Selected Publications

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


[24] Analysis of next- and third-generation RNA-Seq data reveals the structures of alternative transcription units in bacterial genomes.
Qi Wang, Zhaoqian Liu, Bo Yan, Wen-Chi Chou, Laurence M Ettwiller, Qin Ma, Bingqiang Liu$
bioRxiv
[Abstract] [Full paper]


[23] Assessing deep learning algorithms in cis-regulatory motif finding based on genomic sequencing data.
Yan Wang, Shuangquan Zhang, Anjun Ma, Cankun Wang, Zhenyu Wu, Dong Xu, Qin Ma$
bioRxiv (2020)
[Abstract] [Full paper]


[22] 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]


[21] 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]


[20] 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]


[19] 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]


[18] 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]


[17] 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]


[16] 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]


[15] 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]


[14] 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]


[13] 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]


[12] 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]


[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]


[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]


[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]