Full publication lists: Google Scholar, ORCID
Lab members underlined. *,# mark equal contributions.
Current preprints:
Saldana-Guerrero IM*, Montano-Gutierrez LF*, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A#, Halbritter F#. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. bioRxiv. 2022:2022.11.21.515753. https://doi.org/10.1101/2022.11.21.515753
Hafemeister C, Halbritter F. Single-cell RNA-seq differential expression tests within a sample should use pseudo-bulk data of pseudo-replicates. bioRxiv. 2023:2023.03.28.534443. https://doi.org/10.1101/2023.03.28.534443
Buri MC, Shoeb MR, Bykov A, Repiscak P, Baik H, Dupanovic A, David FO, Kovacic B, Hall-Glenn F, Urbanus J, Sippl L, Stofner S, Emminger D, Cosgrove J, Lehner M, Perié L, Schumacher TN, Gotthardt D, Halbritter F, Putz EM. NK cells shape the clonal evolution of B-ALL cells by IFN-γ production. bioRxiv. 2023:2023.11.16.567430. https://doi.org/10.1101/2023.11.16.567430
Main contributions (first | last authorship):
Kirchberger S*, Shoeb MR*, Lazic D, Wenninger-Weinzierl A, Fischer K, Shaw LE, Nogueira F, Rifatbegovic F, Bozsaky E, Ladenstein R, Bodenmiller B, Lion T, Traver D, Farlik M, Schöfer C, Taschner-Mandl S, Halbritter F#, Distel M#. Cross-species analysis identifies conserved transcriptional mechanisms of neutrophil maturation. Nat Commun. 2024;15;1792. https://doi.org/10.1038/s41467-024-45802-1 Code | Code Archive | Data: GSE252788
Santini L*, Halbritter F*, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. Nat Commun. 2021;12:3804. https://doi.org/10.1038/s41467-021-23510-4 Code | Data: GSE152106 | Press@CCRI
Halbritter F*, Farlik M*, Schwentner R, Jug G, Fortelny N, Schnöller T, Pisa H, Schuster LC, Reinprecht A, Czech T, Gojo J, Holter W, Minkov M, Bauer WM, Simonitsch-Klupp I, Bock C#, Hutter C#. Epigenomics and single-cell sequencing define a developmental hierarchy in langerhans cell histiocytosis. Cancer Discov. 2019;9(10):1406-1421. https://doi.org/10.1158/2159-8290.CD-19-0138 Website | Code | Data: GSE133706 | Press@CCRI
Barakat TS*, Halbritter F*, Zhang M, Rendeiro AF, Perenthaler E, Bock C, Chambers I. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Cell Stem Cell. 2018;23(2):276-288. https://doi.org/10.1016/j.stem.2018.06.014 Website | Data: GSE99631
Allison TF, Andrews PW, Avior Y, Barbaric I, Benvenisty N, Bock C, Brehm J, Brüstle O, Damjanov I, Elefanty A, Felkner D, Gokhale PJ, Halbritter F, Healy LE, Hu TX, Knowles BB, Loring JF, Ludwig TE, Mayberry R, et al. Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells. Nat Commun. 2018;9(1):1925. https://doi.org/10.1038/s41467-018-04011-3 Data: GSE97964
Mass E*, Ballesteros I*, Farlik M, Halbritter F*, Günther P*, Crozet L, Jacome-Galarza CE, Händler K, Klughammer J, Kobayashi Y, Gomez-Perdiguero E, Schultze JL, Beyer M#, Bock C#, Geissmann F#. Specification of tissue-resident macrophages during organogenesis. Science (80- ). 2016;353(6304):aaf4238. https://doi.org/10.1126/science.aaf4238 Website | Data: GSE81774 | Press@CeMM | Press@MSKCC
Bock C, Halbritter F, Carmona FJ, Tierling S, Datlinger P, Assenov Y, Berdasco M, Bergmann AK, Booher K, Busato F, Campan M, Dahl C, Dahmcke CM, Diep D, Fernández AF, Gerhauser C, Haake A, Heilmann K, Holcomb T, et al. Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol. 2016;34(7):726-737. https://doi.org/10.1038/nbt.3605 Code | Data: GSE77965 | Press@CeMM
Farlik M*, Halbritter F*, Müller F*, Choudry FA, Ebert P, Klughammer J, Farrow S, Santoro A, Ciaurro V, Mathur A, Uppal R, Stunnenberg HG, Ouwehand WH, Laurenti E, Lengauer T, Frontini M#, Bock C#. DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation. Cell Stem Cell. 2016;19(6):808-822. https://doi.org/10.1016/j.stem.2016.10.019 Website | Data: GSE87196 | Press@CeMM
Halbritter F, Kousa AI, Tomlinson SR. GeneProf data: A resource of curated, integrated and reusable high-throughput genomics experiments. Nucleic Acids Res. 2014;42(D1):D851-8. https://doi.org/10.1093/nar/gkt966 Web service (operated by University of Edinburgh)
Halbritter F, Vaidya HJ, Tomlinson SR. GeneProf: Analysis of high-throughput sequencing experiments. Nat Methods. 2012;9(1):7-8. https://doi.org/10.1038/nmeth.1809 Web service (operated by University of Edinburgh)
Halbritter F, Geibel P. Learning Models of Relational MDPs Using Graph Kernels. In: MICAI 2007: Advances in Artificial Intelligence. Springer; 2007:409-419. https://doi.org/10.1007/978-3-540-76631-5_39
Other contributions:
Karwacki-Neisius V, Cukuroglu E, Tai A, Jiao A, Predes D, Yoon J, Brookes E, Chen J, Iberg A, Halbritter F, Õunap L, Gecz J, Schlaeger TM, Sui SH, Göke J, He X, Lehtinen MK, Pomeroy SL, Shi Y. WNT signalling control by KDM5C during development affects cognition. Nature. 2023; blood.2022018303. https://doi.org/10.1038/s41586-024-07067-y
Kostel Bal S, Giuliani S, Block J, Repiscak P, Hafemeister C, Shahin T, Kasap N, Ransmayr B, Miao Y, van de Wetering C, Frohne A, Jimenez-Heredia R, Schuster MK, Zoghi S, Hertlein V, Thian M, Bykov A, Babayeva R, Eltan SB, Karakoc-Aydiner E, Shaw LE, Chowdury I, Varjosalo M, Argüello RJ, Farlik M, Ozen A, Serfling EAE, Dupré L, Bock C, Halbritter F, Hannich JT, Castanon I, Kraakman MJ, Baris S, Boztug K. Biallelic NFATC1 mutations cause an inborn error of immunity with impaired CD8+ T-cell function and perturbed glycolysis. Blood. 2023; blood.2022018303. https://doi.org/10.1182/blood.2022018303 Code
Grissenberger S, Sturtzel C, Wenninger-Weinzierl A, Radic-Sarikas B, Scheuringer E, Bierbaumer L, Etienne V, Némati F, Pascoal S, Tötzl M, Tomazou E, Metzelder M, Putz EM, Decaudin D, Delattre O, Surdez D, Kovar H, Halbritter F, Distel M. Automated compound testing in zebrafish xenografts identifies combined MCL-1 and BCL-XL inhibition to be effective against Ewing sarcoma. Cancer Letters. 2022; 554:216208. https://doi.org/10.1016/j.canlet.2022.216028
Gogolou A, Souilhol C, Granata I, Wymeersch FJ, Manipur I, Wind M, Frith TJ, Guarini M, Bertero A, Bock C, Halbritter F, Takasato M, Guarracino MR, Tsakiridis A. Early anteroposterior regionalisation of human neural crest is shaped by a pro-mesodermal factor. eLife. 2022; 11: e74263. https://doi.org/10.7554/eLife.74263 Data: GSE184227 | Data: GSE184622 | Data: GSE184620
Shahin T, Mayr D, Shoeb MR, Kuehn HS, Hoeger B, Giuliani S, Gawriyski L, Yüce Petronczki Ö, Hadjadj J, Kostel Bal S, Zoghi S, Haimel M, Jimenez-Heredia R, Boutboul D, Triebwasser MP, Rialland-Battisti F, Costedoat-Chalumeau N, Quartier P, Tangye SG, Fleisher TA, Rezaei N, Romberg N, Latour S, Varjosalo M, Halbritter F, Rieux-Laucat F, Castanon I, Rosenzweig S, Boztug K. Identification of Germline Monoallelic Mutations in IKZF2 in Patients with Immune Dysregulation. Blood Adv. 2021; bloodadvances.2021006367. https://doi.org/10.1182/bloodadvances.2021006367 Code | Data: EGAS00001005874
Shahin T, Kuehn HS, Shoeb MR, Gawriyski L, Giuliani S, Repiscak P, Hoeger B, Yüce Petronczki Ö, Bal SK, Zoghi S, Dmytrus J, Seruggia D, Castanon I, Rezaei N, Varjosalo M, Halbritter F, Rosenzweig SD, Boztug K. Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity. Sci Immunol 2021; 6(65):eabe3981. https://doi.org/10.1126/sciimmunol.abe3981 Code | Data: EGAS00001005675
Rindler K, Jonak C, Alkon N, Thaler FM, Kurz H, Shaw LE, Stingl G, Weninger W, Halbritter F, Bauer WM, Farlik M, Brunner PM. Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma. Mol Cancer. 2021 Sep 28;20(1):124. https://doi.org/10.1186/s12943-021-01419-2 Data: GSE173205
Eder SK, Schwentner R, Ben Soussia P, Abagnale G, Attarbaschi A, Minkov M, Halbritter F, Hutter C. Vemurafenib acts as molecular on-off switch governing systemic inflammation in Langerhans cell histiocytosis. Blood Adv. 2021 Oct 7:bloodadvances.2021005442. https://doi.org/10.1182/bloodadvances.2021005442 Data: GSE175480
Kollmann S, Grausenburger R, Klampfl T, Prchal-Murphy M, Bastl K, Pisa H, Knab VM, Brandstoetter T, Doma E, Sperr WR, Lagger S, Farlik M, Moriggl R, Valent P, Halbritter F, Kollmann K, Heller G, Maurer B, Sexl V. A STAT5B-CD9 axis determines self-renewal in hematopoietic and leukemic stem cells. Blood. 2021. https://doi.org/10.1182/blood.2021010980
Lazic D, Kromp F, Kirr M, Mivalt F, Rifatbegovic F, Halbritter F, Bernkopf M, Bileck A, Ussowicz M, Ambros IM, Ambros PF, Gerner C, Ladenstein R, Ostalecki C, Taschner-Mandl S. Single-cell landscape of bone marrow metastases in human neuroblastoma unraveled by deep multiplex imaging. Cancers. 2021; 13(17), 4311. https://doi.org/10.3390/cancers13174311 Data: Imaging | Data: PXD018267 | Docker | Code | Press@CCRI
Agerer B*, Koblischke M*, Gudipati V*, Montaño-Gutierrez LF, Smyth M, Popa A, Genger JW, Endler L, Florian DM, Mühlgrabner V, Graninger M, Aberle SW, Husa AM, Shaw LE, Lercher A, Gattinger P, Torralba-Gombau R, Trapin D, Penz T, et al. SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8+ T cell responses. Sci Immunol. 2021;6(57). https://doi.org/10.1126/sciimmunol.abg6461 Code | Data: GSE166651
Thomas HF, Kotova E, Jayaram S, Pilz A, Romeike M, Lackner A, Penz T, Bock C, Leeb M, Halbritter F, Wysocka J, Buecker C. Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements. Mol Cell. 2021;81(5):969-982.e13. https://doi.org/10.1016/j.molcel.2020.12.047
Cinquina V, Calvigioni D, Farlik M, Halbritter F, Fife-Gernedl V, Shirran SL, Fuszard MA, Botting CH, Poullet P, Piscitelli F, Máté Z, Szabó G, Yanagawa Y, Kasper S, Di Marzo V, Mackie K, McBain CJ, Bock C, Keimpema E, et al. Life-long epigenetic programming of cortical architecture by maternal ‘Western’ diet during pregnancy. Mol Psychiatry. 2020;25(1):22-36. https://doi.org/10.1038/s41380-019-0580-4 Data: GSE140011
Baumgartner C, Toifl S, Farlik M, Halbritter F, Scheicher R, Fischer I, Sexl V, Bock C, Baccarini M. An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion. Cell Stem Cell. 2018;22(6):879-892. https://doi.org/10.1016/j.stem.2018.05.003 Data: GSE112842
Pham HTT, Maurer B, Prchal-Murphy M, Grausenburger R, Grundschober E, Javaheri T, Nivarthi H, Boersma A, Kolbe T, Elabd M, Halbritter F, Pencik J, Kazemi Z, Grebien F, Hengstschläger M, Kenner L, Kubicek S, Farlik M, Bock C, et al. STAT5B N642H is a driver mutation for T cell neoplasia. J Clin Invest. 2018;128(1):387-401. https://doi.org/10.1172/JCI94509
Festuccia N, Halbritter F, Corsinotti A, Gagliardi A, Colby D, Tomlinson SR, Chambers I. Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation. EMBO J. 2018;37(21):e95476. https://doi.org/10.15252/embj.201695476 Data: GSE118907
Corsinotti A*, Wong FCK*, Tatar T, Szczerbinska I, Halbritter F, Colby D, Gogolok S, Pantier R, Liggat K, Mirfazeli ES, Ponsele EH, Mullin NP, Wilson V, Chambers I. Distinct SoxB1 networks are required for naïve and primed pluripotency. Elife. 2017;6:e27746. https://doi.org/10.7554/eLife.27746 Data: GSE99185
Mistri TK, Devasia AG, Chu LT, Ng WP, Halbritter F, Colby D, Martynoga B, Tomlinson SR, Chambers I, Robson P, Wohland T. Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells. EMBO Rep. 2015;16(9):1177-1191. https://doi.org/10.15252/embr.201540467
Karwacki-Neisius V, Göke J, Osorno R, Halbritter F, Ng JH, Weiße AY, Wong FCK, Gagliardi A, Mullin NP, Festuccia N, Colby D, Tomlinson SR, Ng HH, Chambers I. Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and Nanog. Cell Stem Cell. 2013;12(5):531-545. https://doi.org/10.1016/j.stem.2013.04.023 Data: E-MTAB-1619
Gagliardi A*, Mullin NP*, Ying Tan Z, Colby D, Kousa AI, Halbritter F, Weiss JT, Felker A, Bezstarosti K, Favaro R, Demmers J, Nicolis SK, Tomlinson SR, Poot RA, Chambers I. A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal.EMBO J. 2013;32(16):2231-2247. https://doi.org/10.1038/emboj.2013.161
Festuccia N*, Osorno R*, Halbritter F, Karwacki-Neisius V, Navarro P, Colby D, Wong F, Yates A, Tomlinson SR, Chambers I. Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells. Cell Stem Cell. 2012;11(4):477-490. https://doi.org/10.1016/j.stem.2012.08.002
Lee EK*, Jin YW*, Park JH, Yoo YM, Hong SM, Amir R, Yan Z, Kwon E, Elfick A, Tomlinson S, Halbritter F, Waibel T, Yun BW, Loake GJ. Cultured cambial meristematic cells as a source of plant natural products. Nat Biotechnol. 2010;28(11):1213-1217. https://doi.org/10.1038/nbt.1693