteomic findings, showing elevation of fibrosis in both patient groups and sex differences. Disease-and sex-specific proteomic profiles provide insight into cardiac remodeling in patients with heart valve disease and might help improve the understanding of molecular mechanisms and the development of individualized treatment strategies.},
  language  = {en}
}