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).

 

 

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
>>more
Supervisor:
Jun. Prof. Dr. Redmond Smyth
Promotion Committee: Jun. Prof. Dr. Redmond Smyth, Dr. Antoine-Emmanuel Saliba, Prof. Dr. Bettina Böttcher, Dr. Simone Backes

Picture of Mona Alzheimer

New 3D-infection models based on tissue-engeneering to study the pathogenesis of Helicobacter pylori and Campylobacter jejuni
>>more
Supervisor: Prof. Dr. Cynthia Sharma
Promotion Committee
: Prof. Dr. Cynthia Sharma, Prof. Dr. Heike Walles, Prof. Dr. Jörg Vogel

Riboregulation of meningococcal virulence
>>more
Supervisor:
Prof. Dr. Christoph Schoen
Promotion Committee:
Prof. Dr. Christoph Schoen, Prof. Dr. Jörg Vogel, Prof. Dr. Joachim Morschhäuser

Picture of Nico Dunkel

Regulatory circuits underlying host colonization by C. albicans
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Supervisor:
Dr. J. Christian Pérez
Promotion Committee: Dr. J. Christian Pérez, Prof. Dr. Joachim Morschhäuser, Dr. Till Strowig, Dr. Kai Sohn

Understanding how a family of transcriptional regulators was repurposed to enable Candida albicans to thrive in mammalian hosts
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Supervisor:
Dr. Christian Pérez
Promotion Committee: Dr. Christian Pérez, Prof. Dr. Joachim Morschhäuser, Prof. Dr. T. Nicolai Siegel, Dr. Polly Fordyce

Implementation and application of bioinformatical tools for the analysis of high-throughput sequencing data to detect RNA-protein and RNA-RNA interactions
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Supervisor: Prof. Dr. Konrad Förstner
Promotion Committee
: Prof. Dr. Konrad Förstner, Prof. Dr. Jörg Vogel, Prof. Dr. Thomas Dandekar

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

Identification of auxiliary protein factors in post-transcriptional regulation in Epsilonproteobacteria
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Supervisor:
Prof. Dr. Cynthia Sharma
Promotion Committee:
Prof. Dr. Cynthia Sharma, Prof. Dr. Thomas Rudel, Dr. Gisela Storz

Unraveling the Type VII secretion system (T7S) of Mycobacterium tuberculosis
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Supervisor:
Dr. Sebastian Geibel
Promotion Commitee: Dr. Sebastian Geibel, Prof. Dr. Caroline Kisker, Dr. Clemens Grimm, Dr. Angel Rivera-Calzada

Identification and characterization of pseudouridine in RNAs of the human pathogen Campylobacter jejuni
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Supervisor: Prof. Dr. Cynthia Sharma
Promotion Committee: Prof. Dr. Cynthia Sharma, Prof. Dr. Utz Fischer, Prof. Dr. Dagmar Beier

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

Meningococcal ligands and molecular targets required for adhesion and penetration of the blood-cerebrospinal fluid barrier
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Supervisor: Prof. Dr. Alexandra Schubert-Unkmeir
Promotion Committee:
Prof. Dr. Alexandra Schubert-Unkmeir, Dr. Marco Metzger, Dr. Maria Steinke, Antje Appelt-Menzel

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

Serotonin signaling and mobile genetic elements in E. multiloculari
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Supervisor:
Prof. Dr. Klaus Brehm
Promotion Committee:
Prof. Dr. Klaus Brehm, Prof. Dr. Nicolai Siegel, Prof. Dr. Jörg Schultz

Discovery of novel RNA-protein complexes by Grad-seq
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Supervisor:
Prof. Dr. Jörg Vogel
Promotion Committee:
Prof. Dr. Jörg Vogel, Prof. Dr. Cynthia Sharma, Prof. Dr. Utz Fischer

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

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

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

Picture of Andrea Kühn

Identification of factors responsible for the targeted deposition of histone variants in Trypanosoma brucei
>>more
Supervisor:
Prof. Dr. Nicolai Siegel
Promotion Committee: Prof. Dr. Nicolai Siegel, Dr. Sonja Lorenz, Prof. Dr. Christian Janzen, Prof. Dr. Andreas Schlosser

Picture of Andreas Kalbfleisch

Functional characterization of lipid rafts in bacteria
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Supervisor:
Dr. Daniel López
Promotion Committee:
Dr. Daniel López, Prof. Dr. Kai Papenfort, Prof. Dr. Sibylle Schneider-Schaulies

Identification and functional characterization of novel RNA-binding proteins in Clostridium difficile
>>more

Supervisor:
Dr. Franziska Faber
Promotion Committee: Dr. Franziska Faber, Dr. Lars Barquist, Dr. José Manuel Borrero-de Acuña

Role of host cell microRNAs during infection by Staphylococcus aureus
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Supervisor: Dr. Ana Eulalio
Promotion Committee: Dr. Ana Eulalio, Dr. Daniel López, Prof. Dr. Jörg Wischhusen

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
>>more
Supervisor: Prof. Dr. Jörg Vogel
Promotion Committee: Prof. Dr. Jörg Vogel, Prof. Dr. Kai Papenfort, Dr. Franziska Faber

Investigation of the Type VII secretion system in Staphylococcus aureus
>>more
Supervisor: Dr. Sebastian Geibel
Promotion Committee: Dr. Sebastian Geibel, Prof. Dr. Thomas Müller, Dr. Gilles Phan

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

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

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

Epigenetic regulation of monoallelic expression in Trypanosoma brucei
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Supervisor: Prof. Dr. Nicolai Siegel
Promotion Committee: Prof. Dr. Nicolai Siegel, Prof. Dr. Markus Engstler, Dr. Susanne Fenz, Dr. Konrad Förstner

The roles of the anaphylatoxin receptors during invasive disease as well as mucosal colonization caused by Neisseria meningitidis
>>more
Supervisor:
Dr. Kay Johswich
Promotion Commitee:
Dr. Kay Johswich, Prof. Dr. Alexandra Schubert-Unkmeir, Dr. Martin Fraunholz

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

Analysis of the functional relevance of sphingomyelinases and ceramide in meningococcal pathogenesis
>>more
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.

Evolution of antifungal drug resistance in Candida albicans
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Supervisor: Prof. Dr. Joachim Morschhäuser
Promotion Committee: Prof. Dr. Joachim Morschhäuser, PD Dr. Wilma Ziebuhr, Prof. Dr. Frank Ebel

Identification and functional characterization of in-vivo-relevant sRNAs in Bacteroides thetaiotaomicron
>>more
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

Establishing a human intestinal tissue model to study host and pathogen determinants that restrict Salmonella enterica infection
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Supervisor: Prof. Dr. Jörg Vogel
Promotion Committee: Prof. Dr. Jörg Vogel, Prof. Dr. Nicolai Siegel, Prof. Dr. Jay Hinton

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

Identification and characterization of RNA-binding proteins in mycobacteria
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Supervisor: Dr. Sebastian Geibel
Promotion Committee: Dr. Sebastian Geibel, Prof. Dr. Jörg Vogel, Jun. Prof. Dr. Alexander J. Westermann

Analysis of the changes in the transcriptome of EcN in the presence of human host cells or EHEC
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Supervisor: ADr Dr. Tobias Ölschläger
Promotion Committee: ADr Dr. Tobias Ölschläger, Prof. Dr. Roy Gross, Prof. Dr. Konrad Förstner, Dr. Rudolf von Buenau

Picture of Ean Jeong

Interplay between Shigella infection and host cell microRNAs
>>more
Supervisor:
Dr. Ana Eulalio
Promotion Committee:
Dr. Ana Eulalio, Prof. Dr. Thomas Rudel, Dr. Miguel Mano

Characterization of small proteins in E. coli and Salmonella Typhimurium
>>more
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

Picture of Nina Simon

Structural studies of bacterial lipid rafts
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Supervisor:
Dr. Daniel López
Promotion Committee:
Dr. Daniel López, Prof. Dr. Nicolai Siegel, Prof. Dr. Samuel Wagner

Regulation of methionine metabolism in staphylococci: Impact on fitness and virulence
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Supervisor:
PD Dr. Wilma Ziebuhr
Promotion Committee: PD Dr. Wilma Ziebuhr, PD Dr. Knut Ohlsen, Prof. Dr. Caroline Kisker

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

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

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