2018

  • Jiang P., Sellers W., Liu, XS. Big Data Approaches for Modeling Response and Resistance to Cancer Drugs. Annual Review of Biomedical Data Science, 2018 1:1, 1-27 
  • Köster J., Brown M., Liu, XS. (2018). A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinformatics 2018; epub Oct 15
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  • Chen CH., Xiao T., Xu H., Jiang P., Meyer CA., Li W., Brown M., Liu XS. Improved design and analysis of CRISPR knockout screens. Bioinformatics, 2018 Dec 1;34(23):4095-4101.
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  • Zheng R., Wan C., Mei S., Qin Q., Wu Q., Sun H., Chen CH., Brown M., Zhang X., Meyer CA., Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res. 2018 Nov 20. (epub)
    [Abstract] [Full Paper]
  • Hu X., Zhang J., Liu JS., Li B., Liu XS.Evaluation of immune repertoire inference methods from RNA-seq data. Nat Biotechnol. 2018 Nov 9;36(11):1034.
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  • Zhang X., Xiao W., Hu X. Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. PLoS One. 2018 Apr 10;13(4):e0195410.
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  • Jiang P., Gu S., Pan D., Fu J., Sahu A., Hu X., Li Z., Traugh N., Bu X., Li B., Liu J., Freeman GJ., Brown MA., Wucherpfennig KW., Liu XS. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response Nat Med. 2018; epub August 20. 
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  • Cader FZ, Schackmann RCJ, Hu X, Wienand K, Redd R, Chapuy B, Quyang J, Paul N, Gjini E, Lipshitz M, Armand P, Wu D, Fromm JR, Neuberg D, Liu XS, Rodig SJ, Shipp MA. Mass cytometry of Hodgkin lymphoma reveals a CD4+ exhausted T-effector and T-regulatory cell rich microenvironment. Blood 2018;epub June 7. 
    [Abstract] [Full Paper]
  • Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M*, Liu XS*. Improved design and analysis of CRISPR knockout screens. Bioinformatics 2018;epub June 1. 
    [Abstract] [Full Paper]
  • Jeselsohn R, Bergholz JS, Pun M, Cornwell M, Liu W, Nardone A, Xiao T, Li W, Qiu X, Buchwalter G, Feiglin A, Abell-Hart K, Fei T, Rao P, Long H, Kwiatkowski N, Zhang T, Gray N, Melchers D, Houtman R, Liu XS, Cohen O, Wagle N, WIner EP, Zhao J, Brown M. Allele-specific chromatin recruitment and therapeutic vulnerabilities of ESR1 activating mutations. Cancer Cell 2018;33(2):173-186. 
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  • Jiang P, Lee W, Li X, Johnson C, Liu JS, Brown M, Aster JC*, Liu XS*. Genome-scale signatures of gene interaction from compound screens predict clinical efficacy of targeted cancer therapies. Cell Syst 2018;6(3):343-354. 
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  • Cornwell M*, Vangala M*, Taing L*, Herbert Z, Koster J, Li B, Sun H, Li T, Zhang J, Qiu X, Pun M, Jeselsohn R, Brown M, Liu XS, Long HW#. Visualization pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinformatics 2018;19(1):135. 
    [Abstract] [Full Paper]
  • Chen D, Fang L, Mei S, Li H, Xu X, Des Marais TL, Lu K, Liu XS, Jin C. Erratum: Regulation of chromatin assembly and cell transformation by formaldehyde exposure in human cells. Environ Health Perspect 2018;126(1):019001. 
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  • Sun T, Du SY, Armenia J, Qu F, Fan J, Wang X, Fei T, Komura K. Liu Xs, Lee GSM, Kantoff PW. Expression of IncRNA MIR222HG co-transcribed from the miR-221/222 gene promoter facilitates the development of castration-resistant prostate cancer. Oncogenesis 2018; 7(3):30. 
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  • Pan D*, Kobayashi A*, Jiang P*, Ferrari de Andrade L, Tay RE, Luoma A, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan GC, Doench J, Brown M, Liu XS#, Wucherpfennig KW#. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 2018; 359(6377):770-5.
    [Abstract] [Full Paper]


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