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)
($ Corresponding author)
(# Doctoral supervisor is the first author)

    2016 (at SDSU)

  1. Yu Zhang, Juan Xie, Jinyu Yang, Anne Fennell and Qin Ma$, QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinformatics. (IF=5.766)
  2. Lina Yuan, Yang Yu, Yanmin Zhu, Yulai Li, Changqing Li, Rujiao Li, Qin Ma, Gilman Kit-Hang Siu, Jun Yu, Taijiao Jiang, Jingfa Xiao, Yu Kang, GAAP: Genome-Organization-Framework-Assisted Assembly Pipeline for the Prokaryotic Genome. BMC Genomics. (IF=4)
  3. Bingqiang Liu, Hanyuan Zhang, Chuan Zhou, Guojun Li, Anne Fennell, Guanghui Wang, Yu Kang, Qi Liu and Qin Ma$, An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.BMC Genomics. (IF=4)
  4. Zhenjia Wang, Chuan Zhou, Bingqiang Liu, Qin Ma, Guojun Li, A new insight into species from the same descendents aspect and an application to Clostridia. Current Bioinformatics.
  5. Guishen Wang, Lan Huang, Yan Wang, Wei Pang, and Qin Ma, A link density clustering algorithm based on automatically selecting density peaks for overlapping community detection. International Journal of Modern Physics B.
  6. Guohui Chuai, Fayu Yang, Yanan Chen, Qin Ma, Chi Zhou, Chenyu Zhu, Feng Gu, and Qi Liu, Deciphering determining factors rather than microhomology on the occurrence of in-frame mutation in human CRISPR-based gene knockout. Molecular Therapy - Nucleic Acids. (IF=5.048)
  7. 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)
  8. Jiading Yang, Eric Worley, Qin Ma, Jun Li, Ivone Torres-Jerez, Yi-Ching Lee, Jiyi Zhang, Nick Krom, Fuqi Liao, Yuhong Tang, Patrick X. Zhao, Michael Udvardi, Nitrogen conservation and underlying changes in genome activity associated with annual senescence in perennial Switchgrass Panicum virgatum, New Phytologist. (IF=7.21)
  9. Zhuoyuan Xin, Qin Ma, Guoqing Wang, Shuangchun Ren, Fan Li, The understanding of circular RNAs as special triggers in carcinogenesis, Briefings in functional genomics. (IF=3.124)
  10. Yi Sun, Yunqin Chen, Wei Zhang, Qin Ma, Jia Wei, Qi Liu, Identifying anti-cancer drug response related genes using integrative analysis of transcriptomic and genomic variations with cell line-based drug perturbations. Oncotarget, DOI: 10.18632/oncotarget.7012.
  11. Guishen Wang, Lan Huang, Yan Wang, Qin Ma, Wei Pang, Link community detection based on linear graphs with a novel link similarity measure, International Journal of Modern Physics B, DOI: 10.1142/S0217979216500235.

    2015 (at SDSU)

  12. Qin Ma*, Xizeng Mao*, Bingqiang Liu, Zheng Chang, Chuan Zhou, Hanyuan Zhang, Ying Xu. Revisiting Operons: An Analysis of the Landscape of Transcriptional Units in E. coli, BMC Bioinformatics, DOI: 10.1186/s12859-015-0805-8.
  13. 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.
  14. 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.

    2014 (at UGA)

  15. 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.
  16. Qin Ma*, Xin Chen*, Chao Liu, Hanyuan Zhang, Xizeng Mao, Fei Ji, Chunguo Wu, Ying Xu, Understanding the commonality and differences in genomic organizations across closely related bacteria from energy perspective. Science China, October, 2014, Vol.57 No.10: 1-10.
  17. Chuan Zhou*, Qin Ma*, Guojun Li, Elucidation of operon structures across multiple closely related organisms. PLoS ONE, 2014, Jun 24;9(6):e100999. doi: 10.1371/journal.pone.0100999. Article Metrics.
  18. 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).
  19. 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.
  20. 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.

    2013 (at UGA)

  21. 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.
  22. Charlotte M. Wilson, Shihui Yang, Miguel Rodriguez, Jr., Qin Ma, Courtney M. Johnson, Lezlee Dice, Ying Xu, Steven D. Brown, Clostridium thermocellum transcriptomic profiles after exposure to ethanol, furfural or heat stress. Biotechnology for Biofuels, 2013 Sep 12;6(1):131. doi: 10.1186/1754-6834-6-131. Artical Metrics.
  23. 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.
  24. 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.
  25. 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
  26. Lingpeng Meng, Qin Ma, Han Chuanfeng, Qidi Wu, Determining the Number of Facilities for Large-Scale Emergency, International Journal of Computing Science and Mathematics (EI), Volume 4, 242-251, 2013. doi:10.1504/IJCSM.2013.057253.

    2012 (at UGA)

  27. Shan Wang, Yanbin Yin, Qin Ma, Xiaojia Tang, Kan Bao, Dongyun Hao, Ying Xu, Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis, BMC Plant Biology, 2012, 12:138
  28. Sara Blumer-Schuette, Richard Giannone, Jeffrey Zurawski, Inci Ozdemir, Qin Ma, Yanbin Yin, Ying Xu, etc., Caldicellulosiruptor core and pan genomes reveal determinants for non-cellulosomal thermophilic deconstruction of plant biomass, Journal of Bacteriology, 2012, 194(15):4015-28
  29. 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.
  30. Jing Zhao, Qin Ma, Yuquan Cui, Comparative study on macro-economic regionalization: an application of biclustering algorithm, Journal of Shandong University, 2012, 49(7): 71-77.

    2011 (at UGA)

  31. 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.
  32. 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.

    2010 and earlier (at UGA)

  33. Qin Ma, Elucidation and identification of Regulons for Prokaryotic Genomes, Ph.D. thesis, Shandong University, 2010.
  34. 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-.
  35. Guojun Li, Qin Ma#, Bingqiang Liu, Haibao Tang, Andrew H. Paterson, Ying Xu, A Close-to Optimum Bi-clustering Algorithm for Microarray Gene Expression Data, Computational Systems Bioinformatics (Conference), 2009, 082Li

    2010 and earlier (at SDU)

  36. Qin Ma, Jian-liang Wu, Xiao Yu, Planar graphs without 5-cycles or 6-cycles, Discrete Mathematics, 2009, 309: 2998-3005. (Graph Theory)
  37. Qin Ma, The degree-constrained k-arboricity of outerplanar graphs, Journal of Shandong university, 2007,42 (10): 41-43.