Publications

Yu W, Biyik-Sit R, Uzun Y, Chen CH, Thadi A, Sussman JH, Pang M, Wu C, Grossmann LD, Gao P, Wu D, Yousey A, Zhang M, Turn CS, Zhang Z, Bandyopadhyay S, Huang J, Patel T, Chen C, Martinez D, Surrey L, Hogarty MD, Bernt K, Zhang N, Maris J, Tan K: Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring. Nature Genetics Apr 2025.

Xu J, Chen C, Sussman JH, Yoshimura S, Vincent T, Polonen P, Hu J, Bandyopadhyay S, Elghawy O, Yu W, Timulty J, Chen C, Li EY, Diorio C, Shraim R, Newman H, Uppuluri L, Li A, Chen GM, Wu DW, Ding Y, Xu JA, Karanfilovski D, Lim T, Hus M, Thadi A, Ahn KJ, Wu C, Peng J, Sun Y, Wang A, Mehta R, Frank D, Meyer L, Loh ML, Raetz EA, Chen Z, Wood BL, Devidas M, Dunsmore KP, Winter SS, Chang T, Wu G, Pounds SB, Zhang NR, Carroll W, Hunger SP, Bernt K, Yang JJ, Mullighan CG, Tan K, Teachey DT.: A multiomic atlas identifies a treatment-resistant, bone marrow progenitor-like cell population in T cell acute lymphoblastic leukemia. Nature Cancer 6(1): 102-122, Jan 2025.

Pang M, Roy TK, Wu X, Tan K: CelloType: A unified model for segmentation and classification of tissue images. Nature Methods 22(2): 348-357, Feb 2025.

Bandyopadhyay S, Duffy M, Ahn K, Sussman J, Pang M, Smith D, Duncan G, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen C, Thadi A, Chen C, Xu J, Reichart M, Martinez Z, Diorio C, Chen C, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, and Tan K.: Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging. Cell 187(12): 3120-3140, Jun 2024.

Hu Y, Rong J, Xu Y, Xie R, Peng J, Gao L, Tan K : Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. Nature Methods 21(2): 267-278, Feb 2024.

Melenhorst JJ, Chen GM, Wang M, Porter DL, Chen C, Collins MA, Gao P, Bandyopadhyay S, Sun H, Zhao Z, Lundh S, Pruteanu-Malinici I, Nobles CL, Maji S, Frey NV, Gill SI, Tian L, Kulikovskaya I, Gupta M, Ambrose DE, Davis MM, Fraietta JA, Brogdon JL, Young RM, Chew A, Levine BL, Siegel DL, Alanio C, Wherry EJ, Bushman FD, Lacey SF, Tan K, June CH: Decade-long leukemia remissions with persistence of CD4+ CAR T-cells. Nature 602(7897): 503-509, Feb 2022.

Chen C, Yu W, Alikarami F, Qiu Q, Chen C, Flournoy J, Gao P, Uzun Y, Fang L, Davenport JW, Hu Y, Zhu Q, Wang K, Libbrecht C, Felmeister A, Rozich I, Ding Y, Hunger SP, Felix CA, Wu H, Brown PA, Guest EM, Barrett DM, Bernt KM, Tan K: Single-cell multiomics reveals increased plasticity, resistant populations and stem-cell-like blasts in KMT2A-rearranged leukemia. Blood 139(14): 2198-2211, Apr 2022.

Chen GM, Chen C, Das RK, Gao P, Chen C, Bandyopadhyay S, Ding Y, Uzun Y, Yu W, Zhu Q, Myers RM, Grupp SA, Barrett DM, Tan K : Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy. Cancer Discovery Apr 2021.

Hu Y, Peng T, Gao L, Tan K: CytoTalk: De novo construction of signal transduction networks using single-cell RNA-Seq data. Science Advances 7(16): eabf1356, Apr 2021.

Zhu Q, Gao P, Tober J, Bennett L, Chen C, Uzun Y, Li Y, Howell ED, Mumau M, Yu W, He B, Speck NA, Tan K: Developmental trajectory of prehematopoietic stem cell formation from endothelium. Blood 136(7): 845-856, Aug 2020.