Integrative Cancer Genomics: Single-Cell Transcriptomics and Oxford Nanopore Long-Read Sequencing for Biomarker Discovery Aston University in United Kingdom

Project Overview: This PhD project at Aston University focuses on integrative cancer genomics, leveraging single-cell RNA sequencing (scRNA-seq) and Oxford Nanopore long-read transcriptomics to advance biomarker discovery in sarcoma. Sarcomas are rare, heterogeneous cancers with over 70 subtypes, each presenting unique genomic and molecular features. The project aims to address the clinical challenge of limited reliable biomarkers by generating a high-resolution molecular map of sarcoma, combining cutting-edge sequencing technologies.

Research Objectives: The student will generate and analyze single-cell transcriptomic profiles to identify tumor subclones, immune microenvironment states, stromal interactions, and transcriptional programs linked to metastasis and treatment resistance. Long-read sequencing will enable full-length transcript reconstruction, detection of novel isoforms, and validation of structural and splice variants often missed by short-read approaches. The dual sequencing strategy provides a comprehensive view of cellular heterogeneity and transcriptomic complexity.

Key goals include:

• Characterizing intra-tumor heterogeneity and identifying clinically relevant cellular states.
• Detecting novel fusion transcripts, isoform switches, and long noncoding RNAs associated with metastasis.
• Validating biomarkers across a diverse patient cohort and correlating molecular signatures with clinical and pathological data.
• Generating a comprehensive biomarker catalogue to inform translational research and potential diagnostic or prognostic assays.

Training & Environment: The successful candidate will receive extensive training in wet-lab methods, multi-omics data analysis, long-read informatics, single-cell analysis pipelines, and computational oncology. The project is based at the Aston Campus in Birmingham, UK, within the College of Health and Life Sciences, offering a vibrant research environment and access to state-of-the-art facilities.

Funding: The studentship covers Home tuition fees. Overseas applicants are welcome but must pay the difference between Home and Overseas tuition fees (£17,712 for 2026/7). Applicants must confirm their ability to provide this additional funding if required.

Eligibility: Applicants should hold, or expect to achieve, a First or Upper Second Class undergraduate degree (or equivalent) in a relevant subject, or a Merit (or above) in a relevant postgraduate Masters degree plus an undergraduate degree. Overseas qualifications will be assessed for equivalence. English language proficiency is required.

Application Process: Applications are accepted year-round. Submit a complete application including transcripts, certificates, research statement, personal statement, CV, two academic references, evidence of English proficiency, and a copy of your passport. Incomplete applications will not be considered. Shortlisted candidates will be invited for an online interview via Microsoft Teams.

For formal enquiries, contact Dr Mohammed ‘Mo’ Elasrag at [email protected]. For application process queries, contact [email protected].

Apply for this position here (select 'Research - Biomedical Sciences' on the form).