Pauling Lab - Computational Integrative Omics in Biomedicine

Computational Integrative Omics in Biomedicine

Research Focus

My group focuses on researching and developing computational methods that utilize today's and future compute capabilities to improve and facilitate modern health care. Integrating high dimensional multi-modal data sources is key to unravel disease mechanisms and allows for precise disease sub-typing and accurate stratification of patients. This leads to more effective disease prevention, earlier detection, and tailored individual intervention strategies. Thus, my group's research results are important contributions to data-driven life sciences and translate into improved physician assistance, therapy efficiency, health care, and well-being for patients.

Specific expertise

Computational System Biology
Machine Learning and Artificial Intelligence Computational OMICS Data Science,
Integration, and Mining Mass Spectrometry Network Medicine

Lab Members

Dr. Pauling, Josch K.	Group leader	E-Mail

Professional Experience

Since 2024: Group leader, Institute of Clinical Chemistry and Laboratory Medicine, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Germany
2019 - 2024: Junior Group leader, LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich (TUM), Germany, Bavarian Research Institute of Digital Transformation (bidt), Bavarian Academy of Sciences, Munich, Germany
2016 - 2-18: Postdoc, Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany LiSyM – Liver Systems Medicine
2013 - 2016: Ph.D. in the Functional Lipidomics Group, Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Denmark. Thesis title: Lipid Bioinformatics – Computational Strategies for analyses of shotgun lipidomic data
2011 - 2012: Researcher, Computational Systems Biology, MPI for Informatics, Max Planck Society and Cluster of Excellence of Multi-Modal Computing and Interaction, Saarland University, Germany
2006 - 2011: Interruptions due to hardship.
2001 - 2008: Study program: Informatics in the Natural Sciences (Diplom). Faculty of Technology, Center for Biotechnology (CeBiTec), Bielefeld University, Germany ISAS
Dortmund, Germany. Thesis title: Metabolic Fingerprinting in Mass Spectra

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

Funding and Awards

	2021: Bavarian State Ministry for Science and the Arts: Elite Network Bavaria – International Graduate School “Proteomes that feed the world”, 12 PIs 2018: Bavarian State Ministry for Science and the Arts: Highly competitive research grant, Zentrum Digitalisierung.Bayern (ZD.B), Bavarian Research Institute for Digital Transformation (bidt),
	2018: BMBF Liver Systems Medicine (LiSyM)

Awards	2024 Offered the Associate Professorship of Bioinformatics at the Institute of Mathematics and Informatics at the University of Southern Denmark, Odense, Denmark 2019 Junior Fellow of the Technical University of Munich (for securing highly competitive grants) 2012 German Conference on Bioinformatics Highlight: KeyPathwayMiner - Combining Omics Data and Biological Networks 2012 Travel Award: ACM SIGEvo travel grant (GECCO 2012, Philadelphia, PA, USA)

Selected Collaborations

Collaborator Name	Institute	Collaboration Theme