Pasajlic D^*, Plaschka M^*, Assen FP, Kusienicka A, Shaw LE, Traxler P, Mann U, Petrovic M, Bogdanovic J, Weninger W, Decker T, Halbritter F^#, Farlik M^# A Conserved Chromatin-Driven Checkpoint Defines Late Macrophage Maturation Independent of Tissue Specialization. bioRxiv. 2026. https://doi.org/10.64898/2026.07.01.735834

Zylka MM, Capraz T, Moquin-Beaudry G, Hafemeister C, Bradaric N, Watzke L, Suresh V, Mann U, Ringnalda F, Wachtel M, Dettmer MS, Thuillez C, Farlik M, Sorger H, Marchais A, Sanders K, van de Wetering M, Seidel MG, Liegl-Atzwanger B, Metzelder M, Kameneva P, Halbritter F, Kovar H, Radic-Sarikas B A human lung organoid co-culture model of early bone sarcoma metastasis reveals contact-dependent epithelial remodeling at the metastatic interface. bioRxiv. 2026. https://doi.org/10.64898/2026.06.03.729838

Hafemeister C, Halbritter F Single-cell RNA-seq differential expression tests within a sample should use pseudo-bulk data of pseudo-replicates. bioRxiv. 2023. https://doi.org/10.1101/2023.03.28.534443

Montano-Gutierrez LF^*, Muller S^*, Kutschat AP, Adameyko I, Seruggia D^#, Halbritter F^# Directing stem cell differentiation by chromatin state approximation. Nucleic Acids Research. 2026. https://doi.org/10.1093/nar/gkag124 | Code | Data: GSE291386 | Press@CCRI

Shoeb MR, Schinnerl D, Shaw LE, Farlik M, Strehl S, Halbritter F^#, Fortschegger K^# A stem cell differentiation model reveals two alternative fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation. Communications Biology. 2025. https://doi.org/10.1038/s42003-025-08730-4 | Code | Data: GSE277004 | Interactive: Fig. 3 | Interactive: Fig. 4

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. Nature Communications. 2024. https://doi.org/10.1038/s41467-024-47945-7 | Code | Code Archive | Data: GSE219153 | Interactive Data @R2

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. Nature Communications. 2024. 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. Nature Communications. 2021. 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 Discovery. 2019. 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. 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. Nature Communications. 2018. 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. 2016. 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. Nature Biotechnology. 2016. 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. 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 Research. 2014. https://doi.org/10.1093/nar/gkt966 | Web service

Halbritter F, Vaidya HJ, Tomlinson SR GeneProf: Analysis of high-throughput sequencing experiments. Nature Methods. 2012. https://doi.org/10.1038/nmeth.1809 | Web service

Halbritter F, Geibel P Learning Models of Relational MDPs Using Graph Kernels. MICAI 2007: Advances in Artificial Intelligence. Springer. 2007. https://doi.org/10.1007/978-3-540-76631-5_39

Radic-Sarikas B, Markovic M, Zylka MM, Sturtzel C, Ilg M, Surdez D, Metzelder M, Distel M, Ovsianikov A, Halbritter F, Kovar H Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition. Molecular Therapy Oncology. 2026. https://doi.org/10.1016/j.omton.2026.201229

Watzke L, Palmisani F, Plaschka M, Halbritter F, Radic-Sarikas B, Rezkalla K, Kager L, Kovar H, Kain R, Metzelder M, Sorger H, Amann G, Bergmann M Differential immune infiltrates in histomorphologic Wilms tumor regions identify prognostic macrophages. Molecular Therapy Oncology. 2026. https://doi.org/10.1016/j.omton.2026.201162

Akagha MJ, Georgolopoulos G, Martin D, Meissl K, Amenitsch L, Vogl C, Farlik M, Fortelny N, Halbritter F, Müller M, Decker T, Strobl B IFNγ shapes macrophage inflammatory responses by STAT1 isoform-specific epigenetic and transcriptional mechanisms. BMC Genomics. 2026. https://doi.org/10.1186/s12864-026-12601-5

Suresh V^*, Hafemeister C^*, Konstantinou A, Grissenberger S, Sturtzel C, Zylka MM, Cidre-Aranaz F, Wenninger-Weinzierl A, Queiros K, Kurek D, Distel M, Obenauf A, Gruenewald TGP, Halbritter F, Kovar H^#, Fock V^# Modelling EWS::FLI1 protein fluctuations reveal determinants of tumor plasticity in Ewing sarcoma. EMBO Molecular Medicine. 2026. https://doi.org/10.1038/s44321-025-00364-7

Traxler P^*, Reichl S^*, Folkman L, Shaw L, Fife V, Nemc A, Pasajilic D, Kusienicka A, Barreca D, Fortelny N, Rendeiro AF, Halbritter F, Weninger W, Decker T, Farlik M^#, Bock C^# Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation. Cell Systems. 2025. https://doi.org/10.1016/j.cels.2025.101346 | Code | Data: GSE263763

Noorizadeh R, Sax B, Javaheri T, Radic Sarikas B, Fock V, Kauer M, Bykov A, Suresh V, Schlederer M, Kenner L, Weber G, Mikulits W, Halbritter F, Moriggl R, Kovar H YAP1 is a key regulator of EWS::FLI1-dependent malignant transformation upon IGF-1 mediated reprogramming of bone mesenchymal stem cells. Cell Reports. 2025. https://doi.org/10.1016/j.celrep.2025.115381 | Code | Data: GSE269007

Ressler JM, Plaschka M, Silmbrod R, Bachmayr V, Shaw LE, Silly T, Zila N, Stepan A, Kusienicka A, Tschandl P, Tittes J, Roka F, Haslik W, Petzelbauer P, Koenig F, Kunstfeld R, Farlik M, Halbritter F, Weninger W, Christoph Hoeller C Efficacy and tolerability of neoadjuvant therapy with Talimogene laherparepvec in cutaneous basal cell carcinoma: a phase II trial (NeoBCC trial). Nature Cancer. 2025. https://doi.org/10.1038/s43018-024-00879-x | Code | Data: GSE268728 | Data: EGAD50000000371

Abagnale G, Schwentner R, Ben Soussia-Weiss P, van Midden W, Sturtzel C, Pötschger U, Rados M, Taschner-Mandl S, Simonitsch-Klupp I, Hafemeister C, Halbritter F, Distel M, Eder SK, Hutter C BRAFV600E induces key features of LCH in iPSCs with cell type-specific phenotypes and drug responses. Blood. 2025. https://doi.org/10.1182/blood.2024026066 | Data: GSE270891

Buri MC, Shoeb MR, Bykov A, Repiscak P, Baik H, Dupanovic A, David FO, Kovacic B, Hall-Glenn F, Dopa S, Urbanus J, Sippl L, Stofner S, Emminger D, Cosgrove J, Schinnerl D, Poetsch AR, Lehner M, Koenig X, Perié L, Schumacher TN, Gotthardt D, Halbritter F, Putz EM Natural killer cell–mediated cytotoxicity shapes the clonal evolution of B cell leukaemia. Cancer Immunology Research. 2024. https://doi.org/10.1158/2326-6066.CIR-24-0189 | Code

Ransmayr B, Bal SK, Thian M, Svaton M, van de Wetering C, Hafemeister C, Segarra-Roca A, Block J, Frohne A, Krolo A, Altunbas MY, Bilgic-Eltan S, Kıykım A, Aydiner O, Kesim S, Inanir S, Karakoc-Aydiner E, Ozen A, Abü Ü, Çomak A, Tuğcu GD, Pazdzior R, Huber B, Farlik M, Kubicek S, von Bernuth H, Simonitsch-Klupp I, Rizzi M, Halbritter F, Tumanov AV, Kraakman MJ, Metin A, Castanon I, Erman B, Baris S, Boztug K LTβR deficiency causes lymph node aplasia and impaired B cell differentiation. Science Immunology. 2024. https://doi.org/10.1126/sciimmunol.adq8796

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. 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. 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. 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. 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 Advances. 2021. 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. Science Immunology. 2021. 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. Molecular Cancer. 2021. 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 Advances. 2021. 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. 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. Science Immunology. 2021. 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. Molecular Cell. 2021. 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. Molecular Psychiatry. 2020. 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. 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. Journal of Clinical Investigation. 2018. 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 Journal. 2018. 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. 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 Reports. 2015. 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. 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 Journal. 2013. 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. 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. Nature Biotechnology. 2010. https://doi.org/10.1038/nbt.1693