Fran Supek

Fran Supek

Institut de Recerca Biomèdica de Barcelona

Life & Medical Sciences

Fran Supek is an ICREA professor based at the Institute for Research in Biomedicine (IRB Barcelona), a part of the Barcelona Institute of Science and Technology. Fran leads the Genome Data Science laboratory, which specializes in large-scale statistical analyses of genomic, transcriptomic and epigenomic data. Fran obtained his PhD in Molecular biology in 2010 from the University of Zagreb, while working as an early-stage researcher at the RBI (Croatia). This was followed by a postdoctoral stay at the Centre for Genomic Regulation (as a Marie Curie fellow) and in 2017 he started his group at the IRB as a Ramón y Cajal fellow. Fran is the PI of the ERC Starting Grant HYPER-INSIGHT, an EMBO Young Investigator, and an author on 46 research papers, 3 invited review articles and 2 book chapters, cited 6525 times.

Research interests

My interests focus on computational approaches for elucidating mutational processes that generate genetic diversity within populations and across species, with the goal of understanding mechanisms of mutagenesis and DNA repair. I am also interested in developing statistical frameworks for detecting genomic signatures of negative or positive selection, which are often challenging to distinguish from the background DNA sequence variability that results from accumulated mutations. Such novel methodologies provide opportunities to gain insight into evolution of genomes, by revealing details of the interplay between mutation and selection. The biological questions I addressed include learning about evolution of gene function and regulation, in particular related to mechanisms underlying stress resistance and disease. In addition, I am interested in distributions of genetic variants in the human germline and soma, which can reveal how DNA repair is organized along eukaryotic chromosomes.

Selected publications

– Mas-Ponte D, Supek F. 2020, ‘DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers.’ Nature Genetics ;52(9):958-968.

– Salvadores M, Fuster-Tormo F & Supek F 2020. ‘Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns.’ Science Advances 6(27):eaba1862.

– Rodriguez-Martin B, Alvarez EG*, Baez-Ortega A*, Zamora J*, Supek F*, […44 more authors], PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC; PCAWG Consortium. 2020. ‘Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.’ Nature Genetics ;52(3):306-319.(* equal contribution)

– Madin JS, Nielsen DA, Brbic M, Corkrey R, Danko D, Edwards K, Engqvist MKM, Fierer N, Geoghegan JL, Gillings M, Kyrpides NC, Litchman E, Mason CE, Moore L, Nielsen SL, Paulsen IT, Price ND, Reddy TBK, Richards MA, Rocha EPC, Schmidt TM, Shaaban H, Shukla M, Supek F, Tetu SG, Vieira-Silva S, Wattam AR, Westfall DA, Westoby M. 2020. ‘A synthesis of bacterial and archaeal phenotypic trait data.’ Scientific Data ;7(1):170.

Selected research activities

– invited talks at the HIBIT 2020 health informatics conference and at “Tendiendo Puentes” medical oncology conference; invited department seminars at University College London and at Peking University

– work-package leader on an upcoming Horizon 2020 “Research in Action” collaborative project DECIDER (2021-2026) that will study the evolution of ovarian cancer under therapy