Qin Ma, Ph.D.
Postdoc in Bioinformatics

Computational Systems Biology laboratory (CSBL)
Department of Biochemistry and Molecular Biology
A134, Davison Life Sciences Building
The University of Georgia,
Athens, GA 30602
Phone: (706)542-3930
Fax: (706)542-9751
Email: maqin@csbl.bmb.uga.edu

EDUCATION AND TRAINING

• Postdoc in Computational Systems Biology laboratory (CSBL), University of Georgia, 2011.01-now.
• Ph.D. in Operations Research, School of Mathematics, Shandong University, 2005.09-2010.09.
• Visiting Ph.D. student in Computational Systems Biology laboratory (CSBL), University of Georgia, 2008.10-2010.09.
• B.S. in Applied Mathematics, School of Mathematics, Shandong University, 2001.09-2005.07.

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RESEARCH INTERESTS:

• Biclustering algrithm for gene expression data.
• Evolutionary history of cancer genome.
• Transcriptional regulation mechanism for prokaryotic.
• Graph Theory and Algorithm Design.

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PAPERS:

1. Blumer-Schuette, Sara; Giannone, Richard; Zurawski, Jeffrey; Ozdemir, Inci; Ma, Qin; Yin, Yanbin; Xu, Ying; Kataeva, Irina; Poole, II, Farris; Adams, Mike; Hamilton-Brehm, Scott; Elkins, James; Larimer, Frank; Land, Miriam; Hauser, Loren; Cottingham, Robert; Hettich, Robert; Kelly, Robert, Caldicellulosiruptor core and pan genomes reveal determinants for non-cellulosomal thermophilic deconstruction of plant biomass, Submitted to Genome Biology
2. Fengfeng Zhou, Qin Ma (co-first), Guojun Li, Ying Xu, QServer: a biclustering server for prediction and validation of co-expressed gene clusters, Accepted by PLOS one, 2012
3. Guojun Li, Qin Ma (co-first), 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
   
4. Lingpeng Meng, Qin Ma, Zhenyu Yu, Han Chuanfeng, A Modeling Framework to Identify the Number and Locations of Medical Services Facilities for Large-Scale Emergencies, submitted to european journal of operational research, 2011
5. Jing Zhao, Qin Ma, Yuquan Cui, Comparative study on macro-economic regionalization: an application of biclustering algorithm, Accepted by Journal of Shandong University, 2010
6. Guojun Li, Bingqiang Liu, Qin Ma, Ying Xu, A New Framework for Identifying cis Regulatory Motifs in Prokaryotes, Nucleic Acids Research, 2011, 39(7): e42
7. 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 2009, 082Li
   
8. 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-
   
9. Qin Ma, Jian-liang Wu, Xiao Yu, Planar graphs without 5-cycles or 6-cycles, Discrete Mathematics, 2009, 309: 2998-3005.
   
10. Qin Ma, The degree-constrained k-arboricity of outerplanar graphs, Journal of Shandong university, 2007,42 (10): 41-43.
    

PAPERS IN PREPARED

1. Qin Ma, Yanbin Yin, Han Zhang, Guojun Li, Ying Xu, Elucidation of the Supercoil Packaging Boundaries of Escherichia coli Chromosome
   
2. Shan Wang, Yanbin Yin, Qin Ma, Xiaojia Tang, Kan Bao, Dongyun Hao, Ying Xu, Identification and characterization of plant cell-wall related proteins through bi-clustering coexpression analysis
   
3. Qin Ma, Bingqiang Liu, Guojun Li, Ying Xu, BOBRO2.0: A cis-regulatory elements analysis suite can get specific and discriminative motifs
   
4. Qin Ma, Xiaojia Tang, Guojun Li, Victor Olman, Ying Xu, QUBIC2.0: A new clues to elucidate regulatory mechanism by microarray data for E. coli
   

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PROFESSIONAL ACTIVETIES

• Ph.D. thesis, Elucidation and identification of Regulons for Prokaryotic Genomes, 2010, Shandong University.
  
• Invited talk, QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data, The 8th Annual International Conference on Computational Systems Bioinformatics, 2009, Stanford University, USA.
  
• Invited talk, Elucidation and identification of Regulons for Prokaryotic Genomes, College of computer science and Technology, Jilin University, 2010, Changchun, China
  
• Invited talk, An introduction of Biclustering algorithm in gene microarray analysis. School of Mathematics, Shandong University, 2010.09, Jinan, China.
• Poster, Bingqiang Liu, Phuongan Dam, Guojun Li, Qin Ma, Victor Olman, Fenglou Mao, Jacky Chou, Ying Xu, Reconstruction of the transcriptional regulatory network in prokaryotes, BioEnergy Science Center 3rd retreat, Asheville NC, USA, 2009.
• Program committee member, 6th INTERNATIONAL CONFERENCE ON LANGUAGE AND AUTOMATA THEORY AND APPLICATIONS, LATA 2012.
• Reviewer for Journals PLoSONE Mathematical Biosciences Bioinformatics, BMC Bioinformatics, BMC Research Notes, Journal of Theoretical Biology.
• Reviewer for Conferences, Bioinformatics 2010, Bioinformatics 2011,BIBM 2010, BIBM 2011, ACM-BCB 2010, ACM-BCB 2011, ICIC 2011, ISBRA 2010.
• Member of Conferences, The 5th International Bioinformatics Workshop (IBW 2007), IBW 2008, Georgia Tech-ORNL International Conference on Bioinformatics, 2009.

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DEVELOPED SOFTWARES:

• QUBIC (A Biclustering Tool for Microarray Data)
  
• BoBro (A New Framework for Identifying cis Regulatory Motifs in Prokaryotes)
  
• QServer (A biclustering-based server for prediction and validation of co-expressed gene clusters)
  
• GOST (Globally Optimized Strategy for Orthology Mapping Detection in Prokaryotes)
  
• BBS (A BoBro-Based motif Searching tool by known motif alignment or frequency matrix)
  
• BBC (A BoBro-Based Clustering tool by finding the maximal weighted subgraph in a weight graph)
  

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PROJECTS IN PROCESS:

1. Elucidation of the evolution process of Cancer genome base on Microhomology-Mediated Break-Induced Replication Model.
   
2. A BiCluster-based Method for Predicting Dynamic Transcriptional Regulatory Network in Escherichia coli.
   
3. A Optimized algorithm for identifying horizontal transfer genes (HTGs).
   

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HOBBIES:

• Basketball The NBA players I like best are Shaquille O'Neal and Tim Duncan.
• GouJi A method Playing Poker Cards, need 6 players, originated in Shandong.

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