iTREAT

Bourgery, M., J. P. Bernardes, M. Wittig, F. Kimmig, N. Mishra, A. Franke, K. Aden, S. Schreiber, P. Rosenstiel, and F. Tran. 2025. "P0918 Identification of a serum proteomics signature linked with anti-TNF therapy response outcomes in Inflammatory Bowel Disease." Journal of Crohn's and Colitis, 2025/01/22/. doi.org/10.1093/ecco-jcc/jjae190.1092.

Jantsch, A., T. Vorhaben, F. Yalcin, F. Hinrichsen, J. Lebich, M. Bourgery, L. Welz, J. Labrenz, S. Lüschen, C. Röcken, K. Aden, P. Rosenstiel, S. Schreiber, and F. Tran. 2025. "P0455 An eosinophilic endotype of ulcerative colitis is linked with a more complicated disease phenotype." Journal of Crohn's and Colitis, 2025/01/22/. doi.org/10.1093/ecco-jcc/jjae190.0629.

Mishra, N., F. Tran, F. Kimmig, K. Aden, G. Credidio, C. Wolff, T. Ruge, J. I. Blase, J. P. Bernardes, D. Ellinghaus, R. Zeuner, N. Frey, W. Lieb, A. Franke, S. Schreiber, and P. Rosenstiel. 2025. "P0008 A multi-omics approach across multiple chronic inflammatory diseases identifies a distinct type-1-interferon endotype of Inflammatory Bowel Disease." Journal of Crohn's and Colitis, 2025/01/22/. doi.org/10.1093/ecco-jcc/jjae190.0182.

^{Becker, B., F. Wottawa, M. Bakr, E. Koncina, L. Mayr, J. Kugler, G. Yang, S. J. Windross, L. Neises, N. Mishra, D. Harris, F. Tran, L. Welz, J. Schwärzler, Z. Bánki, S. T. Stengel, G. Ito, C. Krötz, O. I. Coleman, C. Jaeger, D. Haller, S. R. Paludan, R. Blumberg, A. Kaser, L. Cicin-Sain, S. Schreiber, T. E. Adolph, E. Letellier, P. Rosenstiel, J. Meiser, and K. Aden (2024). "Serine metabolism is crucial for cGAS-STING signaling and viral defense control in the gut." iScience 27(3): 109173. doi.org/10.1016/j.isci.2024.109173.
Harris, D. M. M., S. Szymczak, S. Schuchardt, J. Labrenz, F. Tran, L. Welz, H. Graßhoff, H. Zirpel, M. Sümbül, M. Oumari, N. Engelbogen, R. Junker, C. Conrad, D. Thaçi, N. Frey, A. Franke, S. Weidinger, B. Hoyer, P. Rosenstiel, S. Waschina, S. Schreiber, and K. Aden (2024). "Tryptophan degradation as a systems phenomenon in inflammation – an analysis across 13 chronic inflammatory diseases." eBioMedicine 102: 105056. doi.org/10.1016/j.ebiom.2024.105056.
Knoll, R., E. T. Helbig, K. Dahm, O. Bolaji, F. Hamm, O. Dietrich, M. van Uelft, S. Müller, L. Bonaguro, J. Schulte-Schrepping, L. Petrov, B. Krämer, M. Kraut, P. Stubbemann, C. Thibeault, S. Brumhard, H. Theis, G. Hack, E. De Domenico, J. Nattermann, M. Becker, M. D. Beyer, D. Hillus, P. Georg, C. Loers, J. Tiedemann, P. Tober-Lau, L. Lippert, B. Millet Pascual-Leone, F. Tacke, G. Rohde, N. Suttorp, M. Witzenrath, A.-E. Saliba, T. Ulas, J. K. Polansky, B. Sawitzki, L. E. Sander, J. L. Schultze, A. C. Aschenbrenner, and F. Kurth (2024). "The life-saving benefit of dexamethasone in severe COVID-19 is linked to a reversal of monocyte dysregulation." Cell 187(16): 4318–4335.e4320. doi.org/10.1016/j.cell.2024.06.014.
López-Agudelo, V. A., M. Falk-Paulsen, R. Bharti, A. Rehman, F. Sommer, E. M. Wacker, D. Ellinghaus, A. Luzius, L. K. Sievers, M. Liebeke, A. Kaser, and P. Rosenstiel (2024). "Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice." Gut Microbes. doi.org/10.1080/19490976.2024.2429267.}

Effenberger, M., S. Waschina, C. Bronowski, G. Sturm, O. Tassiello, F. Sommer, A. Zollner, C. Watschinger, F. Grabherr, R. Gstir, C. Grander, B. Enrich, R. Bale, D. Putzer, A. Djanani, A. R. Moschen, H. Zoller, J. Rupp, S. Schreiber, R. Burcelin, C. Lass-Flörl, Z. Trajanoski, G. Oberhuber, P. Rosenstiel, T. E. Adolph, K. Aden, and H. Tilg (2023). "A gut bacterial signature in blood and liver tissue characterizes cirrhosis and hepatocellular carcinoma." Hepatology Communications 7(7). doi.org/10.1097/HC9.0000000000000182.

Frishberg, A., E. Kooistra, M. Nuesch-Germano, T. Pecht, N. Milman, N. Reusch, S. Warnat-Herresthal, N. Bruse, K. Händler, H. Theis, M. Kraut, E. van Rijssen, B. van Cranenbroek, H. J. Koenen, H. Heesakkers, M. van den Boogaard, M. Zegers, P. Pickkers, M. Becker, A. C. Aschenbrenner, T. Ulas, F. J. Theis, S. S. Shen-Orr, J. L. Schultze, and M. Kox (2022). "Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19." CR Med 0(0). doi.org/10.1016/j.xcrm.2022.100652.

Le, H. D., T. Pflaum, J. Labrenz, S. Sari, F. Bretschneider, F. Tran, A. Lassen, S. Nikolaus, S. Szymczak, D. Kormilez, P. Rosenstiel, S. Schreiber, K. Aden, and C. Röcken (2022). "Interobserver Reliability of the Nancy Index for Ulcerative Colitis: An Assessment of the Practicability and Ease of Use in a Single-Centre Real-World Setting." J Crohns Colitis. doi.org/10.1093/ecco-jcc/jjac146.

Mishra, N., K. Aden, J. I. Blase, N. Baran, D. Bordoni, F. Tran, C. Conrad, D. Avalos, C. Jaeckel, M. Scherer, S. B. Sørensen, S. H. Overgaard, B. Schulte, S. Nikolaus, G. Rey, G. Gasparoni, P. A. Lyons, J. L. Schultze, J. Walter, V. Andersen, E. T. Dermitzakis, S. Schreiber, and P. Rosenstiel (2022). "Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease." Genome Med 14(1): 1–20. doi.org/10.1186/s13073-022-01112-z.

Weiss, A. S., A. G. Burrichter, A. C. Durai Raj, A. von Strempel, C. Meng, K. Kleigrewe, P. C. Münch, L. Rössler, C. Huber, W. Eisenreich, L. M. Jochum, S. Göing, K. Jung, C. Lincetto, J. Hübner, G. Marinos, J. Zimmermann, C. Kaleta, A. Sanchez, and B. Stecher (2022). "In vitro interaction network of a synthetic gut bacterial community." ISME J 16: 1095–1109. doi.org/10.1038/s41396-021-01153-z.

Welz, L., N. Kakavand, X. Hang, G. Laue, G. Ito, M. G. Silva, C. Plattner, N. Mishra, F. Tengen, C. Ogris, M. Jesinghaus, F. Wottawa, P. Arnold, L. Kaikkonen, S. Stengel, F. Tran, S. Das, A. Kaser, Z. Trajanoski, R. Blumberg, C. Roecken, D. Saur, M. Tschurtschenthaler, S. Schreiber, P. Rosenstiel, and K. Aden (2022). "Epithelial X-Box Binding Protein 1 Coordinates Tumor Protein p53-Driven DNA Damage Responses and Suppression of Intestinal Carcinogenesis." Gastroenterology 162(1): 223-237 e211. www.ncbi.nlm.nih.gov/pubmed/34599932.

Wienbrandt, L., and D. Ellinghaus (2022). "EagleImp: fast and accurate genome-wide phasing and imputation in a single tool." Bioinformatics. doi.org/10.1093/bioinformatics/btac637.

Kassens, J.C., Wienbrandt, L. and Ellinghaus, D. (2021). "BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data." GigaScience 10(6). www.ncbi.nlm.nih.gov/pubmed/34184051.

Knoll, R., Schultze, J.L. and Schulte-Schrepping, J. (2021). "Monocytes and Macrophages in COVID-19." Frontiers in Immunology 12: 720109. doi.org/10.3389/fimmu.2021.720109.

Wottawa, F., Bordoni, D., Baran, N., Rosenstiel, P. and Aden, K. (2021). "The role of cGAS/STING in intestinal immunity." European Journal of Immunology 51(4): 785-797. doi.org/10.1002/eji.202048777.

Zimmermann, J., Kaleta, C. and Waschina, S. (2021). "gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models." Genome Biology 22(1): 1–35. doi.org/10.1186/s13059-021-02295-1.