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.


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    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
    Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System.
    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)
    Molecular Cell 69: 113–125
    Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.
    Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DAC, Schulte LN, Helaine S, Vogel J (2017)
    Nature Microbiology 2: 1–8
    Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA.
    Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV (2017)
    Molecular Cell 66: 558–567.e4
    In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways.
    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)
    Molecular Cell 65: 39–51
    RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.
    Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn JS, Vogel J (2017)
    PNAS 114: 201620772
    Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA.
    Smirnov A, Wang C, Drewry LL, Vogel J (2017)
    EMBO Journal 36: 1029–1045
    Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.
    Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J (2016)
    Nature 529: 496–501
    The TraDIS toolkit: Sequencing and analysis for dense transposon mutant libraries.
    Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J (2016)
    Bioinformatics 32: 1109–1111
    Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.
    Smirnov A, Förstner KU, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J (2016)
    PNAS 113: 11591–11596
    A 3’ UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response.
    Chao Y, Vogel J (2016)
    Molecular Cell 61: 352–363
    Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.
    Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)
    EMBO Journal 35: 991–1011
    Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems.
    Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL (2016)
    Molecular Cell 62: 137–147
    Crosstalk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA.
    Miyakoshi M, Chao Y, Vogel J (2015)
    EMBO Journal 34:1478-92
    Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.
    Papenfort K, Espinosa E, Casadesús J, Vogel J (2015)
    PNAS 112: E4772–E4781
    Programmed -1 frameshifting by kinetic partitioning during impeded translocation.
    Caliskan N, Katunin VI, Belardinelli R, Peske F, Rodnina MV (2014)
    Cell 157: 1619–1631
    Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR/Cas Systems.
    Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL (2014)
    MBio 5: e00928-13
    Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis.
    Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J (2013)
    Cell 153: 426–437
    A small RNA activates CFA synthase by isoform-specific mRNA stabilization.
    Fröhlich KS, Papenfort K, Fekete A, Vogel J (2013)
    EMBO Journal 32: 2963–2979
    An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs.
    Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J (2012)
    EMBO Journal 31: 4005–4019
    The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair.
    Papenfort K, Podkaminski D, Hinton JCD, Vogel J (2012)
    PNAS 109: E757–E764
    CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.
    Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011)
    Nature 471: 602–607
    Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family.
    Schulte LN, Eulalio A, Mollenkopf HJ, Reinhardt R, Vogel J (2011)
    EMBO Journal 30: 1977–1989
    Evidence for an autonomous 5’ target recognition domain in an Hfq-associated small RNA.
    Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010)
    PNAS 107: 20435–20440
    The primary transcriptome of the major human pathogen Helicobacter pylori.
    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)
    Nature 464: 250–255
    Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation.
    Pfeiffer V, Papenfort K, Lucchini S, Hinton JCD, Vogel J (2009)
    Nature Structural & Molecular Biology 16: 840–846
    Small RNA Binding to 5′ mRNA Coding Region Inhibits Translational Initiation.
    Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008)
    Molecular Cell 32: 827–837
    Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation.
    Urban JH, Vogel J (2008)
    PLoS Biology 6: 0631–0642
    Selected Review Articles
    Bacterial RNA Biology on a Genome Scale.
    Hör J, Gorski SA, Vogel J (2018)
    Molecular Cell doi: 10.1016/j.molcel.2017.12.023
    RNA-based Recognition and targeting: Sowing the seeds of specificity.
    Gorski SA, Vogel J, Doudna JA (2017)
    Nature Reviews Molecular Cell Biology 18:215-228
    Resolving host–pathogen interactions by dual RNA-seq.
    Westermann AJ, Barquist L & Vogel J (2017)
    PLoS Pathogens 13: 1–19
    Changed in translation: MRNA recoding by -1 programmed ribosomal frameshifting.
    Caliskan N, Peske F, Rodnina MV (2015)
    Trends in Biochemical Sciences 40: 265–274
    Accelerating discovery and functional analysis of small RNAs with new technologies.
    Barquist L, Vogel J (2015)
    Annual Review of Genetics 49:367-94
    Single-cell RNA-seq: advances and future challenges.
    Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)
    Nucleic Acids Research 42:8845-60
    Dual RNA-seq of pathogen and host.
    Westermann AJ, Gorski SA, Vogel J (2012)
    Nature Reviews Microbiology 10:618-30
    Hfq and its constellation of RNA.
    Vogel J, Luisi BF (2011)
    Nature Reviews Microbiology 9:578-89
    Regulation by Small RNAs in Bacteria: Expanding Frontiers.
    Storz G, Vogel J, Wassarman KM (2011)
    Molecular Cell 43:880-91
    Regulatory RNA in bacterial pathogens.
    Papenfort K, Vogel J (2010)
    Cell Host & Microbe 8:116-27


    Our invited speakers

    • Fabian Theis (Helmholtz Center Munich)
    • Peter Nielsen (University of Copenhagen, Denmark)
    • Renate König (Paul Ehrlich Institute, Langen)
    • Demián Cazalla (University of Utah, USA)
    • Blake Wiedenheft (Montana State University, USA)
    • Tom Cooper (Baylor College of Medicine, USA)
    • Susan Carpenter (UC Santa Cruz, USA)
    • Ciarán Condon (CNRS, Paris, France)
    • Thorsten Stafforst (University Tübingen)
    • Noam Stern-Ginossar (Weizmann Institute of Science, Israel)

    We would like to welcome you

    to the seminar and the following scientific exchange.

    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.


    PhD CRISPR Biology & Technology


    PhD Bacterial RNA Biology in the Gut Microbiota


    Graduate Program

    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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