.Descripción: The Computational Oncology Group (PI Geoff Macintyre) at the Spanish National Cancer Centre (CNIO) is seeking a postdoctoral researcher to develop computational approaches to help guide the chemoprevention of cancer.In the Macintyre Lab, we are using single cell DNA sequencing and computational approaches to identify different types of chromosomal instability and match them with targeted therapies.We are applying this technology at the earliest stages of tumour development in patients to prevent the development of aggressive, difficult-to-treat cancers.We recently pioneered an innovative computational algorithm capable of dissecting different chromosomal instability (CIN) types in a tumour and demonstrated its potential for predicting response to existing therapies (Drews et al. Nature, 2022).Since the development of our signatures, the scientific community has made substantial progress on conducting deep whole-genome sequencing of large collections of pre-malignant, primary, and metastatic samples. This now offers an opportunity to generate a more comprehensive collection of signatures at much higher resolution.Thus, in this four-year project, we propose to adapt our computational algorithms to decompose patterns of CIN at an unprecedented resolution and at different timepoints of tumour evolution.You will develop new AI methodologies to process sequencing data from > 50,000 tumour genomes (the largest collection of whole-genome-sequenced samples to date), reformulate features to encode patterns of copy number changes at base-pair resolution, and decompose CIN in the new feature space by applying deep-learning approaches.Subsequently, you will characterise these signatures by integrating orthogonal data, which will ultimately allow elucidation of the underlying biology of the new CIN signatures.Finally, you will design a web-based tool for leveraging these advances, assisting users in accurately identifying and quantifying mutational processes operating in new tumour samples.You will work closely with lab members, assisting with algorithm development, as well as clinical collaborators across Spain and the UK, to ensure your research can directly benefit patients.The Macintyre Lab strives to provide a supportive, flexible, and fun working environment, free from bias and inequality, to promote the next generation of scientists. We welcome members from all backgrounds who are passionate about research and are interested in translating their work for patient benefit. Come join us!Criterios de evaluaciónA PhD degree in bioinformatics, computational biology, computer science, mathematics, physics, or statistics.Must have proven expertise in bioinformatics, particularly in cancer genomics, tumour evolution, and mutational signature analysis.Must have experience in analysing whole genome sequence data.Coding experience (preferably in R and Python).Experience with high performance and/or cloud computing.Manuscript writing
