Publications

2025 Link to heading

Preprints 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 bioRxiv, 2025 Citation

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