Qin Ma

Qin Ma, PhD

Assistant Professor
South Dakota State University
Plant Science
(605) 688-6315

Dr. Ma is an assistant professor and leads the Bioinformatics and Mathematical Biosciences Lab (BMBL) at South Dakota State University. He obtained his PhD degree in Operational Research at Shandong University, China and his B.S. degree in Applied Mathematics at Shandong University, China. He worked in bioinformatics at University of Georgia for six years. Hence, he is a well-trained bioinformatics researcher and computational modeler of big biological data and systems. His technical strength is in developing combinatorial optimization techniques and data mining and modeling with the advent of high-throughput Omics technologies. His strong and long-term interests mainly focus on (1) elucidation of metabolic networks and associated regulatory systems; (2) characterization of functionally genomic organization in bacteria and plants; and (3) development of enabling computational techniques in support of the above scientific studies. He has published over 30 peer-reviewed journals, including Nucleic acids research, Bioinformatics, Scientific Reports-Nature, BioEnergy Research, BMC Genomics, etc.

Selected publications:
Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, Ying Xu, QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression DataNucleic Acids Research, 2009, 37(15): e101-.

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 viewsNucleic Acids Research, 2014 Jan;42(Database issue):D654-9, doi:10.1093/nar/gkt1048.

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 analysisBMC Plant Biology, 2012, 12:138

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 stressBiotechnology for Biofuels, 2013 Sep 12;6(1):131. doi: 10.1186/1754-6834-6-131. Artical Metrics.

Guojun Li, Bingqiang Liu, Qin Ma, Ying Xu, A new framework for identifying cis-regulatory motifs in prokaryotesNucleic Acids Research, 2011 Apr;39(7):e42.

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 scaleBioinformatics, 2013, Sep 15;29(18):2261-8. doi:10.1093/bioinformatics/btt397.

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 GenomesNucleic Acids Research, 2011, 1-9, doi:10.1093/nar/gkr766.

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 CancerInternational journal of cancer, 11/2014;DOI: 10.1002/ijc.29352.

Qin Ma, Hanyuan Zhang, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu, DMINDA: An integrated web server for DNA motif identification and analysisNucleic Acids Research, 2014, doi: 10.1093/nar/gku315.

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 ConditionsNucleic Acids Research, 2013, 1-10, Jun;41(11):5594-603, doi:10.1093/nar/gkt261.


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