Publikationen

A distinct priming phase regulates CD8 T cell immunity by orchestrating paracrine IL-2 signals

Jobin K, Seetharama D, Rüttger L, Fenton C, Kharybina E, Wirsching A, Huang A, Knöpper K, Kaisho T, Busch DH, Vaeth M, Saliba AE, Graw F, Pulfer A, González SF, Zehn D, Liang Y, Ugur M, Gasteiger G, Kastenmüller W (2025)

Science

Transcriptomic profiling of individual bacteria by MATQ-seq

Homberger C, Imdahl F, Hayward RJ, Barquist L, Saliba AE, Vogel J (2025)

Nature Protocols

Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges 

Espinoza Miranda SS, Abbaszade G, Hess WR, Drescher K, Saliba A-E, Zaburdaev V, Chai L, Dreisewerd K, Grünberger A, Westendorf C, Müller S, Mascher T (2025)

Microbiology and Molecular Biology Reviews

Circulating NK cells establish tissue residency upon acute infection of skin and mediate accelerated effector responses to secondary infection

Torcellan T, Friedrich C, Doucet-Ladevèze R, Ossner T, Solé VV, Riedmann S, Ugur M, Imdahl F, Rosshart SP, Arnold SJ, Gomez de Agüero M, Gagliani N, Flavell RA, Backes S, Kastenmüller W, Gasteiger G (2024)

Immunity

Resident regulatory T cells reflect the immune history of individual lymph nodes

Kaminski A, Hager FT, Kopplin L, Ticconi F, Leufgen A, Vendelova E, Rüttger L, Gasteiger G, Cerovic V, Kastenmüller W, Pabst O, Ugur M (2023)

Science Immunology

Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms

Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, Saliba AE, Groeber-Becker F, Engstler M (2023)

Nature Communications

Brain-to-gut trafficking of alpha-synuclein by CD11c+cells in a mouse model of Parkinson’s disease

McFleder RL, Makhotkina A, Groh J, Keber U, Imdahl F, Peña Mosca J, Peteranderl A, Wu J, Tabuchi S, Hoffmann J, Karl AK, Pagenstecher A, Vogel J, Beilhack A, Koprich JB, Brotchie JM, Saliba AE, Volkmann J, Ip CW (2023)

Nature Communications

Mitochondrial dysfunction promotes the transition of precursor to terminally exhausted T cells through HIF-1α-mediated glycolytic reprogramming

Wu H, Zhao X, Hochrein SM, Eckstein M, Gubert GF, Knöpper K, Mansilla AM, Öner A, Doucet-Ladevèze R, Schmitz W, Ghesquière B, Theurich S, Dudek J, Gasteiger G, Zernecke A, Kobold S, Kastenmüller W, Vaeth M (2023)

Nature Communications

Microglia-mediated demyelination protects against CD8+ T cell-driven axon degeneration in mice carrying PLP defects

Groh J, Abdelwahab T, Kattimani Y, Hörner M, Loserth S, Gudi V, Adalbert R, Imdahl F, Saliba AE, Coleman M, Stangel M, Simons M, Martini R (2023)

Nature Communications

Lymph node medulla regulates the spatiotemporal unfolding of resident dendritic cell networks

Ugur M, Labios RJ, Fenton C, Knöpper K, Jobin K, Imdahl F, Golda G, Hoh K, Grafen A, Kaisho T, (…), Bajénoff M, Kastenmüller W (2023)

Immunity

DOT1L activity affects neural stem cell division mode and reduces differentiation and ASNS expression

Appiah B, Fullio CL, Ossola C, Bertani I, Restelli E, Cheffer A, Polenghi M, Haffner C, Garcia-Miralles M, Zeis P, (…), Taverna E, Vogel T (2023)

EMBO Reports

VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells

Rosales-Alvarez RE, Rettkowski J, Herman JS, Dumbovic G, Cabezas-Wallscheid N, Grün D (2023)

Genome Biology

Integrated single-cell analysis based classification of vascular mononuclear phagocytes in mouse and human atherosclerosis

Zernecke A, Erhard F, Weinberger T, Schulz C, Ley K, Saliba AE, Cochain C (2023)

Cardiovascular Research

Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning

Caliskan A, Caliskan D, Rasbach L, Yu W, Dandekar T, Breitenbach T (2023)

Computational and Structural Biotechnology Journal

Dynamics of monocyte-derived macrophage diversity in experimental myocardial infarction

Rizzo G, Gropper J, Piollet M, Vafadarnejad E, Rizakou A, Bandi SR, Arampatzi P, Krammer T, DiFabion N, Dietrich O, (…), Saliba AE, Cochain C (2023)

Cardiovascular Research

An interferon gamma response signature links myocardial aging and immunosenescence

Ashour D, Rebs S, Arampatzi P, Saliba AE, Dudek J, Schulz R, Hofmann U, Frantz S, Cochain C, Streckfuß-Bömeke K, Ramos GC (2023)

Cardiovascular Research

Cytotoxic CNS-associated T cells drive axon degeneration by targeting perturbed oligodendrocytes in PLP1 mutant mice

Abdelwahab T, Stadler D, Knöpper K, Arampatzi P, Saliba AE, Kastenmüller W, Martini R, Groh J (2023)

iScience

Slow integrin-dependent migration organizes networks of tissue-resident mast cells

Kaltenbach L, Martzloff P, Bambach SK, Aizarani N, Mihlan M, Gavrilov A, Glaser KM, Stecher M, Thünauer R, Thiriot A, (…), Grün D, Lämmermann T (2023)

Nature Immunology

A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection

Däullary T, Imdahl F, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba AE, Zdzieblo D (2023)

Gut Microbes

A MATQ-seq-Based Protocol for Single-Cell RNA-seq in Bacteria

Homberger C, Saliba AE, Vogel J (2023)

Methods in Molecular Biology

Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads

Homberger C, Hayward RJ, Barquist L, Vogel J (2023)

mBio

Myocardial Milieu Favors Local Differentiation of Regulatory T Cells

Delgobo M, Weiß E, Ashour D, Richter L, Popiolkowski L, Arampatzi P, Stangl V, Arias-Loza P, Mariotti-Ferrandiz E, Rainer PP, Saliba AE, Ludewig B, Hofmann U, Frantz S, Campos Ramos G (2023)

Circulation Research

Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19

Zhang B, Zhang Z, Koeken VACM, Kumar S, Aillaud M, Tsay HC, Liu Z, Kraft ARM, Soon CF, ..., Huehn J, Saliba AE, Sander LE, Förster R, Xu CJ, Cornberg M, Schulte LN, Li Y (2023)

Cell Genomics

RNA recording in single bacterial cells using reprogrammed tracrRNAs

Jiao C, Reckstadt C, König F, Homberger C, Yu J, Vogel J, Westermann AJ, Sharma CM, Beisel CL (2023)

Nature Biotechnology

Th17.1 cell driven sarcoidosis-like inflammation after anti-BCMA CAR T cells in multiple myeloma

Leipold AM, Werner RA, Düll J, Jung P, John M, Stanojkovska E, Zhou X, Hornburger H, Ruckdeschel A, Dietrich O, Imdahl F, Krammer T, Knop S, Rosenwald A, Buck A, Sander LE, Einsele H, Kortüm KM, Saliba AE, Rasche L (2023)

Leukemia

Ushering in a new era of single-cell transcriptomics in bacteria

Homberger C, Barquist L, Vogel J (2022)

microLife

Fibroblastic reticular cells mitigate acute GvHD via MHCII-dependent maintenance of regulatory T cells

Shaikh H, Pezoldt J, Mokhtari Z, Gamboa Vargas J, Le DD, Peña Mosca J, Arellano Viera E, Kern MA, Graf C, Beyersdorf N, Lutz MB, Riedel A, Büttner-Herold M, Zernecke A, Einsele H, Saliba AE, Ludewig B, Huehn J, Beilhack A (2022)

JCI Insight

Landscape and age dynamics of immune cells in the Egyptian Rousette Bat

Friedrichs V, Toussaint C, Schäfer A, Rissmann M, Dietrich O, Mettenleiter TC, Pei G, Balkema-Buschmann A, Saliba AE, Dorhoi A (2022)

Cell Reports

Developmental dynamics of two bipotent thymic epithelial progenitor types

Nusser A, Sagar, Swann JB, Krauth B, Diekhoff D, Calderon L, Happe C, Grün D & Boehm T (2022)

Nature

Type 1 conventional dendritic cells maintain and guide the differentiation of precursors of exhausted T cells in distinct cellular niches

Dähling S, Mansilla AM, Knöpper K, Grafen A, Utzschneider DT, (...), Saliba AE, Gasteiger G, Bedoui S, Kastenmüller W (2022)

Immunity

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis

Wendisch D, Dietrich O, Mari T, von Stillfried S, (...), Saliba AE, Sander LE (2021)

Cell

Homozygous BCMA gene deletion in response to anti-BCMA CAR T cells in a patient with multiple myeloma

Da Vià MC, Dietrich O, Truger M, Arampatzi P, Duell J, Heidemeier A, Zhou X, Danhof S, Kraus S, Chatterjee M, (...), Saliba A, Rasche L (2021)

Nature Medicine

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, (...), Saliba AE, Sander LE (2020)

Cell

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

Imdahl F, Vafadarnejad E, Homberger C, Saliba AE, Vogel J (2020)

Nature Microbiology

scSLAM-seq reveals core features of transcription dynamics in single cells

Erhard F, Baptista MA, Krammer T, Hennig T, Lange M, Arampatzi P, Jürges CS, Theis FJ, Saliba AE, Dölken L (2019)

Nature

Salmonella persisters undermine host immune defenses during antibiotic treatment

Stapels DA, Hill PW, Westermann AJ, Fisher RA, Thurston TL, Saliba AE, Blommestein I, Vogel J, Helaine S (2018)

Science

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis

Cochain C, Vafadarnejad E, Arampatzi P, Pelisek J, Winkels H, Ley K, Wolf D, Saliba AE, Zernecke A (2018)

Circulation Research

Genome organization and DNA accessibility control antigenic variation in trypanosomes

Müller LS, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba AE, Sebra RP, Siegel TN (2018)

Nature

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella

Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J (2017)

Nature Microbiology