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Hypermutated tumors: insight into genome maintenance and cancer vulnerabilities provided by an extreme burden of somatic mutations

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Publications

Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns

Author(s): Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
Published in: Science Advances, Issue 6/27, 2020, Page(s) eaba1862, ISSN 2375-2548
DOI: 10.1126/sciadv.aba1862

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

Author(s): Vedrana Vidulin, Tomislav Šmuc, Sašo Džeroski, Fran Supek
Published in: Microbiome, Issue 6/1, 2018, ISSN 2049-2618
DOI: 10.1186/s40168-018-0506-4

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Author(s): Irene Franco, Hafdis T. Helgadottir, Aldo Moggio, Malin Larsson, Peter Vrtačnik, Anna Johansson, Nina Norgren, Pär Lundin, David Mas-Ponte, Johan Nordström, Torbjörn Lundgren, Peter Stenvinkel, Lars Wennberg, Fran Supek, Maria Eriksson
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
DOI: 10.1186/s13059-019-1892-z

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

Author(s): David Mas-Ponte, Fran Supek
Published in: Nature Genetics, Issue 52/9, 2020, Page(s) 958-968, ISSN 1061-4036
DOI: 10.1038/s41588-020-0674-6

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Author(s): Bernardo Rodriguez-Martin, Eva G. Alvarez, Adrian Baez-Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martin Santamarina, Young Seok Ju, Javier Temes, Daniel Garcia-Souto, Harald Detering, Yilong Li, Jorge Rodriguez-Castro, Ana Dueso-Barroso, Alicia L. Bruzos, Stefan C. Dentro, Miguel G. Blanco, Gianmarco Contino, Daniel Ardeljan, Marta Tojo, Nicola D. Roberts, Sonia Zumalave, Paul A. W.
Published in: Nature Genetics, Issue 52/3, 2020, Page(s) 306-319, ISSN 1061-4036
DOI: 10.1038/s41588-019-0562-0

Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours

Author(s): Alexandra Avgustinova, Aikaterini Symeonidi, Andrés Castellanos, Uxue Urdiroz-Urricelqui, Llorenç Solé-Boldo, Mercè Martín, Ivan Pérez-Rodríguez, Neus Prats, Ben Lehner, Fran Supek, Salvador Aznar Benitah
Published in: Nature Cell Biology, Issue 20/12, 2018, Page(s) 1400-1409, ISSN 1465-7392
DOI: 10.1038/s41556-018-0233-x

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype

Author(s): Matej Mihelčić, Tomislav Šmuc, Fran Supek
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
DOI: 10.1038/s41598-019-55984-0

Passenger mutations accurately classify human tumors

Author(s): Marina Salvadores, David Mas-Ponte, Fran Supek
Published in: PLOS Computational Biology, Issue 15/4, 2019, Page(s) e1006953, ISSN 1553-7358
DOI: 10.1371/journal.pcbi.1006953

Scales and mechanisms of somatic mutation rate variation across the human genome

Author(s): Fran Supek, Ben Lehner
Published in: DNA Repair, Issue 81, 2019, Page(s) 102647, ISSN 1568-7864
DOI: 10.1016/j.dnarep.2019.102647

The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy

Author(s): Rik Lindeboom, Michiel Vermeulen, Ben Lehner, Fran Supek
Published in: Nature Genetics, Issue in press, 2019, ISSN 1061-4036
DOI: 10.1038/s41588-019-0517-5

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author(s): Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Ge
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
DOI: 10.1186/s13059-019-1835-8