Qin Ma, Ph.D.
Assistant Professor

Bioinformatics and Mathematical Biosciences Lab
Department of Plant Science
South Dakota State University
100 Administration Lane, Brookings, SD, 57006
Phone: (706)254-4293
Email: maqin2001@gmail.com

Research Gate


(* Equal contribution)
(# Doctoral supervisor is the first author)
  1. Yu Zhang, Juan Xie, Jinyu Yang, Anne Fennell and Qin Ma$, QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinformatics. (IF=5.766)
  2. Bingqiang Liu, Hanyuan Zhang, Chuan Zhou, Guojun Li, Anne Fennell, Guanghui Wang, Yu Kang, Qi Liu and Qin Ma$, An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.BMC Genomics. (IF=4)
  3. Bingqiang Liu, Chuan Zhou, Guojun Li, Hanyuan Zhang, Erliang Zeng, Qin Ma$, Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses. Scientific Reports. (IF=5.228)
  4. Xin Chen*, Qin Ma*, Xiaolan Rao, Yuhong Tang, Yan Wang, Gaoyang Li, Chi Zhang, Xizeng Mao, Richard A. Dixon and Ying Xu, Genome-Scale Identification of Cell-Wall Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data, BioEnergy Research, DOI: 10.1007/s12155-015-9674-2.
  5. Wen-Chi Chou*, Qin Ma*, Shihui Yang, Sha Cao, Dawn M. Klingeman, Steven D. Brown, Ying Xu, Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. Nucleic Acids Research, doi: 10.1093/nar/gkv177, 2015.
  6. Juan Cui, Yanbin Yin, Qin Ma, Guoqing Wang, Victor Olman, Yu Zhang, Wen-chi Zhou, Celing Hong, Chi Zhang, Sha Cao, Xizeng Mao, Steve Qin, Ying Li, Shaying Zhao, Phil Hasting, Fan Li, Ying Xu, Comprehensive Characterization of the Genomic Alterations in Human Gastric Cancer. International journal of cancer, 11/2014; DOI: 10.1002/ijc.29352.
  7. Chuan Zhou*, Qin Ma*, Xizeng Mao, Bingqiang Liu, Yanbin Yin, Ying Xu, New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes. BioEnergy Research, 2014, doi: 10.1007/s12155-014-9486-9 (this paper is highlighted by Bioenergy Science Center of U.S. Department of energy).
  8. Xizeng Mao*, Qin Ma*, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu. DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Research, 2014 Jan;42(Database issue):D654-9, doi:10.1093/nar/gkt1048.
  9. Qin Ma*, Hanyuan Zhang*, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu, DMINDA: An integrated web server for DNA motif identification and analysis. Nucleic Acids Research, 2014, doi: 10.1093/nar/gku315.
  10. Qin Ma, Jaxk Reeves, David A. Liberles, Lili Yu, Zheng Chang, Jing Zhao, Juan Cui, Ying Xu, Liang Liu, A phylogenetic model for understanding the effect of gene duplication on cancer progressing. Nucleic Acids Research, doi:10.1093/nar/gkt1320, 1-9, 2013.
  11. Qin Ma*, Bingqiang Liu*, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu, An integrated toolkit for accurate prediction and analysis of cis regulatory elements at a genome scale. Bioinformatics, 2013, Sep 15;29(18):2261-8. doi:10.1093/bioinformatics/btt397.
  12. Qin Ma, Ying Xu, Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency. Genomics, Proteomics & Bioinformatics, 2013, 11: 66-71
  13. Qin Ma*, Yanbin Yin*, Mark A. Shell, Han Zhang, Guojun Li, Ying Xu, Computational Analyses of Transcriptomic Data Reveal the Dynamic Organization of the E. coli Chromosome under Different Conditions. Nucleic Acids Research, 2013, 1-10, Jun;41(11):5594-603, doi:10.1093/nar/gkt261.
  14. Fengfeng Zhou*, Qin Ma*, Guojun Li, Ying Xu, QServer: a biclustering server for prediction and validation of co-expressed gene clusters, PLoS ONE, 7(3): e32660. doi:10.1371/journal.pone.0032660, 2012. Article Metrics.
  15. Guojun Li*, Qin Ma*#, Xizeng Mao, Yanbin Yin, Xiaoran Zhu, Ying Xu, Integration of Sequence-Similarity and Functional Association Information Can Overcome Intrinsic Problems in Orthology Mapping across Bacterial Genomes, Nucleic Acids Research, 2011, 1-9, doi:10.1093/nar/gkr766.
  16. Guojun Li, Bingqiang Liu, Qin Ma#, Ying Xu, A new framework for identifying cis-regulatory motifs in prokaryotes, Nucleic Acids Research, 2011 Apr;39(7):e42.
  17. Guojun Li, Qin Ma#, Haibao Tang, Andrew H. Paterson, Ying Xu, QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data, Nucleic Acids Research, 2009, 37(15): e101-.