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

Publicaciones

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

Autores: Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
Publicado en: Science Advances, Edición 6/27, 2020, Página(s) eaba1862, ISSN 2375-2548
Editor: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aba1862

Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells

Autores: Josep Biayna; Isabel Garcia-Cao; Miguel M. Álvarez; Marina Salvadores; Jose Espinosa-Carrasco; Marcel McCullough; Fran Supek; Travis H. Stracker
Publicado en: PLoS Biology, Edición 15449173, 2022, Página(s) e3001176, ISSN 1544-9173
Editor: Public Library of Science
DOI: 10.1371/journal.pbio.3001176

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

Autores: Vedrana Vidulin, Tomislav Šmuc, Sašo Džeroski, Fran Supek
Publicado en: Microbiome, Edición 6/1, 2018, ISSN 2049-2618
Editor: BioMed Central
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

Autores: 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
Publicado en: Genome Biology, Edición 20/1, 2019, ISSN 1474-760X
Editor: BioMed Central
DOI: 10.1186/s13059-019-1892-z

The impact of rare germline variants on human somatic mutation processes

Autores: Mischan Vali-Pour, Ben Lehner, Fran Supek
Publicado en: Nature Communications, Edición 20411723, 2022, Página(s) 3724, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31483-1

Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers

Autores: Marina Salvadores, Fran Supek
Publicado en: Nature Cancer, Edición 5, 2024, Página(s) 330-346, ISSN 2662-1347
Editor: Springer Nature
DOI: 10.1038/s43018-023-00707-8

Proton and alpha radiation-induced mutational profiles in human cells

Autores: Tiffany Delhomme, Maia Munteanu, Manuela Buonanno, Veljko Grilj, Josep Biayna, Fran Supek
Publicado en: Scientific Reports, Edición 13, 2023, Página(s) 9791, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-36845-3

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

Autores: David Mas-Ponte, Fran Supek
Publicado en: Nature Genetics, Edición 52/9, 2020, Página(s) 958-968, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-020-0674-6

Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

Autores: Bruno Fito-Lopez, Marina Salvadores, Miguel-Martin Alvarez, Fran Supek
Publicado en: BMC Biology, Edición 21, 2023, Página(s) 92, ISSN 1741-7007
Editor: BioMed Central
DOI: 10.1186/s12915-023-01595-1

Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation

Autores: David Mas-Ponte, Fran Supek
Publicado en: Nucleic Acids Research, 2024, Página(s) gkae252, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkae252

Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy

Autores: David Mas-Ponte, Marcel McCullough, Fran Supek
Publicado en: Clinical Science, Edición 01435221, 2022, Página(s) 383–404, ISSN 0143-5221
Editor: Portland Press, Ltd.
DOI: 10.1042/cs20210682

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

Autores: 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.
Publicado en: Nature Genetics, Edición 52/3, 2020, Página(s) 306-319, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-019-0562-0

To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases.

Autores: Fran Supek; Ben Lehner; Ben Lehner; Rik G.H. Lindeboom
Publicado en: Trends in Genetics, Edición 01689525, 2022, Página(s) 657-668, ISSN 0168-9525
Editor: Elsevier BV
DOI: 10.1016/j.tig.2020.11.002

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

Autores: 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
Publicado en: Nature Cell Biology, Edición 20/12, 2018, Página(s) 1400-1409, ISSN 1465-7392
Editor: Nature Publishing Group
DOI: 10.1038/s41556-018-0233-x

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

Autores: Matej Mihelčić, Tomislav Šmuc, Fran Supek
Publicado en: Scientific Reports, Edición 9/1, 2019, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-019-55984-0

Passenger mutations accurately classify human tumors

Autores: Marina Salvadores, David Mas-Ponte, Fran Supek
Publicado en: PLOS Computational Biology, Edición 15/4, 2019, Página(s) e1006953, ISSN 1553-7358
Editor: Public Library of Science
DOI: 10.1371/journal.pcbi.1006953

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

Autores: Fran Supek, Ben Lehner
Publicado en: DNA Repair, Edición 81, 2019, Página(s) 102647, ISSN 1568-7864
Editor: Elsevier BV
DOI: 10.1016/j.dnarep.2019.102647

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

Autores: Rik Lindeboom, Michiel Vermeulen, Ben Lehner, Fran Supek
Publicado en: Nature Genetics, Edición in press, 2019, ISSN 1061-4036
Editor: Nature Publishing Group
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

Autores: 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
Publicado en: Genome Biology, Edición 20/1, 2019, ISSN 1474-760X
Editor: BioMed Central
DOI: 10.1186/s13059-019-1835-8

A framework for mutational signature analysis based on DNA shape parameters

Autores: Aleksandra Karolak; Jurica Levatić; Fran Supek
Publicado en: PLoS ONE, Edición 19326203, 2022, Página(s) e0262495, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0262495

Mutational signatures are markers of drug sensitivity of cancer cells

Autores: Jurica Levatic, Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
Publicado en: Nature Communications, Edición 20411723, 2022, Página(s) 2926, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-30582-3

TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening

Autores: Miguel Alvarez, Josep Biayna, Fran Supek
Publicado en: Nature Communications, Edición 20411723, 2022, Página(s) 4520, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-32285-1

Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers.

Autores: Park, Solip; Supek, Fran; Lehner, Ben; park
Publicado en: Nature Communications, Edición 20411723, 2021, Página(s) 7051, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-27242-3

Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals

Autores: Guillermo Palou-Marquez, Fran Supek
Publicado en: bioRxiv, Edición 2024.02.29.582778, 2024, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.29.582778

Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver events of human cancer

Autores: Elizaveta Besedina, Fran Supek
Publicado en: bioRxiv, Edición 2023.08.05.552104, 2023, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.05.552104

Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules

Autores: Ignasi Toledano, Fran Supek, Ben Lehner
Publicado en: bioRxiv, Edición 2023.08.07.552350, 2023, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.07.552350

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