Publications

@ARTICLE{teufel2024iimr110368,
  author = {Teufel, L.U.~ and Matzaraki, V.~ and Folkman, L.~ and Ter Horst, R.~ and Moorlag, S.J.C.F.M.~ and Mulders-Manders, C.M.~ and Netea, M.G.~ and Krausgruber, T.~ and Joosten, L.A.B.~ and Arts, R.J.W.~},
  title = {Insights into the Multifaceted Role of Interleukin-37 on Human Immune Cell Regulation.},
  journal = {Clinical Immunology},
  year = {2024},
  volume = {268},
  pages = {110368},
  issn = {1521-7035 1521-6616},
  doi = {10.1016/j.clim.2024.110368},
  keywords = {Inflammation;Autoinflammation;BCG;Interleukin (IL)-37;Trained immunity}
}

@ARTICLE{stolz2024nrc1e78738,
  author = {Stolz, V.~ and Silva, R.d.F.~ and Rica, R.~ and Zhu, C.~ and Preglej, T.~ and Hamminger, P.~ and Hainberger, D.~ and Alteneder, M.~ and Muller, L.~ and Waldherr, M.~ and Waltenberger, D.~ and Hladik, A.~ and Agerer, B.~ and Schuster, M.~ and Frey, T.~ and Krausgruber, T.~ and Knapp, S.~ and Campbell, C.~ and Schmetterer, K.~ and Trauner, M.~ and Bergthaler, A.~ and Bock, C.~ and Boucheron, N.~ and Ellmeier, W.~},
  title = {Nuclear Receptor Corepressor 1 Controls Regulatory T Cell Subset Differentiation and Effector Function.},
  journal = {eLife},
  year = {2024},
  volume = {13},
  pages = {e78738},
  doi = {10.7554/eLife.78738}
}

@ARTICLE{schaefer2024mltt20241015618501,
  author = {Schaefer, M.~ and Peneder, P.~ and Malzl, D.~ and Peycheva, M.~ and Burton, J.~ and Hakobyan, A.~ and Sharma, V.~ and Krausgruber, T.~ and Menche, J.~ and Tomazou, E.M.~ and Bock, C.~},
  title = {Multimodal Learning of Transcriptomes and Text Enables Interactive Single-Cell RNA-Seq Data Exploration with Natural-Language Chats.},
  journal = {bioRxiv},
  year = {2024},
  pages = {2024.10.15.618501},
  doi = {10.1101/2024.10.15.618501},
  url = {http://biorxiv.org/content/early/2024/10/18/2024.10.15.618501.abstract}
}

@ARTICLE{schaefer2024gaab108796,
  author = {Schaefer, M.~ and Reichl, S.~ and Ter Horst, R.~ and Nicolas, A.M.~ and Krausgruber, T.~ and Piras, F.~ and Stepper, P.~ and Bock, C.~ and Samwald, M.~},
  title = {GPT-4 as a Biomedical Simulator.},
  journal = {Computers in Biology and Medicine},
  year = {2024},
  volume = {178},
  pages = {108796},
  issn = {1879-0534 0010-4825},
  doi = {10.1016/j.compbiomed.2024.108796},
  keywords = {Artificial intelligence;Computational biology;Large language models;Biomedical simulation;GPT-4}
}

@ARTICLE{lim2024almm11521164,
  author = {Lim, C.X.~ and Redl, A.~ and Kleissl, L.~ and Pandey, R.V.~ and Mayerhofer, C.~ and El Jammal, T.~ and Mazic, M.~ and Gonzales, K.~ and Sukhbaatar, N.~ and Krausgruber, T.~ and Bock, C.~ and Hengstschl{\"a}ger, M.~ and Calender, A.~ and Pacheco, Y.~ and Stary, G.~ and Weichhart, T.~},
  title = {Aberrant Lipid Metabolism in Macrophages Is Associated with Granuloma Formation in Sarcoidosis.},
  journal = {American Journal of Respiratory and Critical Care Medicine},
  year = {2024},
  volume = {209},
  number = {9},
  pages = {1152--1164},
  issn = {1535-4970 1073-449X},
  doi = {10.1164/rccm.202307-1273OC},
  keywords = {macrophages;mTOR;lipid metabolism;sarcoidosis}
}

@ARTICLE{fortelny2024jsmh847859,
  author = {Fortelny, N.~ and Farlik, M.~ and Fife, V.~ and Gorki, A.-D.~ and Lassnig, C.~ and Maurer, B.~ and Meissl, K.~ and Dolezal, M.~ and Boccuni, L.~ and Ravi Sundar Jose Geetha, A.~ and Akagha, M.J.~ and Karjalainen, A.~ and Shoebridge, S.~ and Farhat, A.~ and Mann, U.~ and Jain, R.~ and Tikoo, S.~ and Zila, N.~ and Esser-Skala, W.~ and Krausgruber, T.~ and Sitnik, K.~ and Penz, T.~ and Hladik, A.~ and Suske, T.~ and Zahalka, S.~ and Senekowitsch, M.~ and Barreca, D.~ and Halbritter, F.~ and Macho-Maschler, S.~ and Weninger, W.~ and Neubauer, H.A.~ and Moriggl, R.~ and Knapp, S.~ and Sexl, V.~ and Strobl, B.~ and Decker, T.~ and M{\"u}ller, M.~ and Bock, C.~},
  title = {JAK-STAT Signaling Maintains Homeostasis in T Cells and Macrophages.},
  journal = {Nature Immunology},
  year = {2024},
  volume = {25},
  number = {5},
  pages = {847--859},
  issn = {1529-2916 1529-2908},
  doi = {10.1038/s41590-024-01804-1},
  keywords = {Animals;Mice;Mice;Inbred C57BL;*Homeostasis;*Signal Transduction;Gene Expression Regulation;*Janus Kinases/metabolism;*Macrophages/immunology/metabolism;*Mice;Knockout;*STAT Transcription Factors/metabolism;CD8-Positive T-Lymphocytes/immunology/metabolism;Interferon-Stimulated Gene Factor 3;gamma Subunit/metabolism/genetics;STAT1 Transcription Factor/metabolism/genetics;TYK2 Kinase/metabolism/genetics}
}

@ARTICLE{suske2024hshte168536,
  author = {Suske, T.~ and Sorger, H.~ and Manhart, G.~ and Ruge, F.~ and Prutsch, N.~ and Zimmerman, M.W.~ and Eder, T.~ and Abdallah, D.I.~ and Maurer, B.~ and Wagner, C.~ and Schonefeldt, S.~ and Spirk, K.~ and Pichler, A.~ and Pemovska, T.~ and Schweicker, C.~ and Poloske, D.~ and Hubanic, E.~ and Jungherz, D.~ and Muller, T.A.~ and Aung, M.M.K.~ and Orlova, A.~ and Pham, H.T.T.~ and Zimmel, K.~ and Krausgruber, T.~ and Bock, C.~ and Muller, M.~ and Dahlhoff, M.~ and Boersma, A.~ and Rulicke, T.~ and Fleck, R.~ and de Araujo, E.D.~ and Gunning, P.T.~ and Aittokallio, T.~ and Mustjoki, S.~ and Sanda, T.~ and Hartmann, S.~ and Grebien, F.~ and Hoermann, G.~ and Haferlach, T.~ and Staber, P.B.~ and Neubauer, H.A.~ and Look, A.T.~ and Herling, M.~ and Moriggl, R.~},
  title = {Hyperactive STAT5 Hijacks T Cell Receptor Signaling and Drives Immature T Cell Acute Lymphoblastic Leukemia.},
  journal = {Journal of Clinical Investigation},
  year = {2024},
  volume = {134},
  number = {8},
  pages = {e168536},
  doi = {10.1172/JCI168536}
}

@ARTICLE{hevesi2024teng2762,
  author = {Hevesi, Z.~ and Bakker, J.~ and Tretiakov, E.O.~ and Adori, C.~ and Raabgrund, A.~ and Barde, S.S.~ and Caramia, M.~ and Krausgruber, T.~ and Ladst{\"a}tter, S.~ and Bock, C.~ and H{\"o}kfelt, T.~ and Harkany, T.~},
  title = {Transient Expression of the Neuropeptide Galanin Modulates Peripheral‑to‑Central Connectivity in the Somatosensory Thalamus during Whisker Development in Mice.},
  journal = {Nature Communications},
  year = {2024},
  volume = {15},
  pages = {2762},
  issn = {2041-1723},
  doi = {10.1038/s41467-024-47054-5},
  keywords = {Animals;Humans;Mice;*Galanin/metabolism;*Vibrissae/physiology;Axons/metabolism;Brain/metabolism;Thalamus/metabolism}
}

@ARTICLE{rica2024hcgm20240228580886,
  author = {Rica, R.~ and Waldherr, M.~ and Schulein, M.~ and Miyakoda, E.~ and Sandner, L.~ and Stolz, V.~ and Waltenberger, D.~ and Krausgruber, T.~ and Bock, C.~ and Boucheron, N.~ and Ellmeier, W.~ and Sakaguchi, S.~},
  title = {HDAC1 Controls the Generation and Maintenance of Effector-Like CD8+ T Cells during Chronic Viral Infection.},
  journal = {bioRxiv},
  year = {2024},
  pages = {2024.02.28.580886},
  doi = {10.1101/2024.02.28.580886}
}

@ARTICLE{braithwaite2024msrse23448,
  author = {Braithwaite, A.T.~ and Akbar, N.~ and Pezzolla, D.~ and Paget, D.~ and Krausgruber, T.~ and Bock, C.~ and Carnicer, R.~ and Choudhury, R.P.~},
  title = {Multi-Organ Single-Cell RNA Sequencing in Mice Reveals Early Hyperglycemia Responses That Converge on Fibroblast Dysregulation.},
  journal = {FASEB Journal},
  year = {2024},
  volume = {38},
  number = {3},
  pages = {e23448},
  issn = {1530-6860 0892-6638},
  doi = {10.1096/fj.202302003R},
  keywords = {Animals;Male;Mice;Mice;Inbred C57BL;gene expression;fibrosis;mice;hyperglycemia;Sequence Analysis;RNA;*Diabetes Mellitus;Type 1/genetics;*Hyperglycemia/genetics;endothelial cells;Endothelial Cells;monocytes;myofibroblast;RRID:IMSR\_JAX:000664;RRID:SCR\_001618;RRID:SCR\_001905;RRID:SCR\_007322;RRID:SCR\_019010;RRID:SCR\_021946;RRID:SCR\_022146;RRID:SCR\_022254;single-cell RNA-seq;Streptozocin/toxicity;streptozotocin;type 1 diabetes}
}

@ARTICLE{redl2024esmie81e91,
  author = {Redl, A.~ and Doberer, K.~ and Unterluggauer, L.~ and Kleissl, L.~ and Krall, C.~ and Mayerhofer, C.~ and Reininger, B.~ and Stary, V.~ and Zila, N.~ and Weninger, W.~ and Weichhart, T.~ and Bock, C.~ and Krausgruber, T.~ and Stary, G.~},
  title = {Efficacy and Safety of mTOR Inhibition in Cutaneous Sarcoidosis: A Single-Centre Trial.},
  journal = {Lancet Rheumatology},
  year = {2024},
  volume = {6},
  number = {2},
  pages = {e81--e91},
  issn = {2665-9913},
  doi = {10.1016/S2665-9913(23)00302-8}
}

@ARTICLE{cheung2024mpio230246e11,
  author = {Cheung, G.~ and Pauler, F.M.~ and Koppensteiner, P.~ and Krausgruber, T.~ and Streicher, C.~ and Schrammel, M.~ and Gutmann-{\"O}zgen, N.~ and Ivec, A.E.~ and Bock, C.~ and Shigemoto, R.~ and Hippenmeyer, S.~},
  title = {Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.},
  journal = {Neuron},
  year = {2024},
  volume = {112},
  number = {2},
  pages = {230--246.e11},
  issn = {1097-4199 0896-6273},
  doi = {10.1016/j.neuron.2023.11.009},
  keywords = {Animals;*Neural Stem Cells/metabolism;*Superior Colliculi/physiology;Cell Lineage/physiology;cell-type diversity;clonal analysis;lineage;MADM;MADM-CloneSeq;Mammals;mosaic analysis with double markers;Neuroglia/metabolism;Neurons/metabolism;radial glial progenitor;RGP;stem cell;superior colliculus}
}

@ARTICLE{moorlag2024maia171187e14,
  author = {Moorlag, S.J.C.F.M.~ and Folkman, L.~ and Ter Horst, R.~ and Krausgruber, T.~ and Barreca, D.~ and Schuster, L.C.~ and Fife, V.~ and Matzaraki, V.~ and Li, W.~ and Reichl, S.~ and Mourits, V.P.~ and Koeken, V.A.C.M.~ and de Bree, L.C.J.~ and Dijkstra, H.~ and Lemmers, H.~ and van Cranenbroek, B.~ and van Rijssen, E.~ and Koenen, H.J.P.M.~ and Joosten, I.~ and Xu, C.-J.~ and Li, Y.~ and Joosten, L.A.B.~ and van Crevel, R.~ and Netea, M.G.~ and Bock, C.~},
  title = {Multi-Omics Analysis of Innate and Adaptive Responses to BCG Vaccination Reveals Epigenetic Cell States That Predict Trained Immunity.},
  journal = {Immunity},
  year = {2024},
  volume = {57},
  number = {1},
  pages = {171--187.e14},
  doi = {10.1016/j.immuni.2023.12.005}
}

@ARTICLE{brazdilova2023mstus348s348,
  author = {Brazdilova, K.~ and Redl, A.~ and Unterluggauer, L.~ and Kleissl, L.~ and Krausgruber, T.~ and Weichhart, T.~ and Bock, C.~ and Stary, G.~},
  title = {Mapping Single-Cell Trajectories upon mTOR Inhibition over Time in Patients with Granulomatous Disease.},
  journal = {Journal of Investigative Dermatology},
  year = {2023},
  volume = {143},
  number = {11, Suppl: Abstracts 5th Inflammatory Skin Disease Summit (ISDS), Vienna, Austria, 15–18 Nov 2023},
  pages = {S348},
  issn = {0022-202X},
  url = {https://doi.org/10.1016/j.jid.2023.09.103}
}

@ARTICLE{redl2023emics360s360,
  author = {Redl, A.~ and Doberer, K.~ and Unterluggauer, L.~ and Krall, C.~ and Mayerhofer, C.~ and Kleissl, L.~ and Reininger, B.~ and Stary, V.~ and Zilla, N.~ and Weninger, W.~ and Weichhart, T.~ and Bock, C.~ and Krausgruber, T.~ and Stary, G.~},
  title = {Effectivity of mTOR Inhibition in Cutaneous Sarcoidosis.},
  journal = {Journal of Investigative Dermatology},
  year = {2023},
  volume = {143},
  number = {11, Suppl: Abstracts 5th Inflammatory Skin Disease Summit (ISDS), Vienna, Austria, 15–18 Nov 2023},
  pages = {S360},
  issn = {0022-202X},
  url = {https://doi.org/10.1016/j.jid.2023.09.176}
}

@ARTICLE{stolz2023ncts128128,
  author = {Stolz, V.~ and Rica, R.~ and Zhu, C.~ and Freitas, E.~ and Preglej, T.~ and Hamminger, P.~ and Hainberger, D.~ and Alteneder, M.~ and M{\"u}ller, L.~ and Agerer, B.~ and Schuster, M.~ and Frey, T.~ and Krausgruber, T.~ and Boucheron, N.~ and Knapp, S.~ and Schmetterer, K.~ and Trauner, M.~ and Bergthaler, A.~ and Bock, C.~ and Ellmeier, W.~},
  title = {NCOR1 Controls Treg Subset Differentiation and Effector Function.},
  journal = {European Journal of Immunology},
  year = {2023},
  volume = {53},
  number = {Suppl 2: Abstracts Joint Conference of the Société Française d’Immunologie (SFI) and the Deutsche Gesellschaft f{\"u}r Immunologie (DGfI), Strasbourg, France, 26–29 Sep 2023},
  pages = {128},
  issn = {0014-2980},
  doi = {DOI: 10.1002/eji.202370300},
  url = {https://onlinelibrary.wiley.com/toc/15214141/2023/53/S2}
}

@ARTICLE{khan2023spur20230810552772,
  author = {Khan, M.~ and Alteneder, M.~ and Reiter, W.~ and Krausgruber, T.~ and Dobnikar, L.~ and Madern, M.~ and Waldherr, M.~ and Bock, C.~ and Hartl, M.~ and Ellmeier, W.~ and Henriksson, J.~ and Boucheron, N.~},
  title = {Single-Cell Profiling Uncovers Regulatory Programs of Pathogenic Th2 Cells in Allergic Asthma.},
  journal = {bioRxiv},
  year = {2023},
  pages = {2023.08.10.552772},
  doi = {10.1101/2023.08.10.552772}
}

@ARTICLE{redl2023ssahs172s172,
  author = {Redl, A.~ and Krausgruber, T.~ and Barreca, D.~ and Lim, C.~ and Doberer, K.~ and Unterluggauer, L.~ and Kleissl, L.~ and Mayerhofer, C.~ and Kopf, A.~ and Weichhart, T.~ and Bock, C.~ and Stary, G.~},
  title = {Single-Cell and Spatial Architecture of Human Tissue Granulomas Reveals an Aberrant Immune-Regulatory Program Underlying Sarcoidosis.},
  journal = {Journal of Investigative Dermatology},
  year = {2023},
  volume = {143},
  number = {5, Suppl: Abstracts 1st International Societies for Investigative Dermatology Meeting (ISID 2023), Tokyo, Japan, 12–13 May 2023},
  pages = {S172},
  issn = {0022-202X},
  url = {https://www.jidonline.org/article/S0022-202X(23)01192-2/fulltext}
}

@ARTICLE{akbar2023rnmb236251,
  author = {Akbar, N.~ and Braithwaite, A.T.~ and Corr, E.M.~ and Koelwyn, G.J.~ and van Solingen, C.~ and Cochain, C.~ and Saliba, A.-E.~ and Corbin, A.~ and Pezzolla, D.~ and Møller Jørgensen, M.~ and Bæk, R.~ and Edgar, L.~ and De Villiers, C.~ and Gunadasa-Rohling, M.~ and Banerjee, A.~ and Paget, D.~ and Lee, C.~ and Hogg, E.~ and Costin, A.~ and Dhaliwal, R.~ and Johnson, E.~ and Krausgruber, T.~ and Riepsaame, J.~ and Melling, G.E.~ and Shanmuganathan, M.~ and Bock, C.~ and Carter, D.R.F.~ and Channon, K.M.~ and Riley, P.R.~ and Udalova, I.A.~ and Moore, K.J.~ and Anthony, D.C.~ and Choudhury, R.P.~},
  title = {Rapid Neutrophil Mobilization by VCAM-1+ Endothelial Cell-Derived Extracellular Vesicles.},
  journal = {Cardiovascular Research},
  year = {2023},
  volume = {119},
  number = {1},
  pages = {236--251},
  issn = {1755-3245 0008-6363},
  doi = {10.1093/cvr/cvac012},
  keywords = {Animals;Mice;Myocardial infarction;*Extracellular Vesicles/metabolism;*MicroRNAs/genetics/metabolism;*Myocardial Infarction/metabolism;Endothelial Cells/metabolism;Exosome;Neutrophils/metabolism;Programming;Spleen;Vascular Cell Adhesion Molecule-1/genetics/metabolism}
}

@ARTICLE{pandey2023ertc109245,
  author = {Pandey, R.V.~ and Strobl, J.~ and Redl, A.~ and Unterluggauer, L.~ and Gail, L.~ and Kleissl, L.~ and M{\"u}ller, S.~ and Atzm{\"u}ller, D.~ and Fife-Gernedl, V.~ and Krausgruber, T.~ and Knaus, H.~ and Mitterbauer, M.~ and Wohlfarth, P.~ and Rabitsch, W.~ and Bock, C.~ and Stary, G.~},
  title = {Epigenetic Regulation of T Cell Lineages in Skin and Blood Following Hematopoietic Stem Cell Transplantation.},
  journal = {Clinical Immunology},
  year = {2023},
  volume = {248},
  pages = {109245},
  issn = {1521-7035 1521-6616},
  doi = {10.1016/j.clim.2023.109245},
  keywords = {T cells;Histone deacetylases;Epigenetic regulation;Hematopoietic stem cell transplantation}
}

@ARTICLE{krausgruber2023sstr289306e7,
  author = {Krausgruber, T.~ and Redl, A.~ and Barreca, D.~ and Doberer, K.~ and Romanovskaia, D.~ and Dobnikar, L.~ and Guarini, M.~ and Unterluggauer, L.~ and Kleissl, L.~ and Atzmuller, D.~ and Mayerhofer, C.~ and Kopf, A.~ and Saluzzo, S.~ and Lim, C.X.~ and Rexie, P.~ and Weichhart, T.~ and Bock, C.~ and Stary, G.~},
  title = {Single-Cell and Spatial Transcriptomics Reveal Aberrant Lymphoid Developmental Programs Driving Granuloma Formation.},
  journal = {Immunity},
  year = {2023},
  volume = {56},
  number = {2},
  pages = {289--306.e7},
  doi = {10.1016/j.immuni.2023.01.014}
}