Selected Publications

Please see Google Scholar for a full list of publications. (# for equal contribution, * for corresponding authors, bold and italic for lab members.)

  1. Discovery of Regulatory Noncoding Variants in Individual Cancer Genomes by Using cis-X.
    Liu Y#*, Li C#, Shen S#, Chen X, Szlachta K, Edmonson MN, Shao Y, Ma X, Hyle J, Wright S, Ju B, Rusch MC, Liu Y, Li B, Macias M, Tian L, Easton J, Qian M, Yang JJ, Hu S, Look AT, Zhang J*. Nature Genetics, 2020

  2. Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia.
    Li B#, Brady SW#, Ma X#, Shen S#, Zhang Y#, Li Y#, Szlachta K, Dong L, Liu Y, Yang F, Wang N, Flasch DA, Myers MA, Mulder HL, Ding L, Liu Y, Tian L, Hagiwara K, Xu K, Zhou X, Sioson E, Wang T, Yang L, Zhao J, Zhang H, Shao Y, Sun H, Sun L, Cai J, Sun HY, Lin TN, Du L, Li H, Rusch M, Edmonson MN, Easton J, Zhu X, Zhang J, Cheng C, Raphael BJ, Tang J, Downing JR, Alexandrov LB, Zhou BS*, Pui CH*, Yang JJ*, Zhang J*. Blood, 2020

  3. Pan-cancer genome and transcriptome analyses of 1,699 pediatric leukemias and solid tumors.
    Ma X#, Liu Y#, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J*. Nature, 2018

  4. MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification.
    Zimmerman MW#, Liu Y#, He S, Durbin AD, Abraham BJ, Easton J, Shao Y, Xu B, Zhu S, Zhang X, Li Z, Weichert-Leahey N, Young RA*, Zhang J*, Look AT*. Cancer Discovery, 2018

  5. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Bolouri H#*, Farrar JE#, Triche T Jr#, Ries RE#, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S*. Nature Medicine, 2018

  6. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia.
    Liu Y#, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, McCastlain K, Edmonson M, Pounds SB, Shi L, Zhou X, Ma X, Sioson E, Li Y, Rusch M, Gupta P, Pei D, Cheng C, Smith MA, Auvil JG, Gerhard DS, Relling MV, Winick NJ, Carroll AJ, Heerema NA, Raetz E, Devidas M, Willman CL, Harvey RC, Carroll WL, Dunsmore KP, Winter SS, Wood BL, Sorrentino BP, Downing JR, Loh ML, Hunger SP*, Zhang J*, Mullighan CG*. Nature Genetics, 2017

  7. APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL.
    Li Z, Abraham BJ, Berezovskaya A, Farah N, Liu Y, Leon T, Fielding A, Tan SH, Sanda T, Weintraub AS, Li B, Shen S, Zhang J, Mansour MR*, Young RA*, Look AT*. Leukemia, 2017

  8. Small genomic insertions form enhancers that misregulate oncogenes.
    Abraham BJ, Hnisz D, Weintraub AS, Kwiatkowski N, Li CH, Li Z, Weichert-Leahey N, Rahman S, Liu Y, Etchin J, Li B, Shen S, Lee TI, Zhang J, Look AT*, Mansour MR*, Young RA*. Nature Communications, 2017

  9. Genomic heterogeneity of multiple synchronous lung cancer.
    Liu Y#, Zhang J#, Li L#, Yin G#, Zhang J#, Zheng S, Cheung H, Wu N, Lu N, Mao X, Yang L, Zhang J, Zhang L, Seth S, Chen H, Song X, Liu K, Xie Y, Zhou L, Zhao C, Han N, Chen W, Zhang S, Chen L, Cai W, Li L, Shen M, Xu N, Cheng S, Yang H, Lee JJ, Correa A, Fujimoto J, Behrens C, Chow CW, William WN, Heymach JV, Hong WK, Swisher S, Wistuba II, Wang J, Lin D, Liu X, Futreal PA*, Gao Y*. Nature Communications, 2016

  10. Exploring genomic alteration in pediatric cancer using ProteinPaint.
    Zhou X, Edmonson MN, Wilkinson MR, Patel A, Wu G, Liu Y, Li Y, Zhang Z, Rusch MC, Parker M, Becksfort J, Downing JR, Zhang J*. Nature Genetics, 2016