Selected Publications

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


[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]


[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]