[29] Graph Fourier transform for spatial omics representation and analyses of complex organs.
Yuzhou Chang, Jixin Liu, Yi Jiang, Anjun Ma, Yao Yu Yeo, Qi Guo, Megan McNutt, Jordan E. Krull, Scott J. Rodig, Dan H. Barouch, Garry P. Nolan, Dong Xu, Sizun Jiang, Zihai Li, Bingqiang Liu$, Qin Ma$,
Nature Communications (2024)
[Abstract] [Full paper] [Springer Nature Research Communities Post] [Editor highlights]
[28] The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors.
Caroline Wheeler, Samuel Coleman, Rebecca Hoyd, Louis Denko, Carlos Chan, Michelle Churchman, Nicholas Denko, Rebecca Dodd, Islam Eljilany, Sheetal Hardikar, Marium Husain, Alexandra Ikeguchi, Ning Jin, Qin Ma, Martin McCarter, Afaf Osman, Lary Robinson, Eric Singer, Gabriel Tinoco, Cornelia Ulrich, Yousef Zakharia, Daniel Spakowicz, Ahmad Tarhini, and Aik Choon Tan
Cancer Research Communications (2024)
[Abstract] [Full paper]
[27] Analysis of community connectivity in spatial transcriptomics data.
Juan Xie, Kyeong Joo Jung, Carter Allen, Yuzhou Chang, Subhadeep Paul, Zihai Li, Qin Ma, Dongjun Chung
Frontiers in Applied Mathematics and Statistics (2024)
[Abstract] [Full paper]
[26] Harnessing the deep learning power of foundation models in single-cell omics.
Qin Ma, Yi Jiang, Hao Cheng, Dong Xu
Nature Reviews Molecular Cell Biology (2024)
[Abstract] [Full paper]
[25] The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer.
Martin Benej, Rebecca Hoyd, McKenzie Kreamer, Caroline Wheeler, Dennis Grencewicz, Fouad Choueiry, Carlos Chan, Yousef Zakharia, Qin Ma, Rebecca Dodd, Cornelia Ulrich, Sheetal Hardikar, Michelle Churchman, Ahmad Tarhini, Lary Robinson, Eric Singer, Alexandra Ikeguchi, Martin McCarter, Gabriel Tinoco, Marium Husain, Ning Jin, Aik Choon Tan, Afaf Osman, Islam Eljilany, Gregory Riedlinger, Bryan Schneider, Ioanna Papandreou, Jiangjiang Zhu, Nicholas Denko, and Daniel Spakowicz
Cancer Research Communications (2024)
[Abstract] [Full paper]
[24] Spatial and functional targeting of intratumoral Tregs reverses CD8+ T cell exhaustion and promotes cancer immunotherapy.
Lei Zhou, Maria Velegraki, Yi Wang, J K Mandula, Yuzhou Chang, Weiwei Liu, No-Joon Song, Hyunwoo Kwon, Tong Xiao, Chelsea Bolyard, Feng Hong, Gang Xin, Qin Ma, Mark P. Rubinstein, Haitao Wen, Zihai Li
The Journal of Clinical Investigation (2024)
[Abstract] [Full paper]
[23] Targeting Metabolic Sensing Switch GPR84 on Macrophages for Cancer Immunotherapy.
Jianying Li, Anjun Ma, Ruohan Zhang, Yao Chen, Chelsea Bolyard, Bao Zhao, Cankun Wang, Thera Pich, Wantong Li, Nuo Sun, Qin Ma, Haitao Wen, Steven K. Clinton, William E. Carson, Zihai Li, Gang Xin
Cancer Immunology, Immunotherapy (2024)
[Abstract] [Full paper]
[22] Human iPSC-based model of COPD to investigate disease mechanisms, predict SARS-COV-2 outcome, and test preventive immunotherapy.
Rania Dagher, Aigul Moldobaeva, Mia Madel Alfajaro, Craig B. Wilen, Elise Gubbin, Sydney Clark, Finn Hawkins, Yang Li, Lori Clarke, Yasuhiro Ikeda, Charles Brown, Qin Ma, Mauricio Rojas, Jonathan L. Koff, Roland Kolbeck, Mahboobe Ghaedi
Stem Cells (2024)
[Abstract] [Full paper]
[21] MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer.
Xiaoying Wang*, Maoteng Duan*, Jingxian Li, Anjun Ma, Gang Xin, Dong Xu, Zihai Li, Bingqiang Liu$, Qin Ma$
Nature Communications (2024)
[Abstract] [Full paper] [Nature Research Community Post] [Editor highlights]
[20] mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T cell responses in lung cancer patients.
No-Joon Song, Karthik Chakravarthy, Hyeongseon Jeon, Chelsea Bolyard, Kelsi Reynolds, Kevin P. Weller, Sarah Reisinger, Yi Wang, Anqi Li, Sizun Jiang, Qin Ma, Dan H Barouch, Mark P. Rubinstein, Peter G. Shields, Eugene M Oltz, Dongjun Chung, Zihai Li
Journal for ImmunoTherapy of Cancer (2024)
[Abstract] [Full paper]
[19] Glioblastoma Pseudoprogression and True Progression Reveal Spatially Variable Transcriptional Differences.
Wesley Wang, Jonah Domingo Tugaoen, Paolo Fadda, Amanda Ewart Toland, Qin Ma, J Brad Elder, Pierre Giglio, James Cancer Center Integrated Neuro-oncology Team, Jose Javier Otero
Acta Neuropathologica Communications (2023)
[Abstract] [Full paper]
[18] Single-Cell Profiling of Murine Bladder Cancer Identifies Sex-Specific Transcriptional Signatures with Prognostic Relevance.
Hany A. Abdel-Hafiz, Saravana Kumar Kailasam Mani, Wesley Huang, Kenneth H. Gouin, Yuzhou Chang, Tong Xiao, Qin Ma, Zihai Li, Simon R.V. Knott, Dan Theodorescu
iScience (2023)
[Abstract] [Full paper]
[17] LRT: T Cell Trajectory Inference by Integrative Analysis of Single Cell TCR-seq and RNA-seq data.
Juan Xie, Gang Xin, Qin Ma, Dongjun Chung
PLOS Computational Biology (2023)
[Abstract] [Full paper]
[16] CD200R signaling contributes to unfavorable tumor microenvironment through regulating production of chemokines by tumor-associated myeloid cells.
chemokines by tumor-associated myeloid cells.
Cho-Hao Lin, Fatemeh Talebian, Li Yang, Jianmin Zhu, Jin-Qing Liu, Bolin Zhao, Ramesh Ganju, Sujit Basu, Wendy Frankel, Xueliang Pan, William E Carson, Gang Xin, Ruoning Wang, Haitao Wen, Zihai Li, Qin Ma, and Xue-Feng Bai
iScience (2023)
[Abstract] [Full paper]
[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] scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data.
Edison Gu, Hao Cheng, Yang Li, Juexin Wang, Anjun Ma, Dong Xu, Qin Ma
Bioinformatics. (2022). PMID: 36250784
[Abstract][Full paper]
[11] SUSD2 suppresses CD8+ T cell antitumor immunity by targeting IL-2 receptor signaling.
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
Nature Immunology (2022) doi.org/10.1038/s41590-022-01326-8.
[Abstract][Full paper]
[10] Epigenetic Remodeling by Vitamin C Potentiates Plasma Cell Differentiation.
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
eLife (2022). PMID: 36069787 PMCID: PMC9451539
[Abstract] [Full paper]
[9] Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning.
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
Computational and Structural Biotechnology Journal (2022). PMID: 36090815 PMCID: PMC9440291
[Abstract] [Full paper]
[8] Selective targeting of GARP-LTGFb axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell anti-tumor immunity.
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
Journal for ImmunoTherapy of Cancer (2022). PMID: 36096533 PMCID: PMC9472209
[Abstract] [Full paper]
[7] A Bayesian Multivariate Mixture Model for High Throughput Spatial Transcriptomics.
Carter Allen, Yuzhou Chang, Brian Neelon, Won Chang, Hang Kim, Zihai Li, Qin Ma, Dongjun Chung$
Biometrics (2022). PMID: 35895854
[Abstract] [Full paper]
[6] The use of single-cell multi-omics in immuno-oncology.
Anjun Ma, Gang Xin, Qin Ma$
Nature Communications (2022). PMID: 35585090 PMCID: PMC9117235
[Abstract] [Full paper]
[5] Androgen conspires with the CD8+ T cell exhaustion program and contributes to sex bias in cancer.
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$
Science Immunology (2022). PMID: 35420889 PMCID: PMC9374385
[Abstract] [Full paper]
[4] Sex-Biased Adaptive Immune Regulation in Cancer Development and Therapy.
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$
iScience (2022). PMID: 35880048 PMCID: PMC9307950
[Abstract] [Full paper]
[3] A Guideline for the Statistical Analysis of Compositional Data in Immunology.
Jinkyung Yoo, Zequn Sun, Qin Ma, Dongjun Chung, Young Min Kim.
Communications for Statistical Applications and Methods (2022)
[Abstract] [Full paper]
[2] Treatment with Soluble CD24 Attenuates COVID-19-Associated Systemic Immunopathology.
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$
Journal of Hematology & Oncology (2022). PMID: 35012610 PMCID: PMC8744064
[Abstract] [Full paper]
[1] IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis.
Yuzhou Chang, Carter Allen, Changlin Wan, Dongjun Chung, Chi Zhang$, Zihai Li$, Qin Ma$
Bioinformatics (2021). PMID: 33595622 PMCID: PMC8479672
[Abstract] [Full paper]