Benutzerspezifische Werkzeuge

Computational Integrative Omics in Biomedicine

Platzhalter Bild

Dr. Josch K. Pauling

Principal Investigator

Research focus

We are developing computational aids to bring the young and surging field of lipidomics to the playbook of systems medicine methods. The establishment of lipidomics and metabolomics as a third dimension in addition to genomics and proteomics is key to achieve precision medicine workflows that are targeted to and benefit groups of patients with common, distinct molecular signatures. This approach is not based on symptoms-based clinical anamneses but allows for novel molecular disease classifications and patient stratification as well as targeted treatment prediction.

Specific expertise

  • Computational tools for omics data
  • Biclustering algorithms and biomarkers
  • Lipid interactions networks
  • Machine learning with neural network 
  • Computational integration of metabolome data

Funding

Selected Publications

  • Tim D Rose, Nikolai Köhler, Lisa Falk, Lucie Klischat, Olga E Lazareva, Josch K Pauling, Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data, Briefings in Bioinformatics, Volume 24, Issue 1, January 2023, bbac572, https://doi.org/10.1093/bib/bbac572
  • T.D. Rose, T. Bechtler, O. Ciora, K. Anh Lilian Le, F. Molnar, N. Köhler, J. Baumbach, R. Röttger, J.K. Pauling, MoSBi: Automated signature mining for molecular stratification and subtyping, Proc. Natl. Acad. Sci. U.S.A. 119 (16) e2118210119, https://doi.org/10.1073/pnas.2118210119 (2022).
  • Vvedenskaya O, Rose TD, Knittelfelder O, Palladini A, Wodke JAH, Schuhmann K, Ackerman JM, Wang Y, Has C, Brosch M, Thangapandi VR, Buch S, Züllig T, Hartler J, Köfeler HC, Röcken C, Coskun Ü, Klipp E, von Schoenfels W, Gross J, Schafmayer C, Hampe J, Pauling JK, Shevchenko A. Nonalcoholic fatty liver disease stratification by liver lipidomics. J Lipid Res. 2021;62:100104. doi: 10.1016/j.jlr.2021.100104. 
  • Galindez, G., Matschinske, J., Rose, T.D., Sadegh S, Salgado-Albarrán M, Späth J, Baumbach J, Pauling JK. . Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies. Nat Comput Sci 1, 33–41 (2021). https://doi.org/10.1038/s43588-020-00007-6
  • Pauling JK, Hermansson M, Hartler J, Christiansen K, Gallego SF, et al. (2017) Proposal for a common nomenclature for fragment ions in mass spectra of lipids. PLOS ONE 12(11): e0188394. https://doi.org/10.1371/journal.pone.0188394
  • Pauling J, Röttger R, Tauch A, Azevedo V, Baumbach J. CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res. 2012 Jan;40(Database issue):D610-4. doi: 10.1093/nar/gkr883.
  • Thangapandi VR, Knittelfelder O, Brosch M, Patsenker E, Vvedenskaya O, Buch S, Hinz S, Hendricks A, Nati M, Herrmann A, Rekhade DR, Berg T, Matz-Soja M, Huse K, Klipp E, Pauling JK, Wodke JA, Miranda Ackerman J, Bonin MV, Aigner E, Datz C, von Schönfels W, Nehring S, Zeissig S, Röcken C, Dahl A, Chavakis T, Stickel F, Shevchenko A, Schafmayer C, Hampe J, Subramanian P. Loss of hepatic Mboat7 leads to liver fibrosis. Gut. 2021 May;70(5):940-950. doi: 10.1136/gutjnl-2020-320853. 
  • Matschinske J, Alcaraz N, Benis A, Golebiewski M, Grimm DG, Heumos L, Kacprowski T, Lazareva O, List M, Louadi Z, Pauling JK, Pfeifer N, Röttger R, Schwämmle V, Sturm G, Traverso A, Van Steen K, de Freitas MV, Villalba Silva GC, Wee L, Wenke NK, Zanin M, Zolotareva O, Baumbach J, Blumenthal DB. The AIMe registry for artificial intelligence in biomedical research. Nat Methods. 2021 Oct;18(10):1128-1131. doi: 10.1038/s41592-021-01241-0. 
  • Wolff J, Pauling J, Keck A, Baumbach J. The Economic Impact of Artificial Intelligence in Health Care: Systematic Review. J Med Internet Res 2020;22(2):e16866. https://www.jmir.org/2020/2/e16866 DOI: 10.2196/16866