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Beisi Xu, PhD

Beisi Xu, PhD

  • Group Lead, Epigenetics


PhD, Polymer - University of Science and Technology of China
Research Fellowship, Bioinformatics - Indiana University-Purdue University at Indianapolis
BS, Polymer - University of Science and Technology of China


Beisi (pronounce /bās/ as bass) is a highly motivated, skilled, communicative, independent and team-oriented PhD biologist with over 10 years of bioinformatics experience (who did not know how to play bass). He has extensive expertise in Epigenomics, Cancer Biology, Developmental Biology, and High Performance Computation.

Research Interests

  • Evaluate and design bioinformatics pipelines for epigenetics Next Generation Sequencing (NGS) data analysis (include but not limited to ChIP-seq, RNA-seq, ATAC-seq, Hi-C, scRNA-seq, scATAC-seq, Cut-and-Run, SLAM-Seq, ChromHMM, MNase-Seq, WGBS/RRBS, DNase-Seq, FAIRE-seq, HiCHIP, PLAC-Seq, CaptureC, 4C-seq, dCas9-ChIPseq).
  • Establish tools/workflows to empower researchers to explore their results easily either by interactive tables or visualization apps.
  • Investigate and understand epigenetics regulation mechanisms in carcinogenesis, development and innate immune response.

Selected Publications

Zong X, Hao X, Xu B, Crawford JC, Wright S, Li J, Zhang Y, Bai L, He M, Jiang M, Fan Y, Connelly JP, Pruett-Miller SM, Berns H, Janke L, Li C, Feng Y.  Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity. J Exp Med 218(8), 2021.

Montefiori LE, Bendig S, Gu Z, Chen X, Polonen P, Ma X, Murison A, Zeng A, Garcia-Prat L, Dickerson K, Iacobucci I, Abdelhamed S, Hiltenbrand R, Mead PE, Mehr CM, Xu B, Cheng Z, Chang TC, Westover T, Ma J, Stengel A, Kimura S, Qu C, Valentine MB, Rashkovan M, Luger S, Litzow MR, Rowe JM, den Boer ML, Wang V, Yin J, Kornblau SM, Hunger SP, Loh ML, Pui CH, Yang W, Crews KR, Roberts KG, Yang JJ, Relling MV, Evans WE, Stock W, Paietta EM, Ferrando AA, Zhang J, Kern W, Haferlach T, Wu G, Dick JE, Klco JM, Haferlach C, Mullighan CG. Enhancer hijacking drives oncogenic BCL11B expression in lineage ambiguous stem cell leukemia. Cancer Discov 2021.

Dikiy S, Li J, Bai L, Jiang M, Janke L, Zong X, Hao X, Hoyos B, Wang ZM, Xu B, Fan Y, Rudensky AY, Feng Y. A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance. Immunity Apr 6, 2021.

Rai M, Coleman Z, Curley M, Nityanandam A, Platt A, Robles-Murguia M, Jiao J, Finkelstein D, Wang YD, Xu B, Fan Y, Demontis F. Proteasome stress in skeletal muscle mounts a long-range protective response that delays retinal and brain aging. Cell Metab Mar 23, 2021.

Williams J, Xu B, Putnam D, Thrasher A, Li C, Yang J, Chen X. MethylationToActivity: A deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors. Genome Biol 22(1):24, 2021.

Xu P, Scott DC, Xu B, Yao Y, Feng R, Cheng L, Mayberry K, Bi W, Palmer LE, King MT, Wang H, Li Y, Fan Y, Alpi AF, Li C, Peng J, Papizan J, Pruett-Miller SM, Spallek R, Bassermann F, Cheng Y, Schulman BA, Weiss MJ. FBXO11-Mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis. Blood Nov 6;blood.2020007809, 2020.  doi: 10.1182/blood.2020007809. Online ahead of print.

Zhang H, Zhang Y, Zhou X, Wright S, Hyle J, Zhao L, An J, Zhao X, Shao Y, Xu B, Lee HM, Chen T, Zhou Y, Chen X, Lu R, Li C. Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen. Elife. Oct 1;9:e57858, 2020. doi: 10.7554/eLife.57858. Online ahead of print.

Xu B*, Mulvey B*, Salie M, Yang X, Matsui Y, Nityanandam A, Fan Y, Peng JC. UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells. Epigenetics Chromatin 13(1):38, 2020.

Wei, J., Long, L., Zheng, W., Dhungana, Y., Lim, S. A., Guy, C., … Xu, B., ..., Chi, H. (2019). Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature. 1–6. DOI: 10.1038/s41586-019-1821-z.

Robles-Murguia, M., Rao, D., Finkelstein, D., Xu, B., Fan, Y., & Demontis, F. (2019). Muscle-derived Dpp regulates feeding initiation via endocrine modulation of brain dopamine biosynthesis. Genes Dev.  DOI: 10.1101/gad.329110.119.

Norrie, J.*, Lupo, M.*, Xu, B.*, AlDiri, I.*, Valentine, M.*, Putnam, D.*, Griffiths, L., Lupo, M., Norrie, J., Zhang, J., Johnson, D., ..., Chen, X., Dyer, M. A. (2019). Nucleome Dynamics during Retinal DevelopmentNeuron, DOI: 10.1016/j.neuron.2019.08.002.

Hyle, J., Zhang, Y., Wright, S., Xu, B., Shao, Y., Easton, J., Tian, L., Feng, R., Xu, P., and Li, C. (2019) Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping. Nucleic Acids Res. 47. 6699DOI: 10.1093/nar/gkz462.

Yang, X.*, Xu, B.*, Mulvey, B., Evans, M., Jordan, S., Wang, Y.-D., … Peng, J. C. (2019). Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1. Nature Neuroscience. 22, 362. DOI: 10.1038/s41593-018-0328-5.

Karmaus, P. W. F., Chen, X., Lim, S. A., Herrada, A. A., Nguyen, T.-L. M., Xu, B., …, Chi, H. (2019). Metabolic heterogeneity underlies reciprocal fates of T H 17 cell stemness and plasticity. Nature. 565, 101. DOI: 10.1038/s41586-018-0806-7.

Larson, J. D., Kasper, L. H., Paugh, B. S., Jin, H., Wu, G., Kwon, C.-H., … Xu, B., …, Baker, S. J. (2019). Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell. 35, 140-155.e7.  DOI: 10.1016/j.ccell.2018.11.015.

Silveira, A. B., Kasper, L. H., Fan, Y., Jin, H., Wu, G., Shaw, T. I., … Xu, B., …, Baker, S. J. (2019). H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathol. 137, 637–655.  DOI: 10.1007/s00401-019-01975-4.

Tian, L., Shao, Y., Nance, S., Dang, J., Xu, B., Ma, X., … Zhang, J. (2019). Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia. Nature Communications. 10, 2789. DOI: 10.1038/s41467-019-10637-8.

Wang, L.*, Hiler, D.*, Xu, B.*, AlDiri, I., Chen, X., Zhou, X., … Dyer, M. A. (2018). Retinal Cell Type DNA Methylation and Histone Modifications Predict Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures. Cell Reports. 22, 2601–2614. DOI: 10.1016/j.celrep.2018.01.075.

Alexander, T. B., Gu, Z., Iacobucci, I., Dickerson, K., Choi, J. K., Xu, B., … Mullighan, C. G. (2018). The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature. 562, 373. DOI: 10.1038/s41586-018-0436-0.

Stewart, E., McEvoy, J., Wang, H., Chen, X., Honnell, V., Ocarz, M., … Xu, B., …, Dyer, M. A. (2018). Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell. DOI: 10.1016/j.ccell.2018.07.012.

Zimmerman, M. W., Liu, Y., He, S., Durbin, A. D., Abraham, B. J., Easton, J., … Xu, B., …, Young, R. A., Zhang, J., Look, A. T. (2018). MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification. Cancer Discov. 8, 320–335. doi: 10.1158/2159-8290.CD-17-0993.

Lavado, A., Park, J. Y., Paré, J., Finkelstein, D., Pan, H., Xu, B., …, Cao, X. (2018). The Hippo Pathway Prevents YAP/TAZ-Driven Hypertranscription and Controls Neural Progenitor Number. Developmental Cell. 47, 576-591.e8. doi: 10.1016/j.devcel.2018.09.021.

Vo, B. T., Kwon, J. A., Li, C., Finkelstein, D., Xu, B., Orr, B. A., …, Roussel, M. F. (2018). Mouse medulloblastoma driven by CRISPR activation of cellular Myc. Scientific Reports. 8, 8733. doi: 10.1038/s41598-018-24956-1.

Aldiri, I.*, Xu, B.*, Wang, L., Chen, X., Hiler, D., Griffiths, L., …, Dyer, M. A. (2017). The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis. Neuron. 94, 550-568.e10. doi: 10.1016/j.neuron.2017.04.022.

Stewart, E., Federico, S. M., Chen, X., Shelat, A. A., Bradley, C., Gordon, B., … Xu, B., …, Dyer, M. A. (2017). Orthotopic patient-derived xenografts of paediatric solid tumours. Nature. 549, 96. DOI: 10.1038/nature23647.

Zhang, J., McCastlain, K., Yoshihara, H., Xu, B., Chang, Y., Churchman, M. L., …, Mullighan, C. G., PCGP. (2016). Deregulation of DUX4 and ERG in acute lymphoblastic leukemia. Nat Genet. 48, 1481–1489. doi: 10.1038/ng.3691.

Hiler, D., Chen, X., Hazen, J., Kupriyanov, S., Carroll, P. A., Qu, C., Xu, B., …, Dyer, M. A. (2015). Quantification of Retinogenesis in 3D Cultures Reveals Epigenetic Memory and Higher Efficiency in iPSCs Derived from Rod Photoreceptors. Cell Stem Cell. 17, 101–115. doi: 10.1016/j.stem.2015.05.015.

Jose, C. C.*, Xu, B.*, Jagannathan, L., Trac, C., Mallela, R. K., Hattori, T., …, Schones, D. E., Cuddapah, S. (2014). Epigenetic dysregulation by nickel through repressive chromatin domain disruption. PNAS. 111, 14631–14636. doi: 10.1073/pnas.1406923111.

Full List of Publications

Last update: June 2021