Finding noncoding cancer drivers

Publications

A compendium of mutational cancer driver genes

Auteurs: Francisco Martínez-Jiménez, Ferran Muiños, Inés Sentís, Jordi Deu-Pons, Iker Reyes-Salazar, Claudia Arnedo-Pac, Loris Mularoni, Oriol Pich, Jose Bonet, Hanna Kranas, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Nature Reviews Cancer, Numéro 20/10, 2020, Page(s) 555-572, ISSN 1474-175X
Éditeur: Nature Publishing Group
DOI: 10.1038/s41568-020-0290-x

Pervasive lesion segregation shapes cancer genome evolution

Auteurs: Aitken, Sarah J.; Anderson, Craig J.; Connor, Frances; Pich, Oriol; Sundaram, Vasavi; Feig, Christine; Rayner, Tim F.; Lukk, Margus; Aitken, Stuart; Luft, Juliet; Kentepozidou, Elissavet; Arnedo-Pac, Claudia; Beentjes, Sjoerd V.; Davies, Susan E.; Drews, Ruben M.; Ewing, Ailith; Kaiser, Vera B.; Khamseh, Ava; López-Arribillaga, Erika; Redmond, Aisling M.; Santoyo-Lopez, Javier; Sentís, Inés; Ta
Publié dans: Nature, Numéro 583, 2020, Page(s) 10.1038/s41586-020-2435-1, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-020-2435-1

The evolution of hematopoietic cells under cancer therapy

Auteurs: Oriol Pich; Albert Cortes-Bullich; Ferran Muiños; Marta Pratcorona; Abel Gonzalez-Perez; Nuria Lopez-Bigas; Nuria Lopez-Bigas
Publié dans: Nature Communications, Numéro 12/1, 2021, Page(s) 4803, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-24858-3

Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites

Auteurs: Joan Frigola, Radhakrishnan Sabarinathan, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Nucleic Acids Research, Numéro 49/2, 2020, Page(s) 891-901, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa1219

The mutational footprints of cancer therapies

Auteurs: Oriol Pich, Ferran Muiños, Martijn Paul Lolkema, Neeltje Steeghs, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Nature Genetics, Numéro 51/12, 2019, Page(s) 1732-1740, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-019-0525-5

Reduced mutation rate in exons due to differential mismatch repair

Auteurs: Joan Frigola, Radhakrishnan Sabarinathan, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, Núria López-Bigas
Publié dans: Nature Genetics, Numéro 49/12, 2017, Page(s) 1684-1692, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/ng.3991

Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets

Auteurs: K Karube, A Enjuanes, I Dlouhy, P Jares, D Martin-Garcia, F Nadeu, G R Ordóñez, J Rovira, G Clot, C Royo, A Navarro, B Gonzalez-Farre, A Vaghefi, G Castellano, C Rubio-Perez, D Tamborero, J Briones, A Salar, J M Sancho, S Mercadal, E Gonzalez-Barca, L Escoda, H Miyoshi, K Ohshima, K Miyawaki, K Kato, K Akashi, A Mozos, L Colomo, M Alcoceba, A Valera, A Carrió, D Costa, N Lopez-Bigas, R Schmitz,
Publié dans: Leukemia, Numéro 32/3, 2017, Page(s) 675-684, ISSN 0887-6924
Éditeur: Nature Publishing Group
DOI: 10.1038/leu.2017.251

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Auteurs: David Tamborero, Carlota Rubio-Perez, Jordi Deu-Pons, Michael P. Schroeder, Ana Vivancos, Ana Rovira, Ignasi Tusquets, Joan Albanell, Jordi Rodon, Josep Tabernero, Carmen de Torres, Rodrigo Dienstmann, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Genome Medicine, Numéro 10/1, 2018, ISSN 1756-994X
Éditeur: BioMed Central
DOI: 10.1186/s13073-018-0531-8

A Pan-cancer Landscape of Interactions between Solid Tumors and Infiltrating Immune Cell Populations

Auteurs: David Tamborero, Carlota Rubio-Perez, Ferran Muiños, Radhakrishnan Sabarinathan, Josep M. Piulats, Aura Muntasell, Rodrigo Dienstmann, Nuria Lopez-Bigas, Abel Gonzalez-Perez
Publié dans: Clinical Cancer Research, Numéro 24/15, 2018, Page(s) 3717-3728, ISSN 1078-0432
Éditeur: American Association for Cancer Research
DOI: 10.1158/1078-0432.ccr-17-3509

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

Auteurs: Claudia Arnedo-Pac, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Bioinformatics, 2019, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz501

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes

Auteurs: Oriol Pich, Ferran Muiños, Radhakrishnan Sabarinathan, Iker Reyes-Salazar, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Cell, Numéro 175/4, 2018, Page(s) 1074-1087.e18, ISSN 0092-8674
Éditeur: Cell Press
DOI: 10.1016/j.cell.2018.10.004

Whole-genome landscapes of major melanoma subtypes

Auteurs: Nicholas K. Hayward, James S. Wilmott, Nicola Waddell, Peter A. Johansson, Matthew A. Field, Katia Nones, Ann-Marie Patch, Hojabr Kakavand, Ludmil B. Alexandrov, Hazel Burke, Valerie Jakrot, Stephen Kazakoff, Oliver Holmes, Conrad Leonard, Radhakrishnan Sabarinathan, Loris Mularoni, Scott Wood, Qinying Xu, Nick Waddell, Varsha Tembe, Gulietta M. Pupo, Ricardo De Paoli-Iseppi, Ricardo E. Vilain, Pi
Publié dans: Nature, Numéro 545/7653, 2017, Page(s) 175-180, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/nature22071

Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer

Auteurs: Francisco Martínez-Jiménez, Ferran Muiños, Erika López-Arribillaga, Nuria Lopez-Bigas, Abel Gonzalez-Perez
Publié dans: Nature Cancer, Numéro 1/1, 2020, Page(s) 122-135, ISSN 2662-1347
Éditeur: Springer Nature
DOI: 10.1038/s43018-019-0001-2

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Auteurs: Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroe
Publié dans: Nature, Numéro 578/7793, 2020, Page(s) 102-111, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-020-1965-x

The repertoire of mutational signatures in human cancer

Auteurs: Ludmil B. Alexandrov, Jaegil Kim, Nicholas J. Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R. Covington, Dmitry A. Gordenin, Erik N. Bergstrom, S. M. Ashiqul Islam, Nuria Lopez-Bigas, Leszek J. Klimczak, John R. McPherson, Sandro Morganella, Radhakrishnan Sabarinathan, David A. Wheeler, Ville Mustonen, Gad Getz, Steven G. Rozen, Michael R. Stratton
Publié dans: Nature, Numéro 578/7793, 2020, Page(s) 94-101, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-020-1943-3

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

Auteurs: Alex H. Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, Kilannin Krysiak, Jordi Deu-Pons, Ryan P. Duren, Jianjiong Gao, Julie McMurry, Sara Patterson, Catherine del Vecchio Fitz, Beth A. Pitel, Ozman U. Sezerman, Kyle Ellrott, Jeremy L. Warner, Damian T. Rieke, Tero Aittokallio, Ethan Cerami, Deborah I. Ritter, Lynn M. Schriml, Robert R. Freimuth, Melissa Haendel, Gordana R
Publié dans: Nature Genetics, Numéro 52/4, 2020, Page(s) 448-457, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-020-0603-8

In silico saturation mutagenesis of cancer genes

Auteurs: Ferran Muiños; Francisco Martínez-Jiménez; Oriol Pich; Abel Gonzalez-Perez; Nuria Lopez-Bigas; Nuria Lopez-Bigas
Publié dans: Nature, Numéro 596/7872, 2021, Page(s) 428, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-021-03771-1

The evolution of relapse of adult T cell acute lymphoblastic leukemia

Auteurs: Inés Sentís, Santiago Gonzalez, Eulalia Genescà, Violeta García-Hernández, Ferran Muiños, Celia Gonzalez, Erika López-Arribillaga, Jessica Gonzalez, Lierni Fernandez-Ibarrondo, Loris Mularoni, Lluís Espinosa, Beatriz Bellosillo, Josep-Maria Ribera, Anna Bigas, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Publié dans: Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur: Genome Biology
DOI: 10.1186/s13059-020-02192-z

The whole-genome panorama of cancer drivers

Auteurs: Sabarinathan R, Pich O, Martincorena I, Rubio-Perez C, Juul M, Wala J, Schumacher S, Shapira O, Sidiropoulos N, Waszak S, Tamborero D, Mularoni L, Rheinbay E, Hornshoj H, Deu-Pons J, Muinos F, Bertl J, Guo Q, Weischenfeldt J, Korbel JO, Getz G, Campbell PJ, Pedersen JS, Beroukhim R, Perez-Gonzalez A, Lopez-Bigas N, PCAWG Drivers and Functional Interpretation Group, ICGC/TCGA Pan-Cancer Analysis of
Publié dans: Pre print, 2017
Éditeur: Biorxive
DOI: 10.1101/190330

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Auteurs: Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Pedersen, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Johanna Bertl, Priyanka Dhingra, Klev Diamanti, Abel Gonzalez-Perez, Qia
Publié dans: pre print, 2017
Éditeur: Biorxiv
DOI: 10.1101/237313

Disruption of ubiquitin mediated proteolysis is a widespread mechanism of tumorigenesis

Auteurs: Francisco Martínez-Jiménez, Ferran Muiños, Erika Lopez-Arribillaga, Nuria Lopez-Bigas, Abel Gonzalez-Perez
Publié dans: Pre print, 2018
Éditeur: Biorxiv
DOI: 10.1101/507764

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