This PhD project, hosted at the University of Udine and Flomics Biotech SL in Barcelona, focuses on the identification and implementation of novel cell-free RNA (cfRNA) biomarkers for early cancer detection using liquid biopsy. Flomics Biotech is pioneering a multi-purpose blood test that leverages optimized cfRNA profiling via Next-generation sequencing (NGS) and advanced machine learning analysis to detect cancer and other complex diseases before symptoms arise. Unlike traditional liquid biopsy approaches that target circulating tumor DNA (ctDNA), this project emphasizes cfRNA, which is more abundant and informative in early disease stages, as it is released from both cancerous and non-cancerous cells, including those from the immune system and stroma. The candidate will utilize proprietary RNA sequencing protocols and analyze a large in-house dataset (~1,100 samples) covering five cancer types and healthy controls. Research will involve developing bioinformatics pipelines to explore RNA-based signals beyond gene expression, such as mitochondria-derived RNAs, circular RNAs, single nucleotide variants, and novel transcripts. The project includes advanced data normalization and removal of unwanted variation, addressing key challenges in cfRNA research. Machine learning models will be developed to classify cancer patients versus healthy controls with high accuracy, integrating novel biomarker types and global gene expression signatures. The position is part of the INT2ACT Doctoral Network, offering strong collaboration and secondments with leading European research groups, including the Institute of Bioorganic Chemistry (Polish Academy of Science) and University of Udine. The host laboratory at Flomics Biotech provides a dynamic environment with cutting-edge genomics and bioinformatics resources. Applicants must have a Master’s degree in a relevant field, proficiency in English, and willingness to travel for collaborative research. Funding is provided, and the application deadline is January 31, 2026.

This PhD position, hosted at IIS Biogipuzkoa Health Research Centre in Donostia-San Sebastián, Spain, is part of the INT2ACT Doctoral Network and affiliated with the University of Udine. The project, BIOCART, aims to identify novel blood-based biomarkers in CAR-T–treated patients with relapsed or refractory B-cell lymphomas. CAR-T therapy has revolutionized treatment for these patients, but resistance and toxicities such as cytokine release syndrome and neurotoxicity remain significant challenges. The project addresses the urgent clinical need for biomarkers to better predict and manage these toxicities and monitor disease progression. Unlike previous studies that relied on single omic approaches and small cohorts, BIOCART employs a comprehensive multi-omics strategy, including cfDNA, miRNA, methylomics, glycomics, and spectroscopy, in a large, prospective, international, multicenter study. Blood samples are collected at multiple time points before and after CAR-T infusion, and the resulting data are used to develop and train machine learning pipelines capable of integrating and harmonizing multi-omics datasets. The goal is to identify biomarkers for early treatment response, disease progression, and therapy-related toxicities. The developed algorithms and biomarkers will be validated in an independent cohort of 120 patients. The PhD student will focus on bioinformatics analyses, data fusion, and the development of new computational tools for data harmonization. The host laboratory, led by Prof. Charles Lawrie, is well-equipped with facilities for cell culture, flow cytometry, microscopy, genomics, histology, and clinical trials, and maintains strong connections with oncology medical services. The project includes secondments to collaborating groups in China (Prof. Lei Zhang, SSIAT, Shanghai University) and Spain (Dr. Marc Weber, Flomics Biotech SL, Barcelona), so willingness to travel is essential. Applicants must have a Master’s degree in a relevant field, not already hold a doctoral degree, and comply with the mobility rule. Experience in bioinformatics, computational biology, and programming (Python, R, C++) is advantageous, as is knowledge of machine learning. Proficiency in English is required. Funding is provided through the INT2ACT Doctoral Network, with details available on the recruitment web page. The application deadline is January 31, 2026. For more information, visit the INT2ACT website or contact Dr. Charles Lawrie.