DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy by Ahmed Khalil, Fran Supek

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Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner. by Tobias Warnecke, Fran Supek, Ben Lehner

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A framework for mutational signature analysis based on DNA shape parameters. by Aleksandra Karolak, Jurica Levatić, Fran Supek

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Joint inference of mutational signatures from indels and single-nucleotide substitutions reveals prognostic impact of DNA repair deficiencies by Patricia Ferrer-Torres, Iván Galván-Femenía, Fran Supek

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Hydroxymethylated cytosines are associated with elevated C to G transversion rates. by Fran Supek, Ben Lehner, Petra Hajkova, Tobias Warnecke

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Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. by Nives Skunca, Matko Bošnjak, Anita Kriško, Panče Panov, Sašo Džeroski, Tomislav Smuc, Fran Supek

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