Dr Johanna Rhodes

Supervisor Details

Contact Details

School of Biosciences, University of Birmingham

Scientific Background

Research Interests

Dr Rhodes’ research leverages large multi-omics datasets to investigate how pathogenic fungi emerge and evolve. She is interested in how human activity drives the evolvability of Candida and Aspergillus species, through the lens of antifungal drug resistance.

Supervision Style

In three words or phrases: I believe that a positive and inclusive culture is fundamental to achieving excellence in research. It requires fostering an environment where individuals feel valued, supported, and empowered to contribute their unique perspectives whilst upholding high standards of research integrity. As a mentor, I work closely with early-career researchers to develop their career goals. I have directly supervised three PhD students (one submitted, two currently supervising) and nine MSc students (100% pass). I have examined two PhD vivas. I mentor students by regularly reviewing their progress and connecting them with external collaborators and encouraging them to present their research at conferences. This has resulted in significant skill growth of my students and high-impact publications (e.g. Kappel et al., Nature AMR 2 2024, Gifford et al., The Lancet Microbe 5(9) 2024). I lead a supportive group and have an open door policy; as such, I encourage early career scientists to take part in my group meetings to foster their own career development and grow their academic networks and helping with research ideas and proposals.

Provision of Training

I prefer to be responsible for your training initially, with support from other group members if their expertise fits the project, leading to more independence later on.

Progression Monitoring and Management

I will set out expectations of progression on a monthly basis, but I am available more regularly for advice and guidance to help you meet your full potential.

Communication

My group has a Slack chat where we regularly communicate during the week. My working hours may not align with a conventional 9-5 due to family commitments, but I expect you to manage your work/life balance and do not expect you to keep to the same hours as me.

Meetings

PhD Students can expect scheduled meetings with me at least once per month. These meetings will be a mixture of face-to-face and via video chat or telephone. I am usually contactable for an instant response on every working day.

Work Patterns

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings), I expect students to manage their own time.

Notice Period for Feedback

I need at least 1 week's notice to provide feedback on written work of up to 5,000 words.

MIBTP Project Details

Primary supervisor for:

Deciphering the Role of Transcription Factor Binding Site Variation in Phenotypic Diversity of Aspergillus fumigatus

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Deciphering the Role of Transcription Factor Binding Site Variation in Phenotypic Diversity of Aspergillus fumigatus

Secondary Supervisor(s): Dr Hung-Ji Tsai

University of Registration: University of Birmingham

BBSRC Research Themes:

Understanding the Rules of Life (Microbiology, Systems Biology)

Project Outline

Aspergillus fumigatus is a major opportunistic pathogen causing invasive aspergillosis, with marked variability in virulence, stress tolerance, and antifungal resistance. While coding sequence changes explain some of this diversity, many phenotypic differences remain unresolved. Variation in transcription factor binding sites (TFBS) within promoter regions could be a key driver, altering transcription factor affinity and gene regulation without changing protein sequences.

This project will test how TFBS variation shapes A. fumigatus phenotypes by combining comparative genomics with experimental mapping of transcription factor occupancy. A diverse strain panel will be assembled, promoter sequences analysed with motif discovery tools, and variation mapped across virulence and stress-response genes. Selected transcription factors will be targeted with ChIP-seq or CUT&RUN to identify their binding landscapes in multiple strains under baseline and stress conditions. These datasets will validate predicted motifs and reveal condition-dependent regulatory interactions.

RNA-seq will link TFBS variation and binding differences to transcriptional changes, while phenotyping will assess growth, stress responses, secondary metabolism, antifungal susceptibility, and virulence in model hosts. Candidate TFBS variants will be validated using CRISPR-Cas9 editing and promoter–reporter assays to measure functional impact.

The project will deliver the first integrated atlas of TFBS sequence variation, in vivo transcription factor binding, and resulting phenotypic effects in A. fumigatus. This will provide new insight into the regulatory genome of fungal pathogens and identify potential biomarkers and targets for antifungal strategies.

APPLY HERE