Selected publications:

• Incomplete paralog compensation generates selective dependency on TRA2A in cancer.
  Lee AR, Tangiyan A, Singh I, Choi PS.
  PLOS Genetics. 2025 May 14;21(5):e1011685.

• Machine learning-optimized targeted detection of alternative splicing.
  Yang K, Islas N, Jewell S, Wu D, Jha A, Radens CM, Pleiss JA, Lynch KW, Barash Y*, Choi PS*.
  Nucleic Acids Research. 2024 Dec 27:gkae1260.

• A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer.
  Tang S*, Sethunath V*, Metaferia NY, Nogueira MF, Gallant DS, Garner ER, Lairson LA, Penney CM, Li J, Gelbard MK, Alaiwi SA, Seo J, Hwang JH, Strathdee CA, Baca SC, AbuHammad S, Zhang X, Doench JG, Hahn WC, Takeda DY, Freedman ML, Choi PS*, Viswanathan SR*.
  Cell Reports. 2022 Feb 22;38(8):110417.

• RNA-binding proteins of COSMIC importance in cancer.
  Choi PS, Thomas-Tikhonenko A.
  Journal of Clinical Investigation. 2021 Sep 15;131(18). Review.

• An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer.
  Li J*, Choi PS*, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC.
  Elife. 2018 Jul 30; 7.

• Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers.
  Zhang X*, Choi PS*, Francis JM*, Imielinski M, Watanabe H, Cherniack AD, Meyerson M.
  Nature Genetics. 2016; 48(2):176-82.

• Targeted genomic rearrangements using CRISPR/Cas technology.
  Choi PS, Meyerson M.
  Nature Communications. 2014; 5:3728.

• Addiction to multiple oncogenes can be exploited to prevent the emergence of therapeutic resistance.
  Choi PS, Li Y, Felsher DW.
  PNAS. 2014; 111(32):E3316-24.

• Lymphomas that recur after MYC suppression continue to exhibit oncogene addiction.
  Choi PS*, van Riggelen J*, Gentles AJ, Bachireddy P, Rakhra K, Adam SJ, Plevritis SK, Felsher DW.
  PNAS. 2011; 108(42):17432-7.

  *equal contribution

Other publications:

• A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer.
  Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD, Zhang X.
  Nature Communications. 2021 Dec 8;12(1):7139.

• Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers.
  Liu Y, Guo B, Aguilera-Jimenez E, Chu VS, Zhou J, Wu Z, Francis JM, Yang X, Choi PS, Bailey SD, Zhang X.
  Cancer Research. 2020 Dec 15;80(24):5464-5477.

• Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma.
  Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M, Zhang X.
  Molecular Cancer Research. 2020 Apr;18(4):574-584.

• Identification and Characterization of Oncogenic SOS1 Mutations in Lung Adenocarcinoma.
  Cai D, Choi PS, Gelbard M, Meyerson M.
  Molecular Cancer Research. 2019 Apr;17(4):1002-1012.

• Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells.
  Gannon HS, Zou T, Kiessling MK, Gao GF, Cai D, Choi PS, Ivan AP, Buchumenski I, Berger AC, Goldstein JT, Cherniack AD, Vazquez F, Tsherniak A, Levanon EY, Hahn WC, Meyerson M.
  Nature Communications. 2018 Dec 21;9(1):5450.

• Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer.
  Viswanathan SR, Nogueira MF, Buss CG, Krill-Burger JM, Wawer MJ, Malolepsza E, Berger AC, Choi PS, Shih J, Taylor AM, Tanenbaum B, Pedamallu CS, Cherniack AD, Tamayo P, Strathdee CA, Lage K, Carr SA, Schenone M, Bhatia SN, Vazquez F, Tsherniak A, Hahn WC, Meyerson M.
  Nature Genetics. 2018 Jul;50(7):937-943.

• Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.
  Zhang X, Choi PS, Francis JM, Gao GF, Campbell JD, Ramachandran A, Mitsuishi Y, Ha G, Shih J, Vazquez F, Tsherniak A, Taylor AM, Zhou J, Wu Z, Berger AC, Giannakis M, Hahn WC, Cherniack AD, Meyerson M.
  Cancer Discovery. 2018 Jan;8(1):108-125.

• MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma.
  Lu X, Peled N, Greer J, Wu W, Choi P, Berger AH, Wong S, Jen KY, Seo Y, Hann B, Brooks A, Meyerson M, Collisson EA.
  Cancer Research. 2017 Aug 15;77(16):4498-4505.

• Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability.
  Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R.
  Elife. 2017 Feb 8;6. doi: 10.7554/eLife.23268.

• BIM mediates oncogene inactivation-induced apoptosis in multiple transgenic mouse models of acute lymphoblastic leukemia.
  Li Y, Deutzmann A, Choi PS, Fan AC, Felsher DW.
  Oncotarget. 2016 May 10;7(19):26926-34.

• Identification of cancer-cytotoxic modulators of PDE3A by predictive chemogenomics.
  de Waal L, Lewis TA, Rees MG, Tsherniak A, Wu X, Choi PS, Gechijian L, Hartigan C, Faloon PW, Hickey MJ, Tolliday N, Carr SA, Clemons PA, Munoz B, Wagner BK, Shamji AF, Koehler AN, Schenone M, Burgin AB, Schreiber SL, Greulich H, Meyerson M.
  Nature Chemical Biology. 2016 Feb;12(2):102-8.

• Activation of Cre recombinase alone can induce complete tumor regression.
  Li Y, Choi PS, Casey SC, Felsher DW.
  PLoS One. 2014;9(9):e107589.

• MYC through miR-17-92 suppresses specific target genes to maintain survival, autonomous proliferation, and a neoplastic state.
  Li Y, Choi PS, Casey SC, Dill DL, Felsher DW.
  Cancer Cell. 2014 Aug 11;26(2):262-72.

• A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events.
  Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M.
  PLoS One. 2014;9(1):e87361.

• Survival and death signals can predict tumor response to therapy after oncogene inactivation.
  Tran PT, Bendapudi PK, Lin HJ, Choi P, Koh S, Chen J, Horng G, Hughes NP, Schwartz LH, Miller VA, Kawashima T, Kitamura T, Paik D, Felsher DW.
  Science Translational Medicine. 2011 Oct 5;3(103):103ra99.

• The interaction between Myc and Miz1 is required to antagonize TGFbeta-dependent autocrine signaling during lymphoma formation and maintenance.
  van Riggelen J, Müller J, Otto T, Beuger V, Yetil A, Choi PS, Kosan C, Möröy T, Felsher DW, Eilers M.
  Genes and Development. 2010 Jun 15;24(12):1281-94.

• Flowing cells through pulsed electric fields efficiently purges stem cell preparations of contaminating myeloma cells while preserving stem cell function.
  Craiu A, Saito Y, Limon A, Eppich HM, Olson DP, Rodrigues N, Adams GB, Dombkowski D, Richardson P, Schlossman R, Choi PS, Grogins J, O’Connor PG, Cohen K, Attar EC, Freshman J, Rich R, Mangano JA, Gribben JG, Anderson KC, Scadden DT.
  Blood. 2005 Mar 1;105(5):2235-8.

• P2Y-like receptor, GPR105 (P2Y14), identifies and mediates chemotaxis of bone-marrow hematopoietic stem cells.
  Lee BC, Cheng T, Adams GB, Attar EC, Miura N, Lee SB, Saito Y, Olszak I, Dombkowski D, Olson DP, Hancock J, Choi PS, Haber DA, Luster AD, Scadden DT.
  Genes and Development. 2003 Jul 1;17(13):1592-604.

Link to complete list of publications