Selected Publications

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* These authors contributed equally to the paper as the first authors
$ To whom correspondence should be addressed


[46] NIH SenNet Consortium: Mapping Senescent Cells in the Human Body to Understand Health and Disease.
Patty Lee, Philip Blood, Katy Börner, Judith Campisi, Feng Chen, Heike Daldrup-Link, Phil De Jager, Li Ding, Francesca E Duncan, Oliver Eickelberg, Rong Fan, Toren Finkel, Vesna Garovic, Nils Gehlenborg, Carolyn Glass, Ziv Bar-Joseph, Pragati Katiyar, So-Jin Kim, Melanie Königshoff, George Kuchel, Haesung Lee, Jun H Lee, Jian Ma, Qin Ma, Simon Melov, Kay Metis, Ana L Mora, Nicolas Musi, Nicola Neretti, João F. Passos, Irfan Rahman, Juan Carlos Rivera-Mulia, Paul Robson, Mauricio Rojas, Ananda L Roy, Birgit Schilling, Pixu Shi, Jonathan Silverstein, Vidyani Suryadevera, Jichun Xie, Jinhua Wang, An-Kwok Ian Wong, Laura Niedernhofer
Nature Aging (in press) (2022)
[Abstract] [Full paper]


[45] 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]


[44] 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)
[Abstract] [Full paper]


[43] scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data.
Haocheng Gu*, Hao Cheng*, Anjun Ma, Yang Li, Juexin Wang, Qin Ma$, Dong Xu$
Bioinformatics (2022)
[Abstract] [Full paper]


[42] FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling.
Dawei Zhou, Zhenyu Wu, Jun-Gyu Park, Guillaume Fiches, Tai-Wei Li, Qin Ma, Huachao Huang, Ayan Biswas, Luis Martinez-Sobrido, Netty Santoso, Jian Zhu$
Nucleic Acids Research (2022)
[Abstract] [Full paper]


[41] Durability of Booster mRNA Vaccine against SARS-CoV-2 BA.2.12.1, BA.4, and BA.5 Subvariants.
Panke Qu, Julia N. Faraone, John P. Evans, Yi-Min Zheng, Lianbo Yu, Qin Ma, Claire Carlin, Gerard Lozanski, Linda J. Saif, Eugene M. Oltz, Richard J. Gumina, Shan-Lu Liu
New England Journal of Medicine (2022)
[Abstract] [Full paper]


[40] 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)
[Abstract] [Full paper]


[39] Deep Learning Analysis of Single-Cell Data in Empowering Clinical Implementation.
Anjun Ma*, Juexing Wang*, Dong Xu$, Qin Ma$
Clinical and Translational Medicine (2022)
[Abstract] [Full paper]


[38] 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)
[Abstract] [Full paper]


[37] Microglia coordinate cellular interactions during spinal cord repair in mice.
Faith Brennan, Yang Li, Cankun Wang, Anjun Ma, Qi Guo, Yi Li, Nicole Pukos, Warren Campbell IV, Kristina Witcher, Zhen Guan, Kristina Kigerl, Jodie Hall, Jonathan Godbout, Andy Fischer, Dana McTigue, Zhigang He, Qin Ma, Phillip G. Popovich$
Nature Communications (2022)
[Abstract] [Full paper]


[36] Provable Second-order Riemannian Gauss-Newton Method for Low-rank Tensor Estimation.
Yuetian Luo, Qin Ma, Chi Zhang, Anru Zhang
IEEE ICASSP (2022)
[Full paper]


[35] A shared disease-associated oligodendrocyte signature among multiple CNS pathologies.
Mor Kenigsbuch, Pierre Bost, Shahar Halevi, Yuzhou Chang, Shuo Chen, Qin Ma, Renana Hajbi, Benno Schwikowski, Bernd Bodenmiller, Elior Peles, Hongjun Fu, Michal Schwartz, Ido Amit$
Nature Neuroscience (2022)
[Abstract] [Full paper]


[34] The use of single-cell multi-omics in immuno-oncology.
Anjun Ma, Gang Xin, Qin Ma$
Nature Communications (2022)
[Abstract] [Full paper]


[33] Deep learning shapes single-cell data analysis.
Qin Ma$ and Dong Xu
Nature Reviews Molecular Cell Biology (2022)
[Abstract] [Full paper]


[32] 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)
[Abstract] [Full paper]


[31] Wolframin is a novel regulator of tau pathology and neurodegeneration.
Shuo Chen, Liangping Li, Diana Acosta, Jiawen Liang, Yuzhou Chang, Cankun Wang, Julie Fitzgerald, Cody Morrison, Chris Goulbourne, Yoshi Nakano, Nancy C. Hernandez Villegas, Lalitha Venkataraman, Cris Brown, Marilin Ivask, Geidy E. Serrano, Rebecca Davis, Trina Wemlinger, Olga N. Kokiko-Cochran, Phillip Popovich, Lawrence S. Honig, Jean Paul Vonsattel, Douglas W. Scharre, Thomas Beach, Qin Ma, Jeff Kuret, Gail V.W. Johnson, Sulev Kõks, Marc Diamond, Fumihiko Urano, Karen Duff, and Hongjun Fu$
Acta neuropathological (2022)
[Abstract] [Full paper]


[30] Assessing deep learning algorithms in cis-regulatory motif finding based on genomic sequencing data.
Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma, Yan Wang$
Briefings in Bioinformatics (2021)
[Abstract] [Full paper]


[29] A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data.
Norah Alghamdi, Wennan Chang, Pengtao Dang, Xiaoyu Lu, Changlin Wan, Silpa Gampala, Zhi Huang, Jiashi Wang, Qin Ma, Yong Zang, Melissa Fishel$, Sha Cao$, Chi Zhang$
Genome Research (2021)
[Abstract] [Full paper]


[28] A novel computational framework for genome-scale alternative transcription units prediction.
Qi Wang, Zhaoqian Liu, Bo Yan, Wen-Chi Chou, Laurence M Ettwiller, Qin Ma$, Bingqiang Liu$
Briefings in Bioinformatics (2021)
[Abstract] [Full paper]


[27] 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)
[Abstract] [Full paper]


[26] scGNN is a novel graph neural network model for single-cell RNA-Seq analysis.
Juexin Wang*, Anjun Ma*, Jianting Gong, Yuexu Jiang, Yuzhou Chang, Ren Qi, Cankun Wang, Hongjun Fu, Qin Ma$, Dong Xu$
Nature Communications (2021)
[Abstract] [Full paper] [Author correction]


[25] Listeria monocytogenes upregulates mitochondrial calcium signaling to inhibit LC3-associated phagocytosis as a survival strategy.
Tianliang Li, Ligang Kong, Xinghui Li, Sijin Wu, Kuldeep S.Attri, Yan Li, Weipeng Gong, Lupeng Li, Laura E. Herring, John M. Asara, Yu Lei, Qin Ma, Stephanie Seveau, John S Gunn, Xiaolin Cheng, Pankaj L. Singh, Douglas R. Green, Haibo Wang$, Haitao Wen$
Nature Microbiology (2021)
[Abstract] [Full paper]


[24] Single-cell Techniques and Deep Learning in Predicting Drug Response.
Zhenyu Wu, Patrick Lawrence, Anjun Ma, Jian Zhu, Dong Xu, Qin Ma$
Trends in Pharmacological Sciences (2020)
[Abstract] [Full paper]


[23] Elucidation of Biological Networks Across Complex Diseases Using Single-Cell Omics.
Yang Li, Anjun Ma, Ewy A. Mathe, Bingqiang Liu, Lang Li, Qin Ma$
Trends in Genetics (2020)
[Abstract] [Full paper]


[22] Inductive Inference of Gene Regulatory Network Using Supervised and Semi-supervised Graph Neural Networks.
Juexin Wang, Anjun Ma, Qin Ma, Dong Xu, Trupti Joshi$
Computational and Structural Biotechnology Journal (2020)
[Abstract] [Full paper]


[21] scREAD: A single-cell RNA-Seq database for Alzheimer’s Disease.
Jing Jiang*, Cankun Wang*, Ren Qi, Hongjun Fu$, Qin Ma$
iScience (2020)
[Abstract] [Full paper] [News]


[20] IRIS3: Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq.
Anjun Ma*, Cankun Wang*, Yuzhou Chang, Faith H. Brennan, Adam McDermaid, Bingqiang Liu, Chi Zhang, Phillip G. Popovich, Qin Ma$
Nucleic Acids Research (2020)
[Abstract] [Full paper] [News]


[19] Integrative Methods and Practical Challenges for Single-cell Multi-omics.
Anjun Ma, Adam McDermaid, Jennifer Xu, Yuzhou Chang, Qin Ma$
Trends in Biotechnology (2020)
[Abstract] [Full paper]


[18] Prediction of Regulatory Motifs from Human ChIP-Sequencing Data using a Deep Learning Framework.
Jinyu Yang, Anjun Ma, Adam D. Hoppe, Cankun Wang, Yang Li, Chi Zhang, Yan Wang, Bingqiang Liu$, Qin Ma$
Nucleic Acids Research (2019)
[Abstract] [Full paper]


[17] LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data.
Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Xiaoyu Lu, Yong Zang, Anru Zhang, Sha Cao, Melissa Fishel, Qin Ma$, Chi Zhang$
Nucleic Acids Research (2019)
[Abstract] [Full paper]


[16] QUBIC2: A novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.
Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang$, Qin Ma$
Bioinformatics (2019)
[Abstract] [Full paper]


[15] IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.
Brandon Monier*, Adam McDermaid*, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma$
PLoS Computational Biology (2019)
[Abstract] [Full paper]


[14] MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.
Anjun Ma*, Minxuan Sun*, Adam McDermaid, Bingqiang Liu$, Qin Ma$
Bioinformatics (2019)
[Abstract] [Full paper]


[13] Clustering and Classification Methods for Single-cell RNA-sequencing Data.
Ren Qi, Anjun Ma, Qin Ma, Quan Zou$
Briefings in Bioinformatics (2019)
[Abstract] [Full paper]


[12] LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property.
Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang, Ying Li$
Briefings in Bioinformatics (2018)
[Abstract] [Full paper] [Highlights from review] [Highlights from application]


[11] QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data.
Yu Zhang*, Juan Xie*, Jinyu Yang, Anne Fennell, Qin Ma$
Bioinformatics (2018)
[Abstract] [Full paper] [Highlights from review]


[10] Interpretation of differential gene expression results of RNA-Seq data: review and integration.
Adam McDermaid*, Brandon Monier*, Jing Zhao, Bingqiang Liu, Qin Ma$
Briefings in Bioinformatics (2018)
[Abstract] [Full paper]


[9] DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.
Jinyu Yang, Xin Chen, Adam McDermaid, Qin Ma$
Bioinformatics (2017)
[Abstract] [Full paper]


[8] Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.
Wen-Chi Chou*, Qin Ma*, Shihui Yang, Sha Cao, Dawn M. Klingeman, Steven D. Brown, Ying Xu$
Nucleic Acids Research (2015)
[Abstract] [Full paper]


[7] DMINDA: An integrated web server for DNA motif identification and analysis.
Qin Ma*, Hanyuan Zhang*, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu$
Nucleic Acids Research (2014)
[Abstract] [Full paper]


[6] DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Xizeng Mao*, Qin Ma, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu$
Nucleic Acids Research (2014)
[Abstract] [Full paper] [Highlights from application]


[5] A phylogenetic model for understanding the effect of gene duplication on cancer progressing. (2013)
Qin Ma, Jaxk Reeves, David A. Liberles, Lili Yu, Zheng Chang, Jing Zhao, Juan Cui, Ying Xu$, Liang Liu$
Nucleic Acids Research (2013)
[Abstract] [Full paper]


[4] Computational Analyses of Transcriptomic Data Reveal the Dynamic Organization of the E. coli Chromosome under Different Conditions.
Qin Ma*, Yanbin Yin, Mark A. Shell, Han Zhang, Guojun Li, Ying Xu$
Nucleic Acids Research (2013)
[Abstract] [Full paper]


[3] Integration of Sequence-Similarity and Functional Association Information Can Overcome Intrinsic Problems in Orthology Mapping across Bacterial Genomes.
Guojun Li, Qin Ma, Xizeng Mao, Yanbin Yin, Xiaoran Zhu, Ying Xu$
Nucleic Acids Research (2011)
[Abstract] [Full paper]


[2] A new framework for identifying cis-regulatory motifs in prokaryotes.
Guojun Li, Bingqiang Liu, Qin Ma, Ying Xu$
Nucleic Acids Research (2011)
[Abstract] [Full paper]


[1] QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data.
Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, Ying Xu$
Nucleic Acids Research (2009)
[Abstract] [Full paper] [Highlights from review]