Cancer Computational Biology Group

More relevant publications 2023

• 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.

All 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..
• 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
• 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
• 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
• 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
• 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