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. Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-lineage Acute Lymphoblastic Leukemia.
    Wu W#, Zhang J#, Sun H, Wu X, Wang H, Cui B, Zhao S, Wu K, Pan Y, Fan R, Zhong Y, Wang X, Wang Y, Chen X, Rao J, Wang R, Luo K, Liu X, Zheng L, Shen S, Yin M*, Xie Y*, Liu Y*. Genomics Proteomics Bioinformatics, 2025

  2. Integrated proteogenomic characterization of ampullary adenocarcinoma.
    Zhang Q#, Xu X#, Jiang D#, Wang Y#, Wang H#, Zhu J, Tang S, Wang R, Zhao S, Li K, Feng J, Xiang H, Yao Z, Xu N, Fang R, Guo W, Liu Y*, Hou Y*, Ding C*. Cell Discovery, 2025

  3. Novel molecular subtypes of intracranial germ cell tumours expand therapeutic opportunities.
    Li B#, Zhao S#, Li S, Li C, Liu W, Li L, Cui B, Liu X, Chen H, Zhang J, Ren Y, Liu F, Yang M, Tao J, Liu Y*, Qiu X*. Neuro-Oncology, 2024

  4. circRNAs as prognostic markers in pediatric acute myeloid leukemia.
    Sun H#, Xie Y#, Wu X, Hu W, Chen X, Wu K, Wang H, Zhao S, Shi Q, Wang X, Cui B, Wu W, Fan R, Rao J, Wang R, Wang Y,Zhong Y, Yu H, Zhou B, Shen S*, Liu Y*. Cancer Letters, 2024

  5. Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia.
    Wang H#, Sun H#, Liang B, Zhang F, Yang F, Cui B, Ding L, Wang X, Wang R, Cai J, Tang Y, Rao J, Hu W, Wu W, Chen X, Wu K, Lai J, Xie Y, Li B, Tang J, Shen S*, Liu Y*. Nature Communications, 2023

  6. Front- and Rear-driving Patterns of Tumor Thrombus Progression in Clear Cell Renal Cell Carcinoma.
    Xie R#, Sun H#, Zhao S, Chen H, Jiang W, Dong X, Shang B, Bi X, Gao Y, Liu Y*, Shou J*. European Urology, 2022

  7. Distinct genomic landscape of Chinese pediatric acute myeloid leukemia impacts clinical risk classification.
    Liu T#, Rao J#, Hu W#, Cui B, Cai J, Liu Y, Sun H, Chen X, Tang Y, Chen J, Wang X, Wang H, Qian W, Mao B, Guo S, Wang R, Liu Y*, Shen S*. Nature Communications, 2022

  8. 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

  9. 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

Before 2018

  1. 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

  2. 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

  3. 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

  4. 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