Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer
A Strakova, TJ Nicholls*, A Baez-Ortega*, M Ní Leathlobhair, AT Sampson, K Hughes, IAG Bolton, K Gori, J Wang, I Airikkala-Otter, JL Allen, KM Allum, CL Arnold, L Bansse-Issa, TN Bhutia, JL Bisson, K Blank, C Briceño, A Castillo Domracheva, AM Corrigan, HR Cran, JT Crawford, SM Cutter, E Davis, KF de Castro, AB De Nardi, AP de Vos, L Delgadillo Keenan, EM Donelan, AR Espinoza Huerta, IA Faramade, M Fazil, E Fotopoulou, SN Fruean, F Gallardo-Arrieta, O Glebova, PG Gouletsou, RF Häfelin Manrique, JJGP Henriques, RS Horta, N Ignatenko, Y Kane, C King, D Koenig, A Krupa, SJ Kruzeniski, M Lanza-Perea, M Lazyan, AM Lopez Quintana, T Losfelt, G Marino, S Martínez Castañeda, MF Martínez-López, BM Masuruli, M Meyer, EJ Migneco, B Nakanwagi, KB Neal, W Neunzig, SJ Nixon, A Ortega-Pacheco, F Pedraza-Ordoñez, MC Peleteiro, K Polak, RJ Pye, JC Ramirez-Ante, JF Reece, J Rojas Gutierrez, H Sadia, SK Schmeling, O Shamanova, AG Sherlock, AE Steenland-Smit, A Svitich, LJ Tapia Martínez, I Thoya Ngoka, CG Torres, EM Tudor, MG van der Wel, BA Vițălaru, SA Vural, O Walkinton, AS Wehrle-Martinez, SAE Widdowson, I Zvarich, PF Chinnery, M Falkenberg, CM Gustafsson, EP Murchison
Nature Communications, 11 (1): 3059 (2020)
DOI: 10.1038/s41467-020-16765-w
*Equal contribution
Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition
B Rodriguez-Martin, EG Alvarez*, A Baez-Ortega*, J Zamora, F Supek, J Demeulemeester, M Santamarina, YS Ju, J Temes, D Garcia-Souto, H Detering, Y Li, J Rodriguez-Castro, A Dueso-Barroso, AL Bruzos, SC Dentro, MG Blanco, G Contino, D Ardeljan, M Tojo, ND Roberts, S Zumalave, PAW Edwards, J Weischenfeldt, M Puiggros, Z Chong, K Chen, EA Lee, JA Wala, K Raine, A Butler, SM Waszak, FCP Navarro, SE Schumacher, J Monlong, F Maura, N Bolli, G Bourque, M Gerstein, PJ Park, D Wedge, R Beroukhim, D Torrents, JO Korbel, I Martincorena, RC Fitzgerald, P Van Loo, HH Kazazian, KH Burns, PJ Campbell, JMC Tubio
Nature Genetics, 52(3): 306–319 (2020)
DOI: 10.1038/s41588-019-0562-0
*Equal contribution
sigfit: flexible Bayesian inference of mutational signatures
K Gori, A Baez-Ortega
bioRxiv, 372896 (2018)
DOI: 10.1101/372896
The origins and vulnerabilities of two transmissible cancers in Tasmanian devils
MR Stammnitz, THH Coorens, KC Gori, D Hayes, B Fu, J Wang, DE Martin-Herranz, LB Alexandrov, A Baez-Ortega, S Barthorpe, A Beck, F Giordano, GW Knowles, YM Kwon, G Hall, S Price, RJ Pye, JMC Tubio, HVT Siddle, S Singh Sohal, GM Woods, U McDermott, F Yang, MJ Garnett, Z Ning, EP Murchison
Cancer Cell, 33(4): 607–619 (2018)
DOI: 10.1016/j.ccell.2018.03.013
Computational approaches for discovery of mutational signatures in cancer
A Baez-Ortega, K Gori
Briefings in Bioinformatics, 20(1): 77–88 (2017)
DOI: 10.1093/bib/bbx082
