Publications

(Taylor lab members in bold)

Shih, J., Sarmashghi, S., Zhakula-Kostadinova, N., Zhang, S., Georgis, Y., Hoyt, S. H., Cuoco, M. S., Gao, G. F., Spurr, L. F., Berger, A. C., Ha, G., Rendo, V., Shen, H., Meyerson, M., Cherniack, A. D., Taylor, A. M.*, & Beroukhim, R.* (2023). Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature, 619(7971), 793–800. https://doi.org/10.1038/s41586-023-06266-3

Wang Y, Fan JL, Melms JC, Amin AD, Georgis Y, Barrera I, Ho P, Tagore S, Abril-Rodriguez G, He S, Jin Y, Biermann J, Hofree M, Caprio L, Berhe S, Khan SA, Henick BS, Ribas A, Macosko EZ, Chen F, Taylor AM, Schwartz GK, Carvajal RD, Azizi E, Izar B. Multi-modal single-cell and whole-genome sequencing of small, frozen clinical specimens. Nat Gen. 2023 Jan 9.

Mezghani N, Yao A, Vasilyeva D, Kaplan N, Shackelford A, Yoon A, Philipone E, Dubey S, Schwartz GK, Taylor AM, Momen-Heravi F. Molecular Subtypes of Head and Neck Cancer in Patients of African Ancestry. Clin Cancer Res. 2022 Dec 12:CCR-22-2258.

Tanagala KKK, Morin-Baxter J, Carvajal R, Cheema M, Dubey S, Nakagawa H, Yoon A, Cheng YL, Taylor A, Nickerson J, Mintz A, Momen-Heravi F. SP140 inhibits STAT1 signaling, induces IFN-γ in tumor-associated macrophages, and is a predictive biomarker of immunotherapy response. J Immunother Cancer. 2022 Dec;10(12):e005088.

Galeano Niño JL, Wu H, LaCourse KD, Kempchinsky AG, Baryiames A, Barber B, Futran N, Houlton J, Sather C, Sicinska E, Taylor A, Minot SS, Johnston CD, Bullman S. Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. Nature. 2022 Nov;611(7937):810-817.

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. “A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer.” Nat Commun. 2021 Dec 8;12(1):7139.

Wu X, Cheng YSL, Matthen M, Yoon A, Schwartz GK, Bala S, Taylor AM*, and Momen-Heravi F*. “Down-regulation of the tumor suppressor miR-34a contributes to head and neck cancer by up-regulating the MET oncogene and modulating tumor immune evasion.” J Exp Clin Canc Res. 2021 Feb 17;40(1):70.

Quinton RJ, DiDomizio A, Vittoria MA, Kotýnková K, Ticas CJ, Patel S, Koga Y, Vakhshoorzadeh J, Hermance N, Kuroda TS, Parulekar N, Taylor AM, Manning AL, Campbell JD, Ganem NJ. Whole-genome doubling confers unique genetic vulnerabilities on tumour cells. Nature. 2021 Jan 27;590:492-497.

Spurr LF, Touat M, Taylor AM, Dubuc AM, Shih J, Meredith DM, Pisano WV, Meyerson ML, Ligon KL, Cherniack AD, Li YY, Beroukhim R. Quantification of aneuploidy in targeted sequencing data using ASCETS. Bioinformatics. 2020 Nov 28.

Taylor AM, Macari ER, Chan IT, Blair MC, Doulatov S, Vo LT, Raiser DM, Siva K, Basak A, Pirouz M, Shah AN, McGrath K, Humphries JM, Stillman E, Alter BP, Calo E, Gregory RI, Sankaran VG, Flygare J, Ebert BL, Zhou Y, Daley GQ, Zon LI. Calmodulin inhibitors improve erythropoiesis in Diamond-Blackfan anemia. Sci Trans Med. 2020 Oct 21;12(566):1-11.

Chen H*, Carrot-Zhang J*, Zhao Y, Hu H, Freeman S, Yu S, Ha G, Taylor AM, Berger AC, Westlake L, Zheng Y, Zhang J, Ramachandran A, Zheng Q, Pan Y, Zheng D, Zheng S, Cheng C, Kuang M, Zhou X, Zhang Y, Li H, Ting Y, Ma Y, Gao Z, Tao X, Han H, Shang J, Yu Y, Bao D, Huang Y, Li X, Zhang Y, Xiang J-Q, Sun Y, Li Y, Cherniack AD, Campbell JD, Shi L, and Meyerson M. “Genomic and immune profiling of pre-invasive lung adenocarcinoma." Nat. Commun. 2019 Nov 29;10(1):5472.

Kim M, Mun H, Sung CO, Jo EJ, Jeon HJ, Lee DS, Kim DK, Chun SM, Choi EK, Jeong SY, Taylor AM, Jain S, Meyerson M, and Jang SJ. “Patient-Derived Lung Cancer Organoids as In Vitro Personalized Models for Therapeutic Screening.” Nat. Commun. 2019 Sept;10:1-15.

Viswanathan SR, Nogueira MF, Buss CG, Krill-Burger JM, Wawer MJ, Malolepsza E, Berger AC, Choi PS, Shih J, Taylor AM, Tanenbaum B, Tamayo P, Pedamallu CS, Cherniack AD, Strathdee CA, Lage K, Carr S, Schenone M, Bhatia SN, Vazquez F, Tsherniack A, Hahn WC, Meyerson M. “Genome-scale Analysis Reveals Paralog Lethality as a Vulnerability of Chromosome 1p Loss in Cancer.” Nat Genet. 2018 Jul;50(7):937-943.

Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cancer Genome Atlas Research Network, Cherniack AD, Beroukhim R, Meyerson M. “Genome and Functional Approaches to Cancer Aneuploidy.” Cancer Cell. 2018 Apr 9;33(4):676-689.

Hoadley KA*, Yau C*, Hinoue T*, Wolf DM*, Lazar AJ*, Drill E*, Shen R*, Taylor AM*, Cherniack AD*, Thorsson V*, Akbani R*, Bowlby R*, Wong CK*, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Cancer Genome Atlas Network, Stuart JM, Benz CC, Laird PW. “Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.” Cell. 2018 Apr 5;173(2):291-304.

Ding L*, Bailey MH*, Porta-Pardo E*, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G, Cancer Genome Atlas Research Network. “Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.” Cell. 2018 Apr 5;173(2):305-320.

Campbell JD*, Yau C*, Bowlby R*, Liu Y*, Brennan K*, Fan H*, Taylor AM*, Wang C*, Walter V*, Akbani R*, Byers LA*, Creighton CJ*, Coarfa C*, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. “Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.” Cell Rep. 2018 Apr 3;23(1):194-212.

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

Doulatov S*, Vo LT*, Macari ER*, Wahlster L, Kinney MA, Taylor AM, Barragan J, Gupta M, McGrath K, Lee HY, Humphries JM, DeVine A, Narla A, Alter BP, Beggs AH, Agarwal S, Ebert BL, Gazda HT, Lodish HF, Sieff CA, Schlaeger TM, Zon LI, and Daley GQ. “Drug Discovery for Diamond-Blackfan anemia using Reprogrammed Hematopoietic Progenitors.” Sci Trans Med. 2017 Feb 8;9(376):1-11.

Mirabello L, Macari ER, Jessop L, Ellis SR, Myers T, Giri N, Taylor AM, McGrath KE, Humphries JM, Ballew BJ, Yeager M, Boland JF, He J, Hicks BD, Burdett L, Alter BP, Zon L, Savage SA. “Whole-exome sequencing and functional studies identify RPS29 as a novel gene mutated in multicase Diamond-Blackfan anemia families.” Blood. 2014 Jul 3;124(1):24-32.

Yen J, White RM, Wedge DC, Van Loo P, de Ridder J, Capper A, Richardson J, Jones D, Raine K, Watson IR, Wu CJ, Cheng J, Martincorena I, Nik-Zainal S, Mudie L, Moreau Y, Marshall J, Ramakrishna M, Tarpey P, Shlien A, Whitmore I, Gamble S, Latimer C, Langdon E, Kaufman C, Dovey M, Taylor A, Menzies A, McLaren S, O Meara S, Butler A, Teague J, Lister J, Chin L, Campbell P, Adams DJ, Zon LI, Patton EE, Stemple DL, Futreal PA. “The genetic heterogeneity and mutational burden of engineered melanoma in zebrafish model.” Genome Biol. 2013 Oct 23:14(10):R113.

Taylor AM, Humphries JM, White RM, Murphey RD, Burns CE, Zon LI.  “Hematopoietic defects in rps29 mutant zebrafish depend upon p53 activation.”  Exp Hematol. 2012 Mar;40(3):228-237.