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Finding noncoding cancer drivers

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Publications

Reduced mutation rate in exons due to differential mismatch repair

Author(s): Joan Frigola, Radhakrishnan Sabarinathan, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, Núria López-Bigas
Published in: Nature Genetics, Issue 49/12, 2017, Page(s) 1684-1692, ISSN 1061-4036
DOI: 10.1038/ng.3991

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

Author(s): 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,
Published in: Leukemia, Issue 32/3, 2017, Page(s) 675-684, ISSN 0887-6924
DOI: 10.1038/leu.2017.251

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

Author(s): 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
Published in: Genome Medicine, Issue 10/1, 2018, ISSN 1756-994X
DOI: 10.1186/s13073-018-0531-8

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

Author(s): David Tamborero, Carlota Rubio-Perez, Ferran Muiños, Radhakrishnan Sabarinathan, Josep M. Piulats, Aura Muntasell, Rodrigo Dienstmann, Nuria Lopez-Bigas, Abel Gonzalez-Perez
Published in: Clinical Cancer Research, Issue 24/15, 2018, Page(s) 3717-3728, ISSN 1078-0432
DOI: 10.1158/1078-0432.ccr-17-3509

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

Author(s): Claudia Arnedo-Pac, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Published in: Bioinformatics, 2019, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz501

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

Author(s): Oriol Pich, Ferran Muiños, Radhakrishnan Sabarinathan, Iker Reyes-Salazar, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Published in: Cell, Issue 175/4, 2018, Page(s) 1074-1087.e18, ISSN 0092-8674
DOI: 10.1016/j.cell.2018.10.004

Whole-genome landscapes of major melanoma subtypes

Author(s): 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
Published in: Nature, Issue 545/7653, 2017, Page(s) 175-180, ISSN 0028-0836
DOI: 10.1038/nature22071

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

Author(s): Francisco Martínez-Jiménez, Ferran Muiños, Erika López-Arribillaga, Nuria Lopez-Bigas, Abel Gonzalez-Perez
Published in: Nature Cancer, Issue 1/1, 2020, Page(s) 122-135, ISSN 2662-1347
DOI: 10.1038/s43018-019-0001-2

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

Author(s): 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
Published in: Nature, Issue 578/7793, 2020, Page(s) 102-111, ISSN 0028-0836
DOI: 10.1038/s41586-020-1965-x

The repertoire of mutational signatures in human cancer

Author(s): 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
Published in: Nature, Issue 578/7793, 2020, Page(s) 94-101, ISSN 0028-0836
DOI: 10.1038/s41586-020-1943-3

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

Author(s): 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
Published in: Nature Genetics, Issue 52/4, 2020, Page(s) 448-457, ISSN 1061-4036
DOI: 10.1038/s41588-020-0603-8

The whole-genome panorama of cancer drivers

Author(s): 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
Published in: Pre print, 2017
DOI: 10.1101/190330

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

Author(s): 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
Published in: pre print, 2017
DOI: 10.1101/237313

Disruption of ubiquitin mediated proteolysis is a widespread mechanism of tumorigenesis

Author(s): Francisco Martínez-Jiménez, Ferran Muiños, Erika Lopez-Arribillaga, Nuria Lopez-Bigas, Abel Gonzalez-Perez
Published in: Pre print, 2018
DOI: 10.1101/507764