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

[16] Mitochondrial Calcium Signaling Facilitates Bacterial Survival by Restraining LC3-associated Phagpcytosis.
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 (2020)
In press

[15] 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]

[14] 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]

[13] scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses.
Juexin Wang*, Anjun Ma*, Yuzhou Chang, Jianting Gong, Yuexu Jiang, Hongjun Fu, Cankun Wang, Ren Qi, Qin Ma$, Dong Xu$
bioRxiv (2020)
[Abstract] [Full paper]

[12] 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]

[11] 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]

[10] 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]

[9] 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]

[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]

[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]