Doctoral Projects

The scientific programme of the Graduate Programme "Infectious Diseases Research" is based on projects of the individual research groups of the Institute for Molecular Infection Biology (IMIB), the Young Investigator Groups of the Research Center for Infectious Diseases (ZINF), and the Helmholtz Institute for RNA-based Infection Research (HIRI).

 

 

Biochemical dissection of RNA-protein complexes in the host response to infection
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Supervisor: Dr. Mathias Munschauer
Promotion Committee: Dr. Mathias Munschauer, Prof. Dr. Utz Fischer, Dr. Simone Backes

Multi-omic characterization of the Salmonella RNA-binding protein ProQ during infection of the murine typhoid model
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Supervisor: Jun. Prof. Dr. Lars Barquist
Promotion Committee: Jun. Prof. Dr. Lars Barquist, Jun. Prof. Dr.  Alexander Westermann, Prof. Dr. Thomas Dandekar, Dr. Sofia Forslund

Influenza virus reassortment
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Supervisor:
Jun. Prof. Dr. Redmond Smyth
Promotion Committee: Jun. Prof. Dr. Redmond Smyth, Dr. Antoine-Emmanuel Saliba, Prof. Dr. Bettina Böttcher, Dr. Simone Backes

Integrating single-cell multi-omics to decipher host-pathogen interactions
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Supervisor:
 Dr. Antoine-Emmanuel Saliba
Promotion Committee
: Dr. Antoine-Emmanuel Saliba , Prof. Dr. Roy Gross, Jun.-Prof. Dr. Florian Erhard, Prof. Dr. Leif Erik Sander

Functional analysis of HSV-1 induced transcription read-through
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Supervisor:
Prof. Dr. Lars Dölken
Promotion Committee:  Prof. Dr. Lars Dölken, Prof. Dr. Utz Fischer, Jun. Prof. Dr. Florian Erhard

Investigating the interplay between bacterial and fungal members of the human gut microbiota 
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Supervisor: Dr. Christian Pérez
Promotion Committee: Dr. Christian Pérez, Dr. Martin Fraunholz, Prof. Dr. Julia-Stefanie Frick, Prof. Dr. Joachim Morschhäuser

Exploring small proteins in the foodborne pathogen Campylobacter jejuni
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Supervisor:
Prof. Dr. Cynthia Sharma
Promotion Committee
: Prof. Dr. Cynthia Sharma, Prof. Dr. Chase Beisel, Prof. Dr. Susanne Engelmann

Global discovery of Hfq associated RNAs in the enteric pathogen Clostridioides difficile
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Supervisor: Dr. Franziska Faber
Promotion Committee: Dr. Franziska Faber, Jun. Prof. Dr. Alexander J. Westermann, Dr. Meina Neumann-Schaal

Biochemical dissection of protein-RNA interaction in viral infections
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Supervisor: Dr. Mathias Munschauer
Promotion Committee: Dr. Mathias Munschauer, Prof. Dr. Utz Fischer, Prof. Dr. Lars Dölken

CRISPR-based combinatorial screens in bacteria
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Supervisor: Prof. Dr. Chase L. Beisel
Promotion Committee: Prof. Dr. Chase L. Beisel, Jun. Prof. Dr. Alexander Westermann, Dr. Ana Rita Brochado, Prof. Dr. Hardt

Molecular characterization of the wnt-signaling pathway in Echinococcus multilocularis
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Supervisor: Prof. Klaus Brehm
Promotion Commitee:
Prof. Klaus Brehm, Prof. Christian Janzen, Prof. Christian Stigloher

Investigating the effect of peptide nucleic acids on the gene expression profile of bacterial pathogenic communities using single-cell RNA-seq
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Supervisor: Prof. Dr. Jörg Vogel
Promotion Committee: Prof. Dr. Jörg Vogel, Prof. Dr. Thomas Rudel, Dr. Antoine-Emmanuel Saliba

Regulation of antibiotic resistance in Staphylococcus aureus by small RNAs
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Supervisor:
PD Dr. Knut Ohlsen
Promotion Commitee:
PD Dr. Knut Ohlsen, PD Dr. Wilma Ziebuhr, Dr. Martin Fraunholz

Development of novel experimental approaches to decipher host-pathogen interactions at the single-cell level 
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Supervisor: Dr. Antoine-Emmanuel Saliba
Promotion Committee
: Dr. Antoine-Emmanuel Saliba, Prof. Dr. Roy Gross, Jun. Prof. Dr. Alexander J. Westerman

Programming antisense oligonucleotides (ASOs)
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Supervisor: Prof. Dr. Jörg Vogel
Promotion committee:
Prof. Dr. Jörg Vogel, Jun. Prof. Dr. Lars Barquist, Dr. Ana Rita Brochado

Developing a programmable mRNA-derived crRNA(mcrRNA) based CRISPR-Cas9 technology
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Supervisor:
Prof. Dr. Chase Beisel
Promotion Committee: Prof. Dr. Chase Beisel, Prof. Dr. Cynthia Sharma, Jun. Prof. Dr. Redmond Smyth

Computional methods for systems virology of herpes viruses
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Supervisor:
Jun. Prof. Dr. Florian Erhard
Promotion Committee: Jun. Prof. Dr. Florian Erhard, Prof. Dr. Lars Dölken, Prof. Dr. Thomas Dandekar, Prof. Dr. Sibylle Schneider-Schaulies

Analysis of the immune and mucosal barrier functions along the gastrointestinal tract of mouse and human using organoids as a model
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Supervisor: Dr. Sina Bartfeld
Promotion Committee: Dr. Sina Bartfeld, Prof. Dr. Thomas Rudel, Dr. Armin Wiegering, Dr. Bon-Kyong Koo

Global discovery and analysis of programmed ribosomal frameshifting in T-cells
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Supervisor: Jun. Prof. Dr. Neva Caliskan
Promotion Committee: Jun. Dr. Prof. Dr. Neva Caliskan, Jun. Prof. Dr. Redmond Smyth, Jun. Prof. Dr. Florian Erhard

Molecular analysis of the flatworms' intra/intercellular signal transduction
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Supervisor:
  Prof. Dr. Klaus Brehm
Promotion Committee
: Prof. Dr. Klaus Brehm,  Prof. Dr. Christian Stigloher, Dr. August Stich

Exploring virulence factors and regulators of the food-borne pathogen Campylobacter jejuni in a human 3D tissue infection model
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Supervisor: Prof. Dr. Cynthia Sharma
Promotion Committee: Prof. Dr. Cynthia Sharma, PD. Dr. Marco Metzger, Prof. Dr. Roy Gross

Establishment of spatial transcriptomics methods to resolve host-pathogen interactions
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Supervisor: Dr. Antoine-Emmanuel Saliba
Promotion Committee:
Dr. Susanne Kramer, Prof. Dr. Sauer, Dr. Georg Zeller

Identification and functional characterization of novel RNA-binding proteins in Clostridium difficile
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Supervisor:
Dr. Franziska Faber
Promotion Committee: Dr. Franziska Faber, Dr. Lars Barquist, Dr. José Manuel Borrero-de Acuña

Comprehensive reannotation of the human and murine cytomegalovirus genomes and characterisation of novel gene products and sORF-encoded peptides
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Supervisor: Prof. Dr. Lars Dölken
Promotion Committee: Prof. Dr. Lars Dölken, Prof. Dr. Utz Fischer, Asst. Prof. Dr. Vanda Juranic Lisnic, Jun. Prof. Florian Erhard

Genomic and Internet based analysis of Coxiella burnetii
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Supervisor: Prof. Dr. Thomas Dandekar
Promotion Committee: Prof. Dr. Thomas Dandekar, Prof. Dr. Konrad Förstner, PD. Dr. Dimitrios Frangoulidis, Prof. Dr. Jörg Schultz

Unveiling the Hfq mediated RNA-RNA interactome of Salmonella Typihmurium
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Supervisor: Prof. Dr. Jörg Vogel
Promotion Committee: Prof. Dr. Jörg Vogel, Prof. Dr. Kai Papenfort, Dr. Franziska Faber

Dual RNA-seq analysis of pathogen and host
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Supervisor:
Dr. Lars Barquist
Promotion Committee:
Dr. Lars Barquist, Jun. Prof. Dr. Alexander Westermann, Prof. Dr. Konrad Förstner, Prof. Dr. Petra Dersch

Interactome study of HSV-1
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Supervisor:
Prof. Dr. med. Lars Dölken
Promotion Committee
: Prof. Dr. med. Lars Dölken, Prof. Dr. rer. nat. Beate Sodeik, Prof. Dr. Florian Erhard, Dr. Michael Weekes

Analysis of Candida albicans protein kinases in signaling pathways
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Supervisor: Prof. Dr. Joachim Morschhäuser
Promotion committee: Prof. Dr. Joachim Morschhäuser, Dr. J. Christian Pérez, Prof. Dr. Bernhard Hube

Integrative analyses of CMV translatomes and MHC-I ligandomes
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Supervisor: Prof. Dr. Florian Erhard
Promotion Committee: Prof. Dr. Florian Erhard , Prof. Dr. Lars Dölken, Prof. Dr. Andreas Schlosser, Dr. Anne Halenius

Establishment of a human primary 3D model for colonization with anaerobic gut bacteria
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Supervisor: Jun. Prof. Dr. Alexander Westermann
Promotion Committee: Jun. Prof. Dr. Alexander Westermann, Prof. Dr. Roy Gross, PD Dr. Marco Metzger

The CRISPR/Cas system in Neisseria meningitidis and its potential role in host cell adhesion
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Supervisor: PD Dr. rer. nat. Dr. med. Christoph Schoen
Promotion Committee: PD Dr. rer. nat. Dr. med. Christoph Schoen, PD Dr. Knut Ohlsen, Prof. Dr. Dagmar Beier

Analysis of innate immune responses of gastrointestinal epithelium to infection using human organoids as model
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Supervisor: Dr. Sina Bartfeld
Promotion Committee: Dr Sina Bartfeld, Priv.-Doz. Dr. Marco Metzger, Prof. Dr. Tomas Rudel

 

Studying human pathogens using organoid systems
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Supervisor:
Dr. Sina Bartfeld
Promotion Committee: Dr. Sina Bartfel, Dr. Antoine-Emmanuel Saliba, Prof. Dr. Redmond Smyt, PD Dr. Vera Kozjak-Pavlovic

Single-molecule approaches to study frameshifting mechanisms and efficiency
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Supervisor: Jun. Prof. Dr. Neva Caliskan
Promotion Committee: Jun. Prof. Dr. Neva Caliskan, Prof. Dr. Utz Fischer, Prof. Dr. Markus Sauer

Analysis of the functional relevance of sphingomyelinases and ceramide in meningococcal pathogenesis
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Supervisor:
Prof. Dr. Alexandra Schubert-Unkmeir
Promotion Committee: Prof. Dr. Alexandra Schubert-Unkmeir, Prof. Dr. Markus Sauer, Dr. Kay Johswich

Investigation of the post-transcriptional regulation in Fusobacterium nucleatum
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Supervisor: Prof. Dr. Jörg Vogel
Promotion Committee: Prof. Dr. Jörg Vogel, Prof. Dr. Chase Beisel, N.N.

Identification and functional characterization of in-vivo-relevant sRNAs in Bacteroides thetaiotaomicron
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Supervisor: Jun. Prof. Dr. Alexander Westermann
Promotion Committee: Jun. Prof. Dr. Alexander Westermann, Prof. Dr. Chase Beisel, Dr. Martin Fraunholz

Mechanisms of host colonisation by the fungus Candida albicans
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Supervisor: Dr. J. Christian Pérez
Promotion Committee
: Dr. J. Christian Pérez, Prof. Dr. Bernhard Hube, Prof. Dr. Joachim Morschhäuser

Implementation and application of bioinformatical tools for the analysis of dual RNA-sequencing data of host and pathogen during infection
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Supervisor:
Prof. Dr. Konrad Förstner
Promotion Committee: Prof. Dr. Konrad Förstner, Prof. Dr. Thomas Dandekar, Jun. Prof. Dr. Alexander Westermann

Generation of novel gene regulatory networks in the pathogenic yeast Candida albicans by hybrid transcription factors
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Supervisor: Prof. Dr. Joachim Morschhäuser
Promotion Committee:
Prof. Dr. Joachim Morschhäuser, Dr. J. Christian Pérez, PD Dr. Brooke Morriswood, Prof. Dr. Christian Janzen

The functional relevance of the intestinal mycobiome in the pathogenesis of non-alcoholic fatty liver disease
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Supervisor:
Prof. Dr. med Oliver Kurzai
Promotion Committee:
Prof. Dr. med Oliver Kurzai, Prof. Dr med Andreas Geier, Prof. Dr. Christian Janzen

Characterizing the temporal dynamics of host-pathogen interactions by combining single-cell nascent RNA-seq and genetic screen
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Supervisor: Dr. Antoine-Emmanuel Saliba
Promotion Committee: Dr. Antoine-Emmanuel Saliba, Prof. Dr. Chase Beisel, Prof. Dr. Thomas Rudel, Prof. Dr. Florian Erhard, Dr. Sophie Helaine

Characterization of small proteins in E. coli and Salmonella Typhimurium
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Supervisor: Prof. Dr. Jörg Vogel
Promotion Committee: Prof. Dr. Jörg Vogel, Prof. Dr. Cynthia Sharma, PD Dr. Wilma Ziebuhr, Prof. Dr. Kai Papenfort

Applications and outcomes of genome targeting by CRISPR-Cas systems in bacteria
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Supervisor: Prof. Dr. Chase Beisel
Promotion Committee: Dr. Ana Rita Brochado, Jun. Prof. Dr. Lars Barquist, Dr. Till Strowig

Identification and Characterization of anti-CRISPR proteins
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Supervisor:
Prof. Dr. Chase Beisel
Promotion Committee:
Prof. Dr. Chase Beisel, PD Dr. Knut Ohlsen, Prof. Dr. Lars Barquist, Prof. Dr. Peter Fineran

Alternative functions of CRISPR-Cas
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Supervisor:
Prof. Dr. Chase Beisel
Promotion Committee
: Prof. Dr. Chase Beisel, Prof. Dr. Cynthia Sharma, Jun. Prof. Dr. Neva Caliskan

Identification and characterization of RNA-binding-proteins in cancer-associated Fusobacterium nucleatum
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Supervisor: Prof. Dr. Jörg Vogel
Promotion Committee: Prof. Dr. Jörg Vogel, Prof. Dr. rer. nat. Dr. med. Christoph U. Schoen, Prof. Dr. Dagmar Beier

Defining quaternary RNA architecture of influenza by RNA-RNA seq
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Supervisor: Jun. Prof. Dr. Redmond Smyth Promotion
Promotion Committee: Jun. Prof. Dr. Redmond Smyth, Prof. Dr. Sibylle Schneider-Schaulies, Prof. Dr. Cynthia Sharma

Development of CRISPR/Cas method for Functional Genomics
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Supervisor: Jun. Prof. Dr. Lars Barquist
Promotion Committee: Jun. Prof. Dr. Lars Barquist; Prof. Dr. Chase Beise; Dr. Ana Rita Brochado; Dr. Tobias Müller

Identification and Characterization of trans-Regulators of Programmed Ribosomal Frameshifting
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Supervisor: Jun. Prof. Dr. Neva Caliskan
Promotion Committee: Jun. Prof. Dr. Neva Caliskan, Prof. Dr. Utz Fischer, Prof. Dr. Thomas Pietschmann