Tan Laboratory Publications

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Below are selected publications from the Tan Lab.

Chen GM, Chen CH, Perazzelli J, Grupp SA, Barrett DM, Tan K. Characterization of Leukemic Resistance to CD19-Targeted CAR T-cell Therapy through Deep Genomic Sequencing. Cancer Immunol Res. 2023 Jan; 11(1):13-19. PMID: 36255409
Melenhorst JJ, Chen GM, Wang M, Porter DL, Chen C, McKensie AC, 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, Davis MM, Fraietta JA, Brogdon JL, Young RM, Ambrose DE, Chew A, Levine BL, Siegel DL, Alanio C, Wherry JE, Bushman FD, Lacey SF, Tan K, June CH. Decade-long remissions of leukemia sustained by the persistence of activated CD4+ CAR T-cells. Nature. 2022 Feb; 602(7897):503-509. PMID: 35110735
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, resistance populations and stem-cell-like blasts in KMT2A-rearranged leukemia. Blood. 2021 Dec; PMID: 34864916. Online ahead of print
Ding YY, et al. Network analysis reveals synergistic genetic dependencies for rational combination therapy in Philadelphia chromosome-like acute lymphoblastic leukemia. Clin Cancer Res. 2021 Sep; 27(18):5109-5122. PMID: 34210682
Hu Y, Peng T, Gao L, Tan K. CytoTalk: de novo construction of signal transduction networks using single-cell RNA-Seq data. Science Advances. 2021 Apr; 7(16):eabf1356. PMID: 33853780
Chen GM, Chen C, Das RK, Gao P, Chen CH, Bandyopadhyay S, Ding YY, 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 Discov. 2021 Apr; PMID: 33820778
Uzun Y, Wu H, Tan K. Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. Genome Res. 2021 Jan; 31(1):101-109. PMID: 33219054
Chen GM, Azzam A, Ding YY, Barrett DM, Grupp SA, Tan K. Dissecting the Tumor-Immune Landscape in Chimeric Antigen Receptor T-cell Therapy: Key Challenges and Opportunities for a Systems Immunology Approach. Clin Cancer Res. 2020 Jul; 26(14): 3505-3513. PMID: 32127393
He B, Gao P, Ding Y, Chen C, Chen GM, Chen C, Kim H, Tasian SK, Hunger SP, Tan K. Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. Science Advances. 2020 Jul; 6(30):eaba3064. PMID: 32832663 PMCID: PMC7439310
Gao P, Chen C, Howell ED, Li Y, Tober J, Uzun Y, He B, Gao L, Zhu Q, Siekmann AF, Speck NA, Tan K. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells. Genes Dev. 2020 Jul; 34(13-14):950-964. PMID: 32499402
Zhu Q, Gao P, Tober J, Bennett L, Chen C, Uzun Y, Li Y, Mumau M, Yu W, He B, Speck NA, Tan K. Developmental trajectory of pre-hematopoietic stem cell formation from endothelium. Blood. 2020 May; blood.2020004801; PMID: 32392346
Yu, W., Uzun, Y., Zhu, Q., Chen, C., & Tan, K. scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data. Genome Bio. 2020 Apr; 21(1):94. PMC7169039
Chen C, Yu W, Tober J, Gao P, He B, Lee K, Trieu T, Blobel GA, Speck NA, Tan K. Spatial genome re-organization between fetal and adult hematopoietic stem cells. Cell Rep. 2019 Dec; 29(12):4200-4211. PMC7262670
Hu Y, Chen CH, Ding YY, Wen X, Wang B, Gao L, Tan K. Optimal control nodes in disease-perturbed networks as targets for combination therapy. Nat Commun. 2019 May; 10(1): 2180. PMID: 31097707
Peng T, Zhu Q, Yin P, Tan K. SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data. Genome Biol. 2019 May; 20(1):88. PMID: 31060596
Gao P, Uzun Y, He B, Salamati SE, Coffey JKM, Tsalikian E, Tan K. Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes. Proc Natl Acad Sci U S A. 2019 Apr; 116(15):7581-7590. PMID: 30910956
Gao L, Uzun Y, Gao P, He B, Ma X, Wang J, Han S, Tan K. Identifying noncoding risk variants using disease-relevant gene regulatory networks. Nat Commun. 2018 Feb; 9(1):702. PMID: 29453388
Yu W, He B, Tan K. Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test. Nat Commun. 2017 Sep; 8(1):535. PMID: 28912419
He B, Xing S, Chen C, Gao P, Teng L, Shan Q, Gullicksrud JA, Martin MD, Yu S, Harty JT, Badovinac VP, Tan K, Xue HH. CD8+ T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections. Immunity. 2016 Dec; 45(6):1341-1354. PMID: 27986453
He B, Chen C, Teng L, and Tan K. Global view of enhancer-promoter interactome in human cells. Proc Natl Acad Sci USA. 2014 May; 111(21):E2191-9. PMID: 24821768