[15] Computational methods and challenges in analyzing intratumoral microbiome data.
Qi Wang, Zhaoqian Liu, Anjun Ma, Zihai Li, Bingqiang Liu, Qin Ma
Trends in Microbiology
[Abstract] [Full paper]
[14] Single-cell biological network inference using a heterogeneous graph transformer.
Anjun Ma*, Xiaoying Wang*, Cankun Wang, Jingxian Li, Tong Xiao, Juexin Wang, Yuzhou Chang, Yang Li, Yuntao Liu, Yuzhou Chang, Duolin Wang, Yuexu Jiang, Jinpu Li, Li Su, Shaopeng Gu, Gang Xin, Zihai Li, Bingqiang Liu$, Dong Xu$, Qin Ma$
Nature Communications
[Abstract] [Full paper] [Editor highlights]
[13] Deep Transfer Learning of Cancer Drug Responses by Integrating Bulk and Single-cell RNA-seq data.
Junyi Chen*, Xiaoying Wang*, Anjun Ma$, Qi-En Wang, Bingqiang Liu, Lang Li, Dong Xu, Qin Ma$
Nature Communications (2022)
[Abstract] [Full paper]
[12] Edison Gu, Hao Cheng, Yang Li, Juexin Wang, Anjun Ma, Dong Xu, Qin Ma. scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. Bioinformatics. (2022). PMID: 36250784
[Abstract][Full paper]
[11] Bao Zhao, Weipeng Gong, Anjun Ma, Jianwen Chen, Hong Dong, Zihao Liu, Lingling Wang, Tamio Okimoto, Devin M. Jones, Yu L. Lei, Meixiao Long, Kenneth J. Oestreich, Qin Ma, Gang Xin, David P. Carbone, Kai He, Zihai Li, Haitao Wen. SUSD2 suppresses CD8+ T cell antitumor immunity by targeting IL-2 receptor signaling. Nature Immunology (2022) doi.org/10.1038/s41590-022-01326-8.
[Abstract][Full paper]
[10] Heng-Yi Chen, Ana Alamonte-Loya, Fang-Yun Lay, Eric Johnson, Edahi Gonzalez-Avalos, Jieyun Yin, Qin Ma, Daniel Wozniak, Fiona Harrison, Chan-Wang, Jerry Lio. Epigenetic Remodeling by Vitamin C Potentiates Plasma Cell Differentiation. eLife (2022). PMID: 36069787 PMCID: PMC9451539
[Abstract] [Full paper]
[9] Yuzhou Chang, Fei He, Juexin Wang, Shuo Chen, Jingyi Li, Jixin Liu, Yang Yu, Li Su, Anjun Ma, Carter Allen, Yu Lin, Shaoli Sun, Bingqiang Liu, Jose Otero, Dongjun Chung, Hongjun Fu, Zihai Li, Dong Xu, Qin Ma. Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning. Computational and Structural Biotechnology Journal (2022). PMID: 36090815 PMCID: PMC9440291
[Abstract] [Full paper]
[8] Anqi Li, Yuzhou Chang, No-joon Song, Xingjun Wu, Dongjun Chung, Brian P Riesenberg, Maria Velegraki, Tamio Okimoto, Hyunwoo Kwon, Karthik B Chakravarthy, Chelsea Bolyard, Lei Zhou, Kai He, Yiping Yang, Qin Ma, David P Carbone, Zihai Li. Selective targeting of GARP-LTGFb axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell anti-tumor immunity. Journal for ImmunoTherapy of Cancer (2022). PMID: 36096533 PMCID: PMC9472209
[Abstract] [Full paper]
[7] Carter Allen, Yuzhou Chang, Brian Neelon, Won Chang, Hang Kim, Zihai Li, Qin Ma, Dongjun Chung$. A Bayesian Multivariate Mixture Model for High Throughput Spatial Transcriptomics. Biometrics (2022). PMID: 35895854
[Abstract] [Full paper]
[6] Anjun Ma, Gang Xin, Qin Ma$. The use of single-cell multi-omics in immuno-oncology. Nature Communications (2022). PMID: 35585090 PMCID: PMC9117235
[Abstract] [Full paper]
[5] Hyunwoo Kwon, Johanna M. Schafer, No-Joon Song, Satoshi Kaneko, Anqi Li, Tong Xiao, Anjun Ma, Carter Allen, Komal Das, Lei Zhou, Brian Riesenberg, Yuzhou Chang, Payton Weltge, Maria Velegraki, David Y. Oh, Lawrence Fong, Qin Ma, Debasish Sundi, Dongjun Chung$, Xue Li$, Zihai Li$. Androgen conspires with the CD8+ T cell exhaustion program and contributes to sex bias in cancer. Science Immunology (2022). PMID: 35420889 PMCID: PMC9374385
[Abstract] [Full paper]
[4] Johanna M. Schafer, Tong Xiao, Hyunwoo Kwon, Katharine Collier, Yuzhou Chang, Chelsea Bolyard, Dongjun Chung, Yuanquan Yang, Debasish Sundi, Qin Ma, Dan Theodorescu, Xue Li, Zihai Li$. Sex-Biased Adaptive Immune Regulation in Cancer Development and Therapy. iScience (2022). PMID: 35880048 PMCID: PMC9307950
[Abstract] [Full paper]
[3] Jinkyung Yoo, Zequn Sun, Qin Ma, Dongjun Chung, Young Min Kim. A Guideline for the Statistical Analysis of Compositional Data in Immunology. Communications for Statistical Applications and Methods (2022)
[Abstract] [Full paper]
[2] No-Joon Song, Carter Allen, Anna E. Vilgelm, Brian P. Riesenberg, Kevin P. Weller, Kelsi Reynolds, Karthik B. Chakravarthy, Amrendra Kumar, Aastha Khatiwada, Zequn Sun, Anjun Ma, Yuzhou Chang, Mohamed Yusuf, Anqi Li, Cong Zeng, John P. Evans, Donna Bucci, Manuja Gunasena, Menglin Xu, Namal P.M. Liyanage, Chelsea Bolyard, Maria Velegraki, Shan-Lu Liu, Qin Ma, Martin Devenport, Yang Liu, Pan Zheng, Carlos D. Malvestutto, Dongjun Chung, Zihai Li$. Treatment with Soluble CD24 Attenuates COVID-19-Associated Systemic Immunopathology. Journal of Hematology & Oncology (2022). PMID: 35012610 PMCID: PMC8744064
[Abstract] [Full paper]
[1] Yuzhou Chang, Carter Allen, Changlin Wan, Dongjun Chung, Chi Zhang$, Zihai Li$, Qin Ma$. IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis. Bioinformatics (2021). PMID: 33595622 PMCID: PMC8479672
[Abstract] [Full paper]