CFAH JOSE A. SEOANE – VHIO – Vall d'Hebron Institute of Oncology

JOSE A. SEOANE



Current positions


Academic Qualifications

  • 2021 Ramón y Cajal Investigator
  • 2019-2021 Instructor, Stanford University School of Medicine (PI: Christina Curtis)
  • 2014-2019 Postdoctoral Research Scholar, Stanford University School of Medicine (PI: Christina Curtis)
  • 2012-2014 Postdoctoral Research Assistant in Bioinformatics, University of Bristol (PI: Tom Gaunt)
  • 2012 PhD in Computer Science, Universidade da Coruña
  • 2010 MSc in Statistical Learning and Data Mining, UNED
  • 2008 MSc in Computer Science, Universidade da Coruña
  • 2004 Degree in Computer Engineering, Universidade da Coruña

Research areas

  • Multi-omic data integration
  • Epigenetic alterations in cancer
  • Biomedical data science

Awards and scholarships

  • Ramón y Cajal Grant (2021-2025)
  • Susan G. Komen PDF – Basic and Translational Grant (2016-2019)
  • 2012 Extraordinary PhD award in Mathematics and Computer Science

Projects

  1. Targeting synthetic lethality in Chromatin Regulatory Genes for gastrointestinal cancer treatment. Ref PID2020-115097RA-I00. Agencia Estatal de Investigación. 9/2021-8/2025. PI: Jose A. Seoane

Publications  

  • Inter-cellular CRISPR screens reveal regulators of cancer cell phagocytosis
    Roarke A. Kamber, Yoko Nishiga, Bhek Morton, Allison M. Banuelos, Amira A. Barkal, Felipe Vences-Catalán, Mingxin Gu, Daniel Fernandez, Jose A. Seoane, David Yao, Katherine Liu, Sijie Lin, Kaitlyn Spees, Christina Curtis, Livnat Jerby-Arnon, Irving L. Weissman, Julien Sage and Michael C. Bassik
    Nature, September 2021
    https://doi.org/10.1038/s41586-021-03879-4
  • DCIS genomic signatures define biology and correlate with clinical outcome: a Human Tumor Atlas Network (HTAN) analysis of TBCRC 038 and RAHBT cohorts
    Siri H. Strand, Belén Rivero-Gutiérrez, Kathleen E. Houlahan, Jose A. Seoane, Lorraine King, Christina Curtis, Rob Tibshirani, Robert Michael Angelo, Allison Hall, Kouros Owzar, Kornelia Polyak, Carlo Maley, Jeffrey R. Marks, Graham A. Colditz, E. Shelley Hwang, Robert B. West
    bioRxiv, June 2021
    10.1101/2021.06.16.448585
  • The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D
    Andrea C. Chaikovsky, Chuan Li, Edwin E, Jeng, Samuel Loebell, Myung Chang Lee, Christopher W. Murray, Ran Cheng, Janos Demeter, Danielle L. Swaney, Si-Han Chen, Billy W. Newton, Jeffrey R. Johnson, Alexandros P. Drainas, Yan Ting Shue, Jose A Seoane, Preethi Srinivasan, Andy He, Akihiro Yoshida, Susan Q. Hipkins, Edel McCrea, Carson D. Poltorack, Nevan J. Krogan, J. Alan Diehl, Christina Kong, Peter K. Jackson, Christina Curtis, Dmitri A. Petrov, Michael C. Bassik, Monte M. Winslow, Julien Sage
    Nature, 592:794-798, April 2021
    URL: https://www.nature.com/articles/s41586-021-03474-7
  • Cell of Origin Influences Pancreatic Cancer Subtype
    Brittany M. Flowers, Hang Xu, Abigail S. Mulligan, Kathryn J. Hanson, Jose A. Seoane, Hannes Vogel, Christina Curtis, Laura D. Wood, Laura D. Attardi
    Cancer Discovery, 11(3):660-677, March 2021
    URL: https://cancerdiscovery.aacrjournals.org/content/11/3/660.abstract
  • A CRISPR/Cas9-engineered ARID1A-deficient human gastric cancer organoid model reveals essential and non-essential modes of oncogenic transformation
    Yuan-Hung Lo, Kevin S. Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter D. Sobba, Kasper Karlsson, Sunny J. Jones, Teri A. Longacre, Amanda T. Mah, Bahar Tercan, Alexandra Sockell, Hang Xu, Jose A. Seoane, Jin Chen, Ilya Shmulevich, Jonathan S. Weissman, Christina Curtis, Andrea Califano, Haian Fu, Gerald R. Crabtree, Calvin J. Kuo
    Cancer Discovery, January 2021
    URL: https://cancerdiscovery.aacrjournals.org/content/early/2021/01/14/2159-8290.CD-20-1109
  • Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program
    Kathryn T. Bieging-Rolett, Alyssa M. Kaiser, David W. Morgens, Anthony M. Boutelle, Jose A. Seoane, Eric L. Van Nostrand, Changyu Zhu, Shauna L. Houlihan, Stephano S. Mello, Brian A. Yee, Jacob McClendon, Sarah E. Pierce, Ian P. Winters, Mengxiong Wang, Andrew J. Connolly, Scott W. Lowe, Christina Curtis, Gene W. Yeo, Monte M. Winslow, Michael C. Bassik, Laura D. Attardi
    Molecular Cell, 80(3):452-469.e9, November 2020
    URL: www.sciencedirect.com/science/article/pii/S1097276520307292
  • The m6A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor
    Yiren Xiao, Kaushik N. Thakkar, Hongjuan Zhao, James Broughton, Yang Li, Jose A. Seoane, Anh N. Diep, Thomas J. Metzner, Rie von Eyben, David L. Dill, James D. Brooks, Christina Curtis, John T. Leppert, Jiangbin Ye, Donna M. Peehl, Amato J. Giaccia, Subarna Sinha, Erinn B. Rankin
    Proceedings of the National Academy of Sciences, 117(35):21441-21449, September 2020
    URL: www.pnas.org/content/117/35/21441.short
  • CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities
    Kyuho Han, Sarah E. Pierce, Amy Li, Kaitlyn Spees, Grace R. Anderson, Jose A. Seoane, Yuan-Hung Lo, Michael Dubreuil, Micah Olivas, Roarke A. Kamber, Michael Wainberg, Kaja Kostyrko, Marcus R. Kelly, Maryam Yousefi, Scott W. Simpkins, David Yao, Keonil Lee, Calvin J. Kuo, Peter K. Jackson, Alejandro Sweet-Cordero, Anshul Kundaje, Andrew J. Gentles, Christina Curtis, Monte M. Winslow, Michael C. Bassik
    Nature, 580(7801):136-141, April 2020
    URL: www.nature.com/articles/s41586-020-2099-x
  • Metabolic profiling reveals a dependency of human metastatic breast cancer on mitochondrial serine and one-carbon unit metabolism
    Albert M Li, Gregory S. Ducker, Yang Li, Jose A. Seoane, Yiren Xiao, Stavros Melemenidis, Yiren Zhou, Ling Liu, Sakari Vanharanta, Edward E. Graves, Erinn B. Rankin, Christina Curtis, Joan Massagué, Joshua D. Rabinowitz, Craig B. Thompson, Jiangbin Ye
    Molecular Cancer Research, 18(4):599-611, April 2020
    URL: mcr.aacrjournals.org/content/18/4/599.abstract
  • Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers
    Nasa Sinnott-Armstrong, Jose A. Seoane, Jonathan K. Pritchard, Christina Curtis, Michael P. Snyder
    bioRxiv, November 2020
    URL: https://www.biorxiv.org/content/10.1101/2020.08.21.239954v1.abstract
  • Chromatin regulators mediate anthracycline sensitivity in breast cancer
    Jose A. Seoane, Jacob G. Kirkland, Jennifer L. Caswell-Jin, Gerald R. Crabtree, Christina Curtis
    Nature Medicine, 25(11):1721-1727, November 2019
    URL: www.nature.com/articles/s41591-019-0638-5
  • Quantitative evidence for early metastatic seeding in colorectal cancer
    Zheng Hu, Jie Ding, Zhicheng Ma, Ruping Sun, Jose A. Seoane, J. Scott Shaffer, Carlos J. Suarez, Anna S. Berghoff, Chiara Cremolini, Alfredo Falcone, Fotios Loupakis, Peter Birner, Matthias Preusser, Heinz-Josef Lenz, Christina Curtis
    Nature Genetics, 51(7):1113-1122, July 2019
    URL: www.nature.com/articles/s41588-019-0423-x
  • Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups
    Oscar M. Rueda, Stephen-John Sammut, Jose A. Seoane, Suet-Feung Chin, Jennifer L. Caswell-Jin, Maurizio Callari, Rajbir Batra, Bernard Pereira, Alejandra Bruna, H. Raza Ali, Elena Provenzano, Bin Liu, Michelle Parisien, Cheryl Gillett, Steven McKinney, Andrew R. Green, Leigh Murphy, Arnie Purushotham, Ian O. Ellis, Paul D. Pharoah, Cristina Rueda, Samuel Aparicio, Carlos Caldas, Christina Curtis
    Nature, 567(7748):399-404, March 2019
    URL: www.nature.com/articles/s41586-019-1007-8
  • Assessment of ERBB2/HER2 status in HER2-equivocal breast cancers by FISH and 2013/2014 ASCO-CAP guidelines
    Michael F. Press, Jose A. Seoane, Christina Curtis, Emmanuel Quinaux, Roberta Guzman, Guido Sauter, Wolfgang Eiermann, John R. Mackey, Nicholas Robert, Tadeusz Pienkowski, John Crown, Miguel Martin, Vicente Valero, Valerie Bee, Yanling Ma, Ivonne Villalobos, Dennis J. Slamon
    JAMA Oncology, 5(3):366-375, March 2019
    URL: jamanetwork.com/journals/jamaoncology/article-abstract/2718266
  • The chromatin accessibility landscape of primary human cancers
    Ryan Corces, Jeffrey M. Granja, Shadi Shams, Bryan H. Louie, Jose A. Seoane, Wanding Zhou, Tiago C. Silva, Clarice Groeneveld, Christopher K. Wong, Seung Woo Cho, Ansuman T. Satpathy, Maxwell R. Mumbach, Katherine A. Hoadley, A. Gordon Robertson, Nathan C. Sheffield, Ina Felau, Mauro A. A. Castro, Benjamin P. Berman, Louis M. Staudt, Jean C. Zenklusen, Peter W. Laird, Christina Curtis, William J. Greenleaf, Howard Y. Chang
    Science, 362(6413), October 2018
    URL: https://science.sciencemag.org/content/362/6413/eaav1898.abstract
  • Comparative molecular analysis of gastrointestinal adenocarcinomas
    Yang Liu, Nilay S. Sethi, Toshinori Hinoue, Barbara G. Schneider, Andrew D. Cherniack, Francisco Sanchez-Vega, Jose A. Seoane, Farshad Farshidfar, Reanne Bowlby, Mirazul Islam, Jaegil Kim, Walid Chatila, Rehan Akbani, Rupa S. Kanchi, Charles S. Rabkin, Joseph E. Willis, Kenneth K. Wang, Shannon J. McCall, Lopa Mishra, Akinyemi I. Ojesina, Susan Bullman, Chandra Sekhar Pedamallu, Alexander J. Lazar, Ryo Sakai, TCGA consortium, Vésteinn Thorsson, Adam J. Bass and Peter W. Laird
    Cancer Cell, 33(4):721-735, April 2018
    URL: https://www.sciencedirect.com/science/article/pii/S1535610818301144
  • Integrated genomic characterization of oesophageal carcinoma
    The Cancer Genome Atlas Research Network
    Nature, 541(7636), January 2017
    URL: https://www.nature.com/articles/nature20805
  • Canonical correlation analysis for gene-based pleiotropy discovery
    Jose A. Seoane, Colin Campbell, Ian N. M. Day, Juan P. Casas, Tom R. Gaunt
    PLoS Computational Biology, 10(10), October 2014
    URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003876
  • A pathway-based data integration framework for prediction of disease progression
    Jose A. Seoane, Ian N. M. Day, Tom R. Gaunt, Colin Campbell
    Bioinformatics, 30(6):838-845, March 2014
    URL: https://academic.oup.com/bioinformatics/article-abstract/30/6/838/285849