Welcome to HIRI

    Welcome to the preliminary website of HIRI - the Helmholtz Institute for RNA-based Infection Research!

    The Helmholtz Institute for RNA-based Infection Research (HIRI) was established in May 2017 as a partnership between the Helmholtz Centre for Infection Research (HZI) and the Julius-Maximilian-University of Würzburg (JMU). HIRI is the first research institution worldwide bridging the fields of RNA biology and infectious disease.


    Applications for spring 2019 recruitment have been completed. Application procedure for next recruitment will be announced soon.


    Our mission

    Rising antimicrobial resistance, chronic infections, and (re-) emerging pathogens are among the major challenges facing humanity. RNA is increasingly understood to contribute to key regulatory and sensory processes in the cell, but the role of RNA in infection biology remains understudied. HIRI will combine interdisciplinary expertise with cutting-edge research infrastructure to exploit the vast potential of RNA as a diagnostic molecule, target, and drug to combat infectious diseases.

    Our Team

    Research at HIRI focuses on four areas—bacterial infections, viral infections, host response, and RNA delivery—complemented by the strategic pursuit of emerging topics in RNA research. Collaboration between groups is core to our mission, and the tight interconnections between our four research areas provide a vibrant research environment for our scientists and trainees.
    Prof. Jörg Vogel

    RNA Biology of Bacterial Infections

    The first HIRI department was established in June 2017 by HIRI’s founding director, Professor Jörg Vogel. The aim of his department is to develop novel procedures to understand the RNA world of bacterial pathogens and use RNA-centric approaches to target pathogens and manipulate the microbiota.

    Prof. Chase Beisel

    Research group
    RNA Synthetic Biology

    The lab of Prof. Chase Beisel (formerly North Carolina State University, USA) will investigate and harness the functional diversity of CRISPR-Cas immune systems for the development of new foundational technologies. They aim to develop a new generation of CRISPR technologies that can be employed to better understand, diagnose, and combat human infections.

    Dr. Antoine-Emmanuel Saliba

    Research group
    Single-cell Analysis

    The research of Dr. Antoine-Emmanuel Saliba (former maître de conférences, Université Strasbourg, France) and his group is dedicated to using single- cell RNA-seq approaches to study heterogeneity in host responses to infections and its impact on disease outcome.

    Dr. Neva Caliskan

    Research group
    Recoding Mechanisms in Infections

    The research of Dr. Neva Caliskan’s group aims to identify and characterize the mechanisms and regulatory implications of translational recoding in RNA viruses and pathogenic bacteria.

    Dr. Lars Barquist

    Research group
    Integrative Informatics for Infection Biology

    The group of Dr. Lars Barquist will develop systems approaches to RNA and infection, using modern visualization, data science, and machine learning technologies to integrate large-scale functional genomics data.

    Jun. Prof. Alexander Westermann

    Research group
    Host-pathogen-microbiota interactions

    The group of Alexander Westermann focuses on investigating molecular RNA-based mechanisms that allow infecting pathogens to outcompete the resident microbiota. Their research centers on the identification and functional characterization of noncoding RNA molecules in pathogens, microbiota members and the host, to identify those RNAs that may serve as biomarkers for diagnostics or as therapeutic targets.

    Jun. Prof. Redmond Smyth

    Research group
    Genome Architecture and Evolution of RNA Viruses (GARV)

    The genomes of RNA viruses are not just passive carriers of protein coding information, but active participants in the viral infection process through the action of non-coding RNA. We study the structure and function of viral non-coding RNA, with the goal of harnessing the resulting knowledge in the design of next generation RNA-based therapies.


    Selected publications from HIRI scientists

    Here’s an overview of the RNA-centric highlights that our team has produced over the past few years.
    Selected experimental work
    Pezoldt J, Pasztoi M, Zou M, Wiechers C, Beckstette M, Thierry GR, Vafadarnejad E, Floess S, Arampatzi P, Buettner M, Schweer J, Fleissner D, Vital M, Pieper DH, Basic M, Dersch P, Strowig T, Hornef M, Bleich A, Bode U, Pabst O, Bajenoff M, Saliba AE, Huehn J
    Neonatally imprinted mesenteric lymph node stromal cell subsets modulate dendritic cell properties
    Nature Communications In press

    Müller SM, 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
    Histone variants restrict chromatin organization and antigenic variation in trypanosomes
    Nature In press

    Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM (2018)
    CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9.
    Molecular Cell 69(5):893-905.e7
    Available at: https://www.sciencedirect.com/science/article/pii/S1097276518300911?via%3Dihub

    Holmqvist E, Li L, Bischler T, Barquist L, Vogel J (2018)
    Global maps of ProQ binding in vivo reveal target recognition via RNA structure and stability control at mRNA 3' ends
    Molecular Cell 70(5):971-982.e6
    Available at: https://www.sciencedirect.com/science/article/pii/S1097276518303137?via%3Dihub

    Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML, Begemann MB, Gray BN, January E, Singer A, He Y, Beisel CL, Noireaux V (2018)
    Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System.
    Molecular Cell 69: 113–125
    Available at: http://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30935-8

    Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV (2017)
    Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA.
    Molecular Cell 66: 558–567.e4
    Available at: http://dx.doi.org/10.1016/j.molcel.2017.04.023

    Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J (2017)
    In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways.
    Molecular Cell 65: 39–51
    Available at: http://www.cell.com/molecular-cell/pdf/S1097-2765(16)30710-9.pdf

    Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn JS, Vogel J (2017)
    RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.
    PNAS 114: 201620772
    Available at: http://www.pnas.org/lookup/doi/10.1073/pnas.1620772114

    Smirnov A, Wang C, Drewry LL, Vogel J (2017)
    Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA.
    EMBO Journal 36: 1029–1045
    Available at: http://emboj.embopress.org/lookup/doi/10.15252/embj.201696127

    Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J (2016)
    Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.
    Nature 529: 496–501
    Available at: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006033

    Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DAC, Schulte LN, Helaine S, Vogel J (2016)
    Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.
    Nature Microbiology 2: 1–8
    Available at: https://www.nature.com/articles/nmicrobiol2016206

    Smirnov A, Förstner KU, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J (2016)
    Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.
    PNAS 113: 11591–11596
    Available at: http://www.pnas.org/lookup/doi/10.1073/pnas.1609981113

    Chao Y, Vogel J (2016)
    A 3’ UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response.
    Molecular Cell 61: 352–363
    Available at: https://www.sciencedirect.com/science/article/pii/S1097276515010059

    Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)
    Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.
    EMBO Journal 35: 991–1011
    Available at: http://emboj.embopress.org/lookup/doi/10.15252/embj.201593360

    Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL (2016)
    Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems.
    Molecular Cell 62: 137–147
    Available at: http://dx.doi.org/10.1016/j.molcel.2016.02.031

    Miyakoshi M, Chao Y, Vogel J (2015)
    Crosstalk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA.
    EMBO Journal 34:1478-92
    Available at: http://emboj.embopress.org/content/embojnl/34/11/1478.full.pdf

    Luo ML, Mullis AS, Leenay RT, Beisel CL (2015)
    Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression
    Nucleic Acids Research 43(1):674-81
    Available at: https://academic.oup.com/nar/article/43/1/674/2903426

    Papenfort K, Espinosa E, Casadesús J, Vogel J (2015)
    Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.
    PNAS 112: E4772–E4781
    Available at: http://www.pnas.org/lookup/doi/10.1073/pnas.1507825112

    Caliskan N, Katunin VI, Belardinelli R, Peske F, Rodnina MV (2014)
    Programmed -1 frameshifting by kinetic partitioning during impeded translocation.
    Cell 157: 1619–1631
    Available at: http://dx.doi.org/10.1016/j.cell.2014.04.041

    Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J (2013)
    Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis.
    Cell 153: 426–437
    Available at: https://doi.org/10.1016/j.cell.2013.03.003

    Papenfort K, Podkaminski D, Hinton JCD, Vogel J (2012)
    The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair.
    PNAS 109: E757–E764
    Available at: http://www.pnas.org/cgi/doi/10.1073/pnas.1119414109

    Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011)
    CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.
    Nature 471: 602–607
    Available at: https://www.nature.com/articles/nature09886

    Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J (2010)
    The primary transcriptome of the major human pathogen Helicobacter pylori.
    Nature 464: 250–255
    Available at: https://www.nature.com/articles/nature08756

    Selected Review Articles

    Holmqvist E, Vogel J (2018)
    RNA-binding proteins in bacteria
    Nature Reviews Microbiology doi: 10.1038/s41579-018-0049-5
    Available at: https://www.nature.com/articles/s41579-018-0049-5

    Hör J, Gorski SA, Vogel J (2018)
    Bacterial RNA Biology on a Genome Scale.
    Molecular Cell doi: 10.1016/j.molcel.2017.12.023
    Available at: http://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30980-2

    Gorski SA, Vogel J, Doudna JA (2017)
    RNA-based Recognition and targeting: Sowing the seeds of specificity.
    Nature Reviews Molecular Cell Biology 18:215-228
    Available at: https://www.nature.com/articles/nrm.2016.174

    Westermann AJ, Barquist L & Vogel J (2017)
    Resolving host–pathogen interactions by dual RNA-seq.
    PLoS Pathogens 13: 1–19
    Available at: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006033

    Caliskan N, Peske F, Rodnina MV (2015)
    Changed in translation: MRNA recoding by -1 programmed ribosomal frameshifting.
    Trends in Biochemical Sciences 40: 265–274
    Available at: https://www.sciencedirect.com/science/article/pii/S0968000415000444?via%3Dihub

    Barquist L, Vogel J (2015)
    Accelerating discovery and functional analysis of small RNAs with new technologies.
    Annual Review of Genetics 49:367-94
    Available at: https://www.annualreviews.org/doi/full/10.1146/annurev-genet-112414-054804?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed

    Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)
    Single-cell RNA-seq: advances and future challenges.
    Nucleic Acids Research 42:8845-60
    Available at: https://academic.oup.com/nar/article/42/14/8845/1269819

    Westermann AJ, Gorski SA, Vogel J (2012)
    Dual RNA-seq of pathogen and host.
    Nature Reviews Microbiology 10:618-30
    Available at: http://dx.doi.org/10.1038/nrmicro2852

    Vogel J, Luisi BF (2011)
    Hfq and its constellation of RNA.
    Nature Reviews Microbiology 9:578-89
    Available at: https://www.nature.com/articles/nrmicro2615


    Noam Stern-Ginossar
    Weizmann Institute of Science, Israel
    "Post-transcriptional Control of Host Gene Expression During Viral infection"

    Tuesday, 5th February 2019 at 5 pm 

    Helmholtz Institute for RNA-based Infection Research
    Institute of Molecular Infection Biology
    Josef-Schneider-Str. 2 / Building D15
    97080 Würzburg
    Seminar room D15.01.002-004

    We would be delighted to welcome you to the seminar and subsequent reception.

    HIRI is hiring

    Your chance to become part of the future of RNA & Infection! We are currently seeking talented and motivated scientific and non-scientific staff at all levels to advance our mission to investigate the role of RNA in infection.


    Technische/r Assistenten/in oder Biologielaborant/in


    Graduate Program


    PhD position: Data science for functional genomics in infection biology

    RNA is our world

    „Advances in RNA biology continue to highlight the importance of this central biomolecule. At HIRI, we aim to make the next generation of discoveries and translate them into the future of disease detection and treatment.“

    - Prof Jörg Vogel -


    With easy connections to major German transport hubs like the Frankfurt and Nuremberg International Airports, Würzburg is readily accessible by car, train, and airplane.

    Visit us in beautiful Würzburg and enjoy the Mainfranken area with its special mix of culture, world heritage, and wine festivals.


    Josef-Schneider-Straße 2
    Building D15
    97080 Würzburg

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