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From Gene to Whole Cell : Modeling, Visualization, and Analysis

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2025

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https://doi.org/10.1007/978-1-0716-4152-1_5
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ALLMER, Jens, Hrsg., Abhishek KUMAR, Hrsg.. Proteogenomics : Methods and Protocols. 1. New York, NY: Springer, 2025, S. 65-92. Methods in Molecular Biology (MIMB). 2859. ISBN 978-1-0716-4151-4. Verfügbar unter: doi: 10.1007/978-1-0716-4152-1_5

Zusammenfassung

Proteogenomics combines proteomic and genetic data to gain new insights in molecular mechanisms. Here, we extend this approach toward structural biology from a tool perspective. The chapter starts with tools which can be used to explore genetic information and then enrich those with proteomic data. Based on the corresponding identifiers, three-dimensional structures of proteins are identified and used to embed them in their molecular environment, here the surrounding membrane. This membrane is then mapped onto the surface of an interpretative three-dimensional cell model. Then, the embedded protein and the cell environment are associated with a metabolic pathway, again based on the identifiers provided by biomedical databases. Accompanying the different chapters, related work is discussed which can alternatively be used. Finally, an outlook toward immersive analytics is given.

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ISO 690SOMMER, Björn, Sabrina JAEGER-HONZ, 2025. From Gene to Whole Cell : Modeling, Visualization, and Analysis. In: ALLMER, Jens, Hrsg., Abhishek KUMAR, Hrsg.. Proteogenomics : Methods and Protocols. 1. New York, NY: Springer, 2025, S. 65-92. Methods in Molecular Biology (MIMB). 2859. ISBN 978-1-0716-4151-4. Verfügbar unter: doi: 10.1007/978-1-0716-4152-1_5
BibTex
@incollection{Sommer2025Whole-71131,
  year={2025},
  doi={10.1007/978-1-0716-4152-1_5},
  title={From Gene to Whole Cell : Modeling, Visualization, and Analysis},
  edition={1},
  number={2859},
  isbn={978-1-0716-4151-4},
  publisher={Springer},
  address={New York, NY},
  series={Methods in Molecular Biology (MIMB)},
  booktitle={Proteogenomics : Methods and Protocols},
  pages={65--92},
  editor={Allmer, Jens and Kumar, Abhishek},
  author={Sommer, Björn and Jaeger-Honz, Sabrina}
}
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