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The instruments and services of the CFFlowCyt at BMC contributed to the following publications (list not exhaustive): 
last updated: 2024-05-21/BT


  • Albanese et al.: Receptor transfer between immune cells by autoantibody-enhanced, CD32-driven trogocytosis is hijacked by HIV-1 to infect resting CD4 T cells. Cell Rep Med. 2024 Apr 16, 5(4):101483, DOI: 10.1016/j.xcrm.2024.101483
  • Xiao et al.: Genomic deletion of Bcl6 differentially affects conventional dendritic cell subsets and compromises Tfh/Tfr/Th17 cell responses. Nat Commun. 2024 Apr 30, 15:3554, DOI: 10.1038/s41467-024-46966-6


  • Thomann et al.: A B cell-driven EAE mouse model reveals the impact of B cell-derived cytokines on CNS autoimmunity. Proc Natl Acad Sci USA. 2023 Nov 13, 120(47):e2300733120, DOI: 10.1073/pnas.2300733120
  • Kendirli et al.: A genome-wide in vivo CRISPR screen identifies essential regulators of T cell migration to the CNS in a multiple sclerosis model. Nat. Neurosci. 2023 Sep 14, 26(10):1713-1725, DOI: 10.1038/s41593-023-01432-2
  • Kolabas, ..., Khosravani, Tast, Richter, ... et al.: Distinct molecular profiles of skull bone marrow in health and neurological disorders. Cell. 2023 Aug 17,186(17), doi: 10.1016/j.cell.2023.07.009
  • Radmer et al.: Generation and Maintenance of Primate Induced Pluripotent Stem Cells Derived from Urine. J. Vis. Exp. 2023 July 28, (197), e64922,  doi: 10.3791/64922
  • Bauer et al.: Visualizing the activation of encephalitogenic T cells in the ileal lamina propria by in vivo two-photon imaging. PNAS. 2023 July 19, 120 (30) e2302697120,
  • Kalgudde Gopal et al.: Wound infiltrating adipocytes are not myofibroblasts . Nat Commun. 2023 May 25, 14(1):3020, DOI: 10.1038/s41467-023-38591-6
  • Rausch et al.: Phosphatidylserine-positive extracellular vesicles boost effector CD8+ T cell responses during viral infection. 2023 Apr 18, 120120(16):e2210047120; DOI: 10.1073/pnas.2210047120
  • Rohwedder et al.: A20 and the non-canonical NF-κB pathway are key regulators of neutrophil recruitment during fetal ontogeny. JCI Insight. 2023 Jan 12,e155968.; 10.1172/jci.insight.155968 
  • Chao et al.: Human TH17 cells engage gasdermin E pores to release IL-1α on NLRP3 inflammasome activation. Nat. Immunol.2023 Jan 05; 10.1038/s41590-022-01386-w


  • Windheim et al.: Distinct and dynamic activation profiles of circulating dendritic cells and monocytes in mild COVID-19 and after yellow fever vaccination. Eur. J. Immunol. 2022 Nov 20, 0: 1-14;
  • Boushehri et al.: scifAI: Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies. preprint. 2022 Oct 25;
  • Ito-Kureha et al.: The function of Wtap in N6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells. Nature Immunology. 2022 Jul 25; 23:1208-1221; DOI: 10.1038/s41590-022-01268-1
  • Götz et al.: Cobra Venom Factor Boosts Arteriogenesis in Mice. Int J Mol Sci. 2022 Jul 30; 23:8454; DOI: 10.3390/ijms23158454
  • Kendirli et. al.: Identification of essential modules regulating T cell migration to the central nervous system in multiple sclerosis. preprint. 2022 Jun 17;
  • Preisendörfer et al.: FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. Cells. 2022 Apr 14; 11(8), 1341;
  • Fessler et al.: DELE1 tracks perturbed protein import and processing in human mitochondria.
    Nat Commun. 2022 Apr 6; 13:1853;
  • Stutte et al.: High-Fat Diet Rapidly Modifies Trafficking, Phenotype, and Function of Plasmacytoid Dendritic Cells in Adipose Tissue.
    J Immunol. 2022 Feb 18, 2022; ji2100022;
  • Ingelfinger et al.: Twin study reveals non-heritable immune perturbations in multiple sclerosis.
    Nature. 2022 Feb 16; 603:152–158.
  • Noack et al.: Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler.
    Nat Neurosci. 2022 Feb 07; 25:154–167;
  • Albanese et al.: Rapid, efficient and activation-neutral gene editing of polyclonal primary human resting CD4 + T cells allows complex functional analyses. Nat. Methods. 2022 Jan; 19:81-89;



  • Blessing et al.: The Oncogenic Helicase ALC1 Regulates PARP Inhibitor Potency by Trapping PARP2 at DNA Breaks.
    Molecular Cell. 2020 Dec 3; 80, 1–14; doi:10.1016/j.molcel.2020.10.009; PMID: 33275888
  • Loy et al.: Semaphorin 7A restricts serotonergic innervation and ensures recovery after spinal cord injury.
    Cell. Mol. Life Sci. 2020 Oct 30; doi:10.1007/s00018-020-03682-w; PMID: 33128105
  • Chlis et al.: Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning.
    Nucleic Acids Research. 2020 Oct 29; gkaa926; doi: 10.1093/nar/gkaa926; PMID: 33119742
  • Alterauge et al.: Continued Bcl6 Expression Prevents the Transdifferentiation of Established Tfh Cells into Th1 Cells during Acute Viral Infection.
    Cell Reports. 2020 Oct 6; 33, 108232; doi: 10.1016/j.celrep.2020.108232; PMID: 33027650
  • Zeiträg et al.: T cell‐expressed microRNAs critically regulate germinal center T follicular helper cell function and maintenance in acute viral infection in mice.
    Eur J Immunol. 2020 Sept 30; doi: 10.1002/eji.202048867; PMID: 32996581
  • Panagiotopoulos et al.: Antisense Oligonucleotide- and CRISPR-Cas9-Mediated Rescue of mRNA Splicing for a Deep Intronic CLRN1 Mutation.
    Mol Ther Nucleic Acids. 2020 Sept 4; 21:1050-1061. doi: 10.1016/j.omtn.2020.07.036; PMID: 32841912
  • Noack et al.: Multiomics analysis reveals extensive epigenome remodeling during cortical development. 
    bioRxiv. 2020 Aug 7;
  • Matthias et al.: Salt Generates Anti-Inflammatory Th17 Cells but Amplifies Their Pathogenicity in Pro-Inflammatory Cytokine Microenvironments.
    J Clin Invest 2020 Jun 2; 137786. doi: 10.1172/JCI137786; PMID: 32484796
  • Konda, ... Richter, ... et al.: A Simple and Effective Flow Cytometry-Based Method for Identification and Quantification of Tissue Infiltrated Leukocyte Subpopulations in a Mouse Model of Peripheral Arterial Disease.
    Int. J. Mol. Sci. 2020 May; 21, 3593; doi:10.3390/ijms21103593; PMID: 32438752
  • Huber et al.: Dynamic changes in circulating T follicular helper cell composition predict neutralising antibody responses after yellow fever vaccination.
    Clin Transl Immunology 2020 May 13; 9(5):e1129. doi:10.1002/cti2.1129; PMID: 32419947
  • Bararia et al.: Cathepsin S Alterations Induce a Tumor-Promoting Immune Microenvironment in Follicular Lymphoma.
    Cell Reports. 2020 May 5; 31, 107522. doi:org/10.1016/j.celrep.2020.107522; PMID: 32330423
  • Kranich et al.: In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning.
    J Extracell Vesicles. 2020 Jul 16;9(1):1792683; doi: 10.1080/20013078.2020.1792683; PMID: 32944180  
  • Schmidt et al.: Complex human adenoid tissue-based ex vivo culture systems reveal anti-inflammatory drug effects on germinal center T and B cells.
    EBioMedicine. 2020 Feb; 53 102684; doi: 10.1016/j.ebiom.2020.102684; PMID: 32114393
  • Zeiträg et al.: Gene dose matters: Considerations for the use of inducible CD4‐CreERT2 mouse lines.
    Eur J Immunol. 2020 Feb 20; doi: 10.1002/eji.201948461; PMID: 32087088
  • Matthias et al.: Sodium Chloride Is an Ionic Checkpoint for Human TH2 Cells and Shapes the Atopic Skin Microenvironment. 
    Sci Transl Med
    . 2019 Feb 20;11(480):eaau0683. doi: 10.1126/scitranslmed.aau0683. PMID: 30787167 
  • Huber et al.: Fingolimod Profoundly Reduces Frequencies and Alters Subset Composition of Circulating T Follicular Helper Cells in Multiple Sclerosis Patients.
    J Immunol. 2020 Feb 7; pii: ji1900955; doi: 10.4049/jimmunol.1900955; PMID: 32034063 
  • Salei et al.: The Kidney Contains Ontogenetically Distinct Dendritic Cell and Macrophage Subtypes throughout Development That Differ in Their Inflammatory Properties. 
    JASN. 2020 Jan 13; pii: ASN.2019040419; doi: 10.1681/ASN.2019040419; PMID: 31932472


  • Tavernier et al.: A human immune dysregulation syndrome characterized by severe hyperinflammation with a homozygous nonsense Roquin-1 mutation.
    Nature Commun. 2019 Dec; doi: 10.1038/s41467-019-12704-6; PMID: 31636267
  • Cossarizza, ... Richter, ... et al.: Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition).
    Eur J Immunol. 2019 Oct;49(10):1457-1973. doi: 10.1002/eji.201970107. PMID: 31633216
  • Winklmeier et al.: Identification of circulating MOG-specific B cells in patients with MOG antibodies.
    Neurol Neuroimmunol Neuroinflamm. 2019 Oct;6:e625.; doi: 10.1212/NXI.0000000000000625; PMID: 31611268
  • Beltrán et al.: Early adaptive immune activation detected in monozygotic twins with prodromal multiple sclerosis. 
    J Clin Invest. 2019 Sept 30; doi: 10.1172/JCI128475; PMID: 31566584
  • Hassler et al.: Inventories of naive and tolerant mouse CD4 T cell repertoires reveal a hierarchy of deleted and diverted T cell receptors. 
    PNAS. 2019 Aug 26; doi: 10.1073/pnas.1907615116; PMID: 31451631
  • Cernilogar et al.: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2. 
    Nucleic Acids Research. 2019 July 27; doi: 10.1093/nar/gkz627; PMID: 31350899
  • Bartolomé-Casado, ... Richter, ... et al.: Resident memory CD8 T cells persist for years in human small intestine. 
    J Ex Med. 2019 Jul 23; doi: 10.1084/jem.20190414; PMID: 31337737
  • Rosenbaum et al.: Bcl10-controlled Malt1 par-acaspase activity is key for the immune suppressive function of regulatory T cells.
    Nature Commun. 2019 May 28;10(1):2352. doi: 10.1038/s41467-019-10203-2; PMID: 31138793
  • Götzl et al.: Opposite microglial activation stages upon loss of PGRN or TREM2 result in reduced cerebral glucose metabolism.
    EMBO Mol Med 2019 May 23; 11:e9711;
  • Baumann et al.: Targeted removal of epigenetic barriers during transcriptional reprogramming. 
    Nature Commun. 2019 May 9; doi: 10.1038/s41467-019-10146-8.; PMID: 31073172
  • Souren et al.: DNA methylation signatures of monozygotic twins clinically discordant for multiple sclerosis.
    Nature Commun. 2019 May 7; DOI: 10.1038/s41467-019-09984-3; PMID: 31064978
  • Yamano et al.: Aire-expressing ILC3-like cells in the lymph node display potent APC features.
    J Ex Med. 2019 Mar; doi: 10.1084/jem.20181430; PMID: 30918005
  • Zwick et al.: Expression of the Phosphatase Ppef2 Controls Survival and Function of CD8+ Dendritic Cells.
    Front. Immunol. 2019 Feb; doi: 10.3389/fimmu.2019.00222; PMID: 30809231
  • Yamano et al.: B cells latently infected with murine gammaherpesvirus 68 (MHV‐68) are present in the mouse thymus – A step toward immune evasion?
    Eur J Immunol. 2019 Feb;49(2):351-352. doi: 10.1002/eji.201847886; PMID: 30488950
  • Matthias et al.: Sodium chloride is an ionic checkpoint for human Th2 cell responses and shapes the atopic skin microenvironment.
    Sci Transl Med. 2019 Feb;11(480). pii: eaau0683. doi: 10.1126/scitranslmed.aau0683. PMID: 30787167 
  • Ogrinc-Wagner et al.: Strain specific maturation of Dendritic cells and production of IL-1β controls CD40-driven colitis. 
    PLoS One. 2019 Jan 17;14(1):e0210998. doi: 10.1371/journal.pone.0210998. eCollection 2019; PMID: 30653608


  • Essig et al.: Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation.
    Nat Commun. 2018 Sep 19;9(1):3810. doi: 10.1038/s41467-018-06184-3; PMID: 30232334
  • Matthias et al.: Sodium chloride is an ionic checkpoint for human Th2 cell responses and shapes the atopic skin microenvironment.
    bioRxiv. 2018 Aug 13; doi: 10.1101/390393
  • Souren et al.: DNA methylation signatures of a large cohort monozygotic twins clinically discordant for multiple sclerosis.
    bioRxiv. 2018 Aug 1; doi: 10.1101/381822
  • Richter et al.: Transcriptional profiling reveals monocyte-related macrophages phenotypically resembling DC in human intestine. 
    Mucosal Immunol. 2018 Jul 23; doi: 10.1038/s41385-018-0060-1; PMID: 30038215
  • Spadaro et al.: Pathogenicity of human antibodies against myelin oligodendrocyte glycoprotein.
    Ann Neurol. 2018 Jul 16; doi: 10.1002/ana.25291; PMID: 30014603
  • Salvermoser et al.: Clec9a-Mediated Ablation of Conventional Dendritic Cells Suggests a Lymphoid Path to Generating Dendritic Cells In Vivo.
    Front Immunol. 2018 Apr 16; 9:699. doi: 10.3389/fimmu.2018.00699; PMID: 29713321
  • Ederle et al.: Nuclear egress of TDP-43 and FUS occurs independently of Exportin-1/CRM1.
    Sci Rep. 2018 May 4; 8(1):7084. doi: 10.1038/s41598-018-25007-5; PMID: 29728564
  • Rehage et al.: Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA. 
    Nat Commun2018 Jan 19; 9(1):299. doi: 10.1038/s41467-017-02582-1; PMID: 29352114


  • Essig et al.: Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells.
    Immunity. 2017 Dec 19; 47(6):1067-1082.e12. doi: 10.1016/j.immuni.2017.11.008; PMID: 29246441
  • Montoya et al.: A distinct inhibitory function for miR-18a in Th17 cell differentiation. 
    J Immunol. 2017 July 15; 199 (2) 559-569. doi: 10.4049/jimmunol.1700170; PMID: 28607111
  • Zhou et al.: Antibodies inhibit transmission and aggregation of C9orf72 polyGA dipeptide repeat proteins.
    EMBO Mol Med. 2017 May 1; 9(5):687-702. doi: 10.15252/emmm.201607054; PMID: 28351931
  • Schuh et al.: Human Plasmacytoid Dendritic Cells Display and Shed B Cell Maturation Antigen upon TLR Engagement.
    J Immunol. 2017 Apr 15;198(8):3081-3088. doi: 10.4049/jimmunol.1601746. Epub 2017 Mar 10. PMID: 28283566
  • Barthels et al.: CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis. 
    Nat Commun. 2017 Mar 9;8:14715. doi: 10.1038/ncomms14715; PMID: 28276457
  • Ponce et al.: SIRPα-antibody fusion proteins stimulate phagocytosis and promote elimination of acute myeloid leukemia cells.
    Oncotarget. 2017 Feb 14; 8(7):11284-11301. doi: 10.18632/oncotarget.14500; PMID: 28061465


  • Dursun et al.: Continuous single cell imaging reveals sequential steps of plasmacytoid dendritic cell development from common dendritic cell progenitors.
    Sci Rep. 2016 Nov 28; 6:37462. doi: 10.1038/srep37462; PMID: 27892478
  • von Rohrscheidt et al.: Thymic CD4 T cell selection requires attenuation of March8-mediated MHCII turnover in cortical epithelial cells through CD83.
    J Exp Med. 2016 Aug 22; 213(9):1685-94. doi: 10.1084/jem.20160316; PMID: 27503071
  • Pasquarella et al.: Retrotransposon derepression leads to activation of the unfolded protein response and apoptosis in pro-B cells.
    Development. 2016 May 17; 143: 1788-1799; doi: 10.1242/dev.130203; PMID: 27013243
  • Meininger et al.: Alternative splicing of MALT1 controls signalling and activation of CD4(+) T cells.
    Nat Commun. 2016 Apr 12; 7:11292. doi: 10.1038/ncomms11292; PMID: 27068814