Isidro Cortés Ciriano

EMBL's European Bioinformatics Institute, EMBL-EBI

Biography

Isidro Cortés-Ciriano leads the Cancer Genomics group at the EMBL-EBI and is Associate Faculty at the Sanger Institute. His laboratory focuses on the development of computational methods for early cancer detection and to study the mechanisms underpinning cancer evolution using whole-genome sequencing. Recent work by his group includes the discovery of novel mechanisms of cancer development, such as Loss-Translocation-Amplification chromothripsis in osteosarcoma, and the development of novel methods for the analysis of single cell and long-read sequencing data, such as SComatic and SAVANA. His laboratory is leading the application of long-read sequencing technologies for tumour profiling and liquid biopsy analysis through various international studies initiatives, such as the CRUK-funded Stratified Medicine Paediatrics (SMPEDS) programme. Before joining EMBL-EBI, Isidro trained as a postdoctoral fellow at Harvard Medical School, and received his PhD from the Pasteur Institute.

Relevant Publications

Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution

Espejo Valle-Inclan J., De Noon S., Trevers K., Elrick H., van Belzen I. A. E. M., Zumalave S., Sauer C. M., Tanguy M., Butters T., Muyas F., Rust A. G., Amary F., Tirabosco R., Giess A., Sosinsky A., Elgar G., Flanagan A. M., Cortés-Ciriano I., Cell (2025).

https://doi.org/10.1016/j.cell.2024.12.005
SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing

Elrick H., Sauer C. M., Espejo Valle-Inclan J., Trevers K., Tanguy M., Zumalave S., De Noon S., Muyas F., Cascão R., Afonso A., Rust A. G., Amary F., Tirabosco R., Giess A., Freeman T., Sosinsky A., Piculell K., Miller D. T., Faria C. C., Elgar G., Flanagan A. M., Cortés-Ciriano I., Nature Methods (2025).

https://doi.org/10.1038/s41592-025-02708-0
De novo detection of somatic mutations in high-throughput single-cell profiling data sets

Muyas F., Sauer C. M., Espejo Valle-Inclán J., Li R., Rahbari R., Mitchell T. J., Hormoz S., Cortés-Ciriano I., Nature Biotechnology (2024).

https://doi.org/10.1038/s41587-023-01863-z
Mitotic clustering of pulverized chromosomes from micronuclei

Lin Y.-F., Hu Q., Mazzagatti A., Espejo Valle-Inclán J., Maurais E. G., Dahiya R., Guyer A., Sanders J. T., Engel J. L., Nguyen G., Bronder D., Bakhoum S. F., Cortés-Ciriano I., Ly P., Nature (2023).

https://doi.org/10.1038/s41586-023-05974-0
Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity

Westcott P. M. K., Muyas F., Hauck H., Smith O. C., Sacks N. J., Ely Z. A., Jaeger A. M., Rideout W. M. III, Zhang D., Bhutkar A., Beytagh M. C., Canner D. A., Jaramillo G. C., Bronson R. T., Naranjo S., Jin A., Patten J. J., Cruz A. M., Shanahan S.-L., Cortes-Ciriano I., Jacks T., Nature Genetics (2023).

https://doi.org/10.1038/s41588-023-01499-4
Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA

Cortes-Ciriano I., Steele C. D., Piculell K., Al-Ibraheemi A., Eulo V., Bui M. M., Chatzipli A., Dickson B. C., Borcherding D. C., Feber A., Galor A., Hart J., Jones K. B., Jordan J. T., Kim R. H., Lindsay D., Miller C., Nishida Y., Proszek P. Z., Serrano J., Sundby R. T., Szymanski J. J., Ullrich N. J., Viskochil D., Wang X., Snuderl M., Park P. J., Flanagan A. M., Hirbe A. C., Pillay N., Miller D. T., Cancer Discovery (2023).

https://doi.org/10.1158/2159-8290.CD-22-0786
ReConPlot: an R package for the visualization and interpretation of genomic rearrangements

Espejo Valle-Inclán J., Cortés-Ciriano I., Bioinformatics (2023).

https://doi.org/10.1093/bioinformatics/btad719
The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

Muyas F., Gómez Rodriguez M. J., Cascão R., Afonso A., Sauer C. M., Faria C. C., Cortés-Ciriano I., Flores I., Nature Communications (2024).

https://doi.org/10.1038/s41467-023-44287-8
Computational analysis of cancer genome sequencing data

Cortés-Ciriano I., Gulhan D. C., Lee J. J.-K., Melloni G. E. M., Park P. J., Nature Reviews Genetics (2021).

https://doi.org/10.1038/s41576-021-00431-y
Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms

Van Egeren D., Escabi J., Nguyen M., Liu S., Reilly C. R., Patel S., Kamaz B., Kalyva M., DeAngelo D. J., Galinsky I., Wadleigh M., Winer E. S., Luskin M. R., Stone R. M., Garcia J. S., Hobbs G. S., Camargo F. D., Michor F., Mullally A., Cortes-Ciriano I., Hormoz S., Cell Stem Cell (2021).

https://doi.org/10.1016/j.stem.2021.02.001