Job Title: Post-doctoral fellow Department: School of Pharmacy & Biomolecular Sciences Reporting to: Dr. Sudipto Das Location: Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, Dublin 2, Ireland Contract/Duration: 2-years full-time, with the possibility of extension Remuneration: Appointable at Post-doctoral researcher level 2- PD1 Point 1 of the IUA researcher salary scale (Dec, 2024 onwards) Closing Date: 24th June, 2025 RCSI is a community of academic, research, clinical and professional staff working collaboratively to lead the world to better health. Here, you will thrive in an innovative and inclusive atmosphere and your personal development and wellbeing will be supported. We invite you to join us to help deliver on our exciting mission "To educate, nurture and discover for the benefit of human health". We seek candidates whose experience to date has prepared them to contribute to our commitment to the "Race Equality Action Plan 2021-2024" at RCSI. Our students come from all walks of life and so do we. We hire great people from a wide variety of backgrounds. This makes our university stronger and ensures we hire the best talent. Innovating for a Healthier Future 2023-2027 is RCSI's new five-year strategic plan. Through it, RCSI will enhance human health by meeting the health workforce needs of society, creating the insights and inventions that drive health improvements, and working in partnership with patients and the public in support of better health and well-being for all. The strategy unites the RCSI community in supporting the UN Sustainable Development Goals - with a particular focus on Goal 3, which targets good health and well-being. For each of the last six years, RCSI has been positioned in the Top 300 of universities worldwide in the Times Higher World University Rankings. We are proud that RCSI ranks fifth in the world for "Good Health and Well-being" in the Times Higher Education #SDG #SDG Impact Rankings 2024. This reflects our commitment to supporting people of all ages to live healthy lives and our work to promote the concepts of well-being and positive health. Our values of Respect, Collaboration, Scholarship and Innovation continue to unite and direct our purpose. About Our Research RCSI recognises that excellence in research is critical to the quality of its educational activities, its credibility, and, overall, to its mission to enhance human health. RCSI's research strategy aims to build upon its strength in translational biomedical and clinical research to deliver transformational, high impact changes in health care. Targeting both Irish national and EU funding, along with increased collaboration with industry, is a major part of the RCSI research strategy. Forging increased collaboration between RCSI PIs and industry is of critical importance to achieving success in this area. RCSI is also committed to provide its researchers with the supports and developmental opportunities to enable them to continuously grow and support their overall career development. Summary of Post Standardized Profiling of Epigenetic Loci for decentralized ClAssification of Sinonasal Tumours and IdEntification of therapy Response markers - SPELCASTER ProjectSummary: Sinonasal and salivary gland tumors represent a complex group of over 40 different types of cancer, sharing an overlapping anatomical compartment and ranging from benign to highly malignant biology. Many tumors show morphologic similarities that present significant challenges to diagnosis and result in substantial diagnostic discrepancy. Further, methods to predict treatment response or to predict tumor progression or metastasis are lacking. Epigenetic classification based on DNA methylation and machine learning has demonstrated tremendous power in unifying diagnostics in brain tumors. This multi-institutional European project brings together 6 centers of excellence from 5 countries (Germany, Ireland, France, Spain and Italy) to focus on developing a unified, DNA methylation-based classification system for sinonasal and salivary gland tumours (forms of Head and Neck cancer). Leveraging machine learning and a robust reference cohort, we aim to enhance diagnostic accuracy, predict clinical outcomes, and gain insights into tumor progression and heterogeneity. The project bridges epigenomics, computational biology, and clinical oncology to deliver impactful translational tools for improved patient management across Europe ( ) Hypothesis: It has been shown that machine learning algorithms can identify tumor-specific DNA methylation signatures to classify tumors and predict clinical behavior for many types of cancer. We hypothesize that this technology can be extended to a new set of head and neck cancers to help predict treatment response, recurrence, and metastasis. Key Objectives: Work with consortium members to develop and validate a DNA methylation-based machine learning classifier for sinonasal and salivary gland tumors. Harmonize tumor diagnostics across multiple European centers using decentralized validation. Investigate spatial and temporal epigenetic changes related to tumor progression and metastasis. Correlate DNA methylation patterns with clinical outcomes to support prognostication and therapeutic decision-making. Methodology: Construction and expansion of a reference DNA methylation dataset across >40 tumor entities. Development of classification algorithms using machine learning tools. Decentralized validation across six European pathology laboratories. Analysis of progression models, including inverted papilloma and recurrent/metastatic tumors. Outcome-based analyses linking methylation profiles to clinical trial and retrospective cohort data. Description of research group at RCSI: The Epigenetics of Gastrointestinal Diseases research group (EpigastroDRG) led by Dr. Das is a highly dynamic team that includes researchers from various scientific disciplines. The group aims to apply novel bioinformatics approaches to epigenomic/multi- omic data and more recently histopatholigcal as well as digital health data generated from large patient cohorts, in order to identify novel biomarkers of treatment response and disease progression in diseases such as Inflammatory Bowel Diseases (IBD) and Colorectal cancer. In addition, the group is actively involved in validating the phenotypic role of these candidate biomarkers as well as various epigenetic targeting agents using novel models of IBD and Colorectal cancer, working in extensive partnership with clinical, academic and industry-based experts. Training and career development opportunities: This project involves collaborations with 5 international partners including both academic and clinical experts. The role will therefore allow the post-doctoral researcher to interact and collaborate with these partners enabling them to enhance their skill sets from a clinical perspective while increasing their own collaborative network. Opportunity to work with state-of-art multi-omic data sets including epigenetic, histopatholgical and electronic health record data Opportunity to receive hands-on training in advanced bioinformatic skills thorugh in-person training sessions organised by collaborating partner in Germany. Opportunity to contribute to any ongoing projects beyond head and neck cancer within the group including colorectal cancer and IBD, enabling co-/senior authorship on high impact peer-review publications. Support from Dr. Das as well as the RCSI Office of Research & Innovation to apply for national and international competitive post-doctoral fellowships across both academic and industry sectors Support from the highly active post-doctoral society with RCSI that regularly organises career development and social events for post-doctoral staff Opportunity to facilitate tutorials, lectures and practical's for undergraduate and post-graduate degree programmes within the school of pharmacy & biomolecular sciences therefore enhancing teaching portfolio. Specifically, the duties of the post are: The successful candidate will be expected to be highly motivated to perform with a high level of independence. The successful candidate will work with external collaborators (academic, clinical and industry) and internally within RCSI The candidate would be expected to support bioinformatic analysis of ongoing projects within the group as well as any collaborative opportunities The candidate would be expected to write scientific reports and reviews The successful applicant will represent the labs work at national and international conferences The candidate will work in the laboratory with researchers at various training levels and would be expected to provide training and supervision of students and other staff Undergo appropriate training for specialised technical procedures, career training and development both in Ireland and overseas as may be required from time to time Participate in other research programmes within the laboratories Ensure that all RCSI policies and procedures are adhered to Comply with statutory legislation and RCSI rules and requirements in furtherance of your own and general staff welfare and safety Represent the best interests of RCSI at all times Qualifications - (Essential): Applicants should have a PhD in bioinformatics/computational biology/genetics/machine learning or related biological subject Knowledge & Experience - (Essential): Experience in analysis of next-generation sequencing and microarray-derived epigenetic/omic-data Proficiency in at least one programming language; familiarity with R, python, and version-controlled collaborative software development. Familiarity with machine-learning (ML) classification (e.g. random forest, neural networks). Strong research and scientific English writing skills Self-motivated, hard-working and willing to contribute towards the growing research in the area of head and neck cancers. Ability to work successfully and engage positively with colleagues, collaborators, students and project stakeholders Excellent communication style and proficient in report writing and presentation skill Knowledge & Experience (Desirable): Experience in handling digital health data such as electronic health records Experience with terminal-based computer management and basic shell scripting. Experience with statistical hypothesis testing and survival statistics techniques (e.g. Kaplan-Meier)