Publications

2026 Link to heading

Navigating the Lipid Universe with LipidLibrarian: A Cross-Linked Database for Lipidomics Data Integration
Felix Niedermaier, Konstantinos Mechteridis, Konstantin Pelz, Vivian Wuerf, Nikolai Köhler, Josch K Pauling
Journal of Lipid Research, 2025
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2025 Link to heading

Journal Articles Link to heading

Endoscopic healing in pediatric IBD perpetuates a persistent signature defined by Th17 cells with molecular and microbial drivers of disease
Kolja Siebert, Tim Faro$^{\dagger}$, Nikolai Köhler$^{\dagger}$, Hannes Hölz, Sebastian Jarosch, Monica Matchado, Deborah Häcker, Federica De Zen, Mohammad Samer Hajji, Eberhard Lurz, Sibylle Koletzko, Josch K Pauling, Katja Steiger, Klaus Neuhaus, Caspar Ohnmacht, Markus List, Dirk H Busch, Dirk Haller, Tobias Schwerd
Cell Reports Medicine, 2025
Citation

ATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation
Olivia I Colema\(^\dagger\)n, Adam Sorbie\(^\dagger\), Alessandra Riva, Miriam von Stern, Stephanie Kuhls, Denise M Selegato, Nikolai Köhler, Jakob Wirbel, Tim Kacprowski, Andreas Dunkel, Josh K Pauling, Johannes Plagge, Diego Mediel-Cuadra, Sophia Wagner, Ines Chadly, Sandra Bierwith, Tingying Peng, Thomas Metzler, Clemens Schafmayer, Sebastian Hinz, Christian Röder, Christoph Röcken, Michael Zimmermann, Philip Rosenstiel, Katja Steiger, Moritz Jesinghaus, Gerhard Liebisch, Josef Ecker, Christina Schmidt, Georg Zeller, Klaus-Peter Janssen, Dirk Haller
Nature Metabolism, 2025
Citation

2024 Link to heading

Preprints Link to heading

LipiDetective-a deep learning model for the identification of molecular lipid species in tandem mass spectra
Vivian Würf, Nikolai Köhler, Florian Molnar, Lisa Hahnefeld, Robert Gurke, Michael Witting, Josch Konstantin Pauling
bioRxiv, 2024
Citation

Journal Articles Link to heading

Exclusive Enteral Nutrition Initiates Individual Protective Microbiome Changes to Induce Remission in Pediatric Crohn’s Disease
Deborah Haecker, Kolja Siebert, Byron J Smith, Nikolai Köhler, Alessandra Riva, Aritra Mahapatra, Helena Heimes, Jiatong Nie, Amira Metwaly, Hannes Hölz, Quirin Manz, Federica De Zen, Jeannine Heetmeyer, Katharina Socas, Giang Le Thi, Chen Meng, Karin Kleigrewe, Josch K Pauling, Klaus Neuhaus, Markus List, Katherine S Pollard, Tobias Schwerd, Dirk Haller
Cell Host & Microbe, 2024
Citation

2023 Link to heading

Preprints Link to heading

Identification and Integration of Key-Metabolic Reactions from Untargeted Metabolomics Data
Nikolai Köhler, Vivian Würf, Tim Daniel Rose and Josch Konstantin Pauling
bioRxiv, 2023
Citation

Barley shows reduced Fusarium Head Blight under drought and modular expression of differential expressed genes under combined stress
Felix Hoheneder\(^\dagger\), Christina E Steidele$^{\dagger}$, Maxim Messerer, Klaus Mayer, Nikolai Köhler, Christine Wurmser, Michael Heß, Michael Gigl, Corinna Dawid, Remco Stam, Ralph Hückelhoven
bioRxiv, 2023
Citation

Journal Articles Link to heading

Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data
Tim Daniel Rose\(^\dagger\), Nikolai Köhler\(^\dagger\), Lisa Falk, Lucie Klischat, Olga Lazareva and Josch Konstantin Pauling
Briefings in Bioinformatics, 2023
Citation

Software and Computational Tools for LC-MS-Based Epilipidomics: Challenges and Solutions
Tito Damiani, Stefano Bonciarelli, Gerhard G Thallinger, Nikolai Köhler, Christoph A Krettler, Arif K Salihoğlu, Ansgar Korf, Josch K Pauling, Tomáš Pluskal, Zhixu Ni, Laura Goracci
Analytical Chemistry, 2023
Citation

2022 Link to heading

Journal Articles Link to heading

MoSBi: Automated signature mining for molecular stratification and subtyping
Tim Daniel Rose, Thibault Bechtler, Octavia-Andreea Ciora, Kim Anh Lilian Le, Florian Molnar, Nikolai Köhler, Jan Baumbach, Richard Roettger, Josch Konstantin Pauling
Proceedings of the National Academy of Science U.S.A. (PNAS), 2022
Citation

Kupffer cells are protective in alcoholic steatosis.
Nikolai Köhler\(^\dagger\), Marcus Höring\(^\dagger\), Beate Czepukojc\(^\dagger\), Tim Daniel Rose\(^\dagger\), Christa Buechler, Tarek Kröhler, Johannes Haybaeck, Gerhard Liebisch, Josch K. Pauling, Sonja M. Kessler, Alexandra K. Kiemer
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2022
Citation

2021 Link to heading

Journal Articles Link to heading

Investigating Global Lipidome Alterations with the Lipid Network Explorer.
Nikolai Köhler\(^\dagger\), Tim Daniel Rose\(^\dagger\), Lisa Falk and Josch Konstantin Pauling
Metabolites, 2021
Citation

Liver Lipids of Patients with Hepatitis B and C and Associated Hepatocellular Carcinoma.
Haberl EM, Weiss TS, Peschel G, Weigand K, Köhler N, Pauling JK, Wenzel JJ, Höring M, Krautbauer S, Liebisch G, Buechler C
International Journal of Molecular Sciences, 2021
Citation

Susceptibility to diet induced obesity at thermoneutral conditions is independent of UCP1
Sebastian Dieckmann, Akim Strohmeyer, Monja Willershäuser, Stefanie Maurer, Wolfgang Wurst, Susan Marschall, Martin Hrabe de Angelis, Ralf Kühn, Anna Worthmann, Marceline M Fuh, Joerg Heeren, Nikolai Köhler, Josch K. Pauling, Martin Klingenspor
American Journal of Physiology-Endocrinology and Metabolism, 2021
Citation

2019 Link to heading

Journal Articles Link to heading

Pyrrolizidine Alkaloids: Biosynthesis, Biological Activities and Occurrence in Crop Plants
Sebastian Schramm, Nikolai Köhler, Wilfried Rozhon
Molecules, 2019
Citation

\(^{\dagger}\) these authors contributed equally