Mayr M, Monroy LCR, Maier A, Gupta P, Koestler H, Wellein G. Beyond Frozen Features: Block Expansion of Pathology Foundation Models for Glioblastoma Sub-Region Classification. MICCAI 2026 Challenge BraTS-Path, 2026 (accepted).
Ghirotto B, Gonçalves LE, Ruder V, James C, Gerasimova E, Rizo T, Wend H, Farrell M, Gerez JA, Prymaczok NC, Kuijs M, Shulman M, Hartebrodt A, Prots I, Gessner A, Zunke F, Winkler J, Blumenthal DB, Theis FJ, Riek R, Günther C, Neurath M, Gupta P, Winner B. TNF-α disrupts the malate–aspartate shuttle, driving metabolic rewiring in iPSC-derived enteric neural lineages from Parkinson’s disease patients. Nature Communications, 2026. doi: 10.1101/2025.03.25.644826. (shared last authorship)
Rius Rigau A, Xu M, Chenguiti Fakhouri S, Auth J, Garantziotis P, Selvaraju MK, Raimondo M, Tur C, Filla T, Eckstein M, Müller F, Atzinger A, Ronicke M, Ekici A, Schmid R, Wirsching A, Hagen M, Boeltz S, Krickau T, Horch R, Berking C, Grieshaber-Bouyer R, Ramming A, Gupta P, Bozec A, Mackensen A, Distler J, Schett G, Li Y-N, Kuwert T, Liu Z, Zoli A, Gehringer P, Bergmann C. Deep phenotyping of skin tissue remodeling in systemic sclerosis patients in response to CD19 CAR T-cell therapy. Nature Communications, 2026.doi: 10.1038/s41467-026-72817-7.
Wei X, Degen S, Hironimus T, Rechenauer T, Yankouskaya K, Rückel A, Schmid M, Rieger D, Ehrsam C, Regensburger AP, Schnell A, Rabe A, Schmidt-Choudhury A, Tannapfel A, De Laffolie J, Schumann S, Schwerd T, Hoelz H, Allabauer I, Gupta P, Krebs W, Hartmann A, Woelfle J, Rieker R, Hoerning A. PSMB8 stratifies therapy response in eosinophilic esophagitis. Clinical and Experimental Immunology, 2026. doi:10.1093/cei/uxag012.
Guliyeva G, Nguemedjio Foko Takile F, Stallfort V, Derer A, Frey B, Gupta P, Weber M, Trumet L, Schett G, Bozec A, Grötsch B. AnnexinA1–Dectin-1 axis is a key regulator of osteoclastogenesis underlying irradiation-induced bone loss in male mice. Journal of Bone and Mineral Research, 2026. doi:10.1093/jbmr/zjag062.
Gonzalez-Acera M, Patankar JV, Erkert L, Cineus R, Gamez-Belmonte R, Leupold T, Bubeck M, Bao L-L, Dinkel M, Wang R, Schickedanz L, Limberger H, Stolzer I, Gerlach K, Diemand L, Mascia F, Gupta P, Naschberger E, Koop K, Plattner C, Sturm G, Weigmann B, Günther C, Wirtz S, Stürzl M, Hildner K, Kühl AA, Siegmund B, Gießl A, Atreya R, TRR241 IBDome Consortium, Hegazy AN, Trajanoski Z, Neurath MF, Becker C. Integrated multimodel analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD. Gut, 2025. doi:10.1136/gutjnl-2024-333729.
Boerstler T, Kachkin D, Gerasimova E, Zagha N, Furlanetto F, Nayebzade N, Zappia L, Boisvert M, Farrell M, Ploetz S, Prots I, Regensburger M, Günther C, Winkler J, Gupta P, Theis F, Karow M, Falk S, Winner B, Krach F. Deciphering brain organoid heterogeneity by identifying key quality determinants. Communications Biology, 2025. doi:10.1038/s42003-025-08855-6.
John N, Fleming T, Kolb J, Lyraki O, Vásquez-Sepúlveda S, Parmar A, Kim K, Tarczewska M, Gupta P, Singh K, Marini F, Singh SP, Tsata V, Falk S, Franze K, Guck J, Wehner D. Biphasic inflammation control by fibroblasts enables spinal cord regeneration in zebrafish. Cell Reports, 2025. doi:10.1016/j.celrep.2025.116469.
Menche C, Schuhwerk H, Armstark I, Gupta P, Fuchs K, van Roey R, Mosa MH, Hartebrodt A, Hajjaj Y, Clavel Ezquerra A, Selvaraju MK, Geppert CI, Bärthel S, Saur D, Greten FR, Brabletz S, Blumenthal DB, Weigert A, Brabletz T, Farin HF, Stemmler MP. ZEB1-mediated fibroblast polarization controls inflammation and sensitivity to immunotherapy in colorectal cancer. EMBO Reports, 2024. doi:10.1038/s44319-024-00186-7.
Schuhwerk H, Kleemann J, Gupta P, van Roey R, Armstark I, Kreileder M, Feldker N, Ramesh V, Hajjaj Y, Fuchs K, Mahapatro M, Hribersek M, Volante M, Groenewoud A, Engel FB, Ceppi P, Eckstein M, Hartmann A, Müller F, Kroll T, Stemmler MP, Brabletz S, Brabletz T. The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response. Cell Reports, 2022. doi:10.1016/j.celrep.2022.111819.
Gupta P, Peter S, Jung M, Lewin A, Hemmrich-Stanisak G, Franke A, von Kleist M, Schütte C, Einspanier R, Sharbati S, zur Bruegge J. Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Scientific Reports, 2019. doi:10.1038/s41598-018-38141-x.
Gupta P, Gramatke A, Einspanier R, Schütte C, von Kleist M, Sharbati J. In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements. Toxicology in Vitro, 2017. doi:10.1016/j.tiv.2017.02.021.
Bienefeld K, Zautke F, Gupta P. A novel method for undisturbed long-term observation of honey bee behaviour—illustrated by hygienic behaviour towards Varroa destructor infestation. Journal of Apicultural Research, 2016. doi:10.1080/00218839.2016.1174465.
Spötter A, Gupta P, Schauser L, Bienefeld K. Genome-wide association study of a varroa-specific defense behavior in honey bees (Apis mellifera). Journal of Heredity, 2016. doi:10.1093/jhered/esw005.
Gupta P, Reinsch N, Spötter A, Conrad T, Bienefeld K. Accuracy of the unified approach in composite traits—illustrated by a simulation study in honey bee (Apis mellifera). BMC Genetics, 2013. doi:10.1186/1471-2156-14-36.
Gupta P, Conrad T, Spötter A, Reinsch N, Bienefeld K. Simulating a base population in honey bee for molecular genetic studies. Genetics Selection and Evolution, 2012. doi:10.1186/1297-9686-44-14.
Spötter A, Gupta P, Nürnberg G, Reinsch N, Bienefeld K. Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica). Molecular Ecology Resources, 2012. doi:10.1111/j.1755-0998.2011.03106.x.