Jose Antonio Seoane
joseaseoane@vhio.net
Current position
- Group Leader of VHIO´s Cancer Computational Biology Group
Academic Qualifications
- 2023 Consolidación Investigadora Grant from the State Investigation Agency (Agencia Estatal de Investigación – AEI).
- 2021 Ramón y Cajal Investigator
- 2019-2021 Instructor at Stanford University School of Medicine (PI: Christina Curtis)
- 2014-2019 Postdoctoral Research Scholar at Stanford University School of Medicine (PI: Christina Curtis)
- 2012-2014 Postdoctoral Research Assistant in Bioinformatics at University of Bristol (PI: Tom Gaunt)
- 2012 PhD in Computer Science by the Universidade da Coruña
- 2010 MSc in Statistical Learning and Data Mining by the UNED
- 2008 MSc in Computer Science by the Universidade da Coruña
- 2004 Degree in Computer Engineering by the Universidade da Coruña
Areas of Research
- Multi-omic data integration
- Epigenetic alterations in cancer
- Biomedical data science
Prizes and Scholarships
- Ramón y Cajal Grant (2021-2025)
- Susan G Komen PDF Basic Translational Grant (2016-2019)
- 2012 Extraordinary PhD award in Mathematics and Computer Science
Projects
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
Identificación in Silico de Respuesta a fármacos especifica de metastasis
Entidad Financiadora: MCIN/AEI/10.13039/501100011033
Ref: CNS2022-135424
Periodo de Ejecución: 01/09/2023 – 31/08/2025. PI: Jose Antonio Seoane
Grant funded by the European Union NextGenerationEU/Plan de Recuperación, Transformación y Resilencia (PRTR)
Most relevant scientific publications
- Salahudeen AA, Seoane JA, Yuki K, Mah AT, Smith AR, Kolahi K, De la O SM, Hart DJ, Ding J, Ma Z, Barkal SA, Shukla ND, Zhang CH, Cantrell MA, Batish A, Usui T, Root DE, Hahn WC, Curtis C, Kuo CJ. Functional screening of amplification outlier oncogenes in organoid models of early tumorigenesis. Cell Rep. 2023 Nov 28;42(11):113355.
- Kaiser AM, Gatto A, Hanson KJ, Zhao RL, Raj N, Ozawa MG, Seoane JA, Bieging-Rolett KT, Wang M, Li I, Trope WL, Liou DZ, Shrager JB, Plevritis SK, Newman AM, Van Rechem C, Attardi LD. p53 governs an AT1 differentiation programme in lung cancer suppression. Nature. 2023 Jul;619(7971):851-859.
- Strand SH, Rivero-Gutiérrez B, Houlahan KE, Seoane JA, King LM, Risom T, Simpson LA, Vennam S, Khan A, Cisneros L, Hardman T, Harmon B, Couch F, Gallagher K, Kilgore M, Wei S, DeMichele A, King T, McAuliffe PF, Nangia J, Lee J, Tseng J, Storniolo AM, Thompson AM, Gupta GP, Burns R, Veis DJ, DeSchryver K, Zhu C, Matusiak M, Wang J, Zhu SX, Tappenden J, Ding DY, Zhang D, Luo J, Jiang S, Varma S, Anderson L, Straub C, Srivastava S, Curtis C, Tibshirani R, Angelo RM, Hall A, Owzar K, Polyak K, Maley C, Marks JR, Colditz GA, Hwang ES, West RB. Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts. Cancer Cell. 2022 Dec 12;40(12):1521-1536.e7.
- Nobre AR, Dalla E, Yang J, Huang X, Wullkopf L, Risson E, Razghandi P, Anton ML, Zheng W, Seoane JA, Curtis C, Kenigsberg E, Wang J, Aguirre-Ghiso JA. ZFP281 drives a mesenchymal-like dormancy program in early disseminated breast cancer cells that prevents metastatic outgrowth in the lung. Nat Cancer. 2022 Oct;3(10):1165-1180.
- Raj N, Wang M, Seoane JA, Zhao RL, Kaiser AM, Moonie NA, Demeter J, Boutelle AM, Kerr CH, Mulligan AS, Moffatt C, Zeng SX, Lu H, Barna M, Curtis C, Chang HY, Jackson PK, Attardi LD. The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Mol Cell. 2022 Jul 7;82(13):2370-2384.e10.
- Liñares-Blanco J, Fernandez-Lozano C, Seoane JA, López-Campos G. Machine Learning Based Microbiome Signature to Predict Inflammatory Bowel Disease Subtypes. Front Microbiol. 2022 May 17;13:872671
- 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 & Michael C. Bassik
Nature, Sep. 2021 - 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, Jun 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 ,, Apr. 2021 - 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 - 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, Jan. 2021 - 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 ,, Nov. 2020 - 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, Sep. 2020 - 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 - 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 - 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, Nov. 2020 - 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, Nov. 2019 - 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, Jul. 2019 - 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, Mar. 2019 - 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, Mar. 2019 - The chromatin accessibility landscape of primary human cancers
M 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 AA Castro, Benjamin P Berman, Louis M Staudt, Jean C Zenklusen, Peter W Laird, Christina Curtis, William J Greenleaf, Howard Y Chang
Science, 362(6413), Oct. 2018 - 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, VésteinnThorsson, Adam J.Bass and Peter W.Laird
Cancer Cell, 33(4):721-735, April 2018 - Integrated genomic characterization of oesophageal carcinoma
The Cancer Genome Atlas Research Network
Nature, 541(7636), Jan. 2017 - Canonical correlation analysis for gene-based pleiotropy discovery
Jose A Seoane, Colin Campbell, Ian NM Day, Juan P Casas, Tom R Gaunt
PLoS Computational Biology, 10(10), Oct. 2014 - A pathway-based data integration framework for prediction of disease progression
Jose A Seoane, Ian NM Day, Tom R Gaunt, Colin Campbell
Bioinformatics, 30(6):838-845, Mar. 2014
