One genome, three outcomes: a unified honeybee developmental trajectory atlas from rich multiomic data
- Primary Supervisor: Dr Paul J. Hurd
- Co-supervisor(s): Dr Elena Torlai Triglia
- Studentship Funding: Awaiting CSC Funding Decision
- Application Deadline: 28th January 2026
- PhD Programme: PhD Biological Sciences
Project Overview
This project tackles a central unresolved question in biology: how can one genotype generate contrasting morphological, physiological, behavioural, and reproductive phenotypes? One of the most remarkable examples across any phyla, is the capacity of the honeybee (Apis mellifera) to produce three phenotypically distinct organisms (two female; queens and sterile workers, and haploid male drones). The molecular basis of this differential development remains unclear; however, we have generated a rich and comprehensive, multiscale multiomic resource, spanning chromatin, transcription, 3D genome architecture, proteins, metabolites, and single-cell profiles, to address it. This 4-year computational PhD will create a single, shared “honeybee atlas” that brings all these modalities together at once. The end goal is a compact representation that clearly separates honeybee phenotype and developmental time, while revealing what each modality contributes.
In this project, you will process every data type with robust, reproducible workflows (e.g., nf-core) to generate clean, bias-aware inputs. By selecting existing known biological features, you will set the scaling and normalisation, so no modality dominates. You will benchmark familiar ways to reduce complexity (PCA, factor analysis, variance decomposition) and keep the methods that best preserve signal across layers. All code will be open source, documented, and easy to reuse, forming a toolkit for future honeybee and broader multiomic studies. You will combine in-house ChIP-seq/CUT&RUN, EM-seq, ATAC-seq, RNA-seq, Hi-C, metabolomics, proteomics, and single-cell multiome (scRNA and scATAC) and public datasets from larva to adult. Success means clear separation of honeybee phenotypes and stages, balanced contributions from each modality, accurate predictions from partial data, and identification of modality-specific drivers, yielding testable targets for experiments. You will gain expertise in bioinformatics, computational modelling, scalable optimisation and multiomics.
Research Environment
The Hurd Lab (http://www.hurdlab.co.uk) is a vibrant, diverse, and inclusive group exploring how genome–environment interactions shape animal development. We combine molecular biology, biochemistry, proteomics, metabolomics, genomics/epigenomics, and computational analysis to deliver integrative functional genomics in the honeybee. The lab currently includes one postdoctoral researcher and two PhD students and is supported by the UK national funding research council (BBSRC). As a PhD researcher, you’ll join a tailored Researcher Development Programme to build core skills and plan your next career steps. I’ll provide hands-on training, encourage independence, and support you in growing collaborations. You’ll also gain project-management and presentation skills and engage with international partners. We are also founding members of the QMUL Centre for Epigenetics (http://www.qmul.ac.uk/epigenetics/), where bi-weekly joint meetings provide an additional stimulating and supportive learning and training environment.
Find out more about the School of Biological and Behavioural Sciences on our website.
Keywords: bioinformatics, computational modelling, epigenetics, multiomics, large data analysis, honeybee.
Funding & Eligibility
Queen Mary University of London has partnered with the China Scholarship Council (CSC) to offer a joint scholarship programme to enable Chinese students to study for a PhD programme at Queen Mary. Under the scheme, Queen Mary will provide scholarships to cover all tuition fees, whilst the CSC will provide living expenses and one return flight ticket to successful applicants.
Applicants must:
- Be applying for CSC funding.
- Be a citizen and permanent resident of the People’s Republic of China and hold a Chinese passport.
- Satisfy all eligibility criteria set out by the CSC and must refer to the CSC website for full details.
- Apply to QMUL by 28th January 2026. Late applications will not be considered.
- Submit ALL required documentation, including evidence of their English Language ability ahead of the CSC application deadline.
CSC application rules differ slightly for domestic applicants (students applying from China) and overseas applicants (students applying from overseas). Therefore, ALL applicants are advised to see the CSC website for full details on eligibility and conditions on the scholarship.
Entry Requirements
We are looking for candidates to have or expecting to receive a first or upper-second class honours degree and a Master’s degree in an area relevant to the project such as bioinformatics and computational biology.
Knowledge of bioinformatics (coding skills, use of command line tools and R) would be highly advantageous but are not required.
You must meet the IELTS requirements for your course and upload evidence before CSC’s application deadline, ideally by 1st March 2026. You are therefore strongly advised to sit an approved English Language test as soon as possible, where your IELTS test must still be valid when you enrol for the programme.
Please find further details on our English Language requirements page.
How to Apply
Formal applications must be submitted through our online form by 28th January 2026 for consideration. Please identify yourself as a ‘CSC Scholar’ in the funding section of the application.
Applicants are required to submit the following documents:
- Your CV
- Personal Statement
- Evidence of English Language e.g.) IELTS Certificate
- Copies of academic transcripts and degree certificates
- References
Find out more about our application process on our SBBS website.
Informal enquiries about the project can be sent to Dr Paul J. Hurd
Admissions-related queries can be sent to sbbs-pgadmissions@qmul.ac.uk
Shortlisted applicants will be invited for a formal interview by the supervisor. If you are successful in your QMUL application, then you will be issued an QMUL Offer Letter, conditional on securing a CSC scholarship along with academic conditions still required to meet our entry requirements.
Once applicants have obtained their QMUL Offer Letter, they should then apply to CSC for the scholarship with the support of the supervisor.
For further information, please go to the QMUL China Scholarship Council webpage.
Apply online